Starting phenix.real_space_refine on Sat Sep 28 22:22:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo4_32638/09_2024/7wo4_32638.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo4_32638/09_2024/7wo4_32638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo4_32638/09_2024/7wo4_32638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo4_32638/09_2024/7wo4_32638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo4_32638/09_2024/7wo4_32638.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo4_32638/09_2024/7wo4_32638.cif" } resolution = 4.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 300 5.16 5 C 45084 2.51 5 N 11820 2.21 5 O 14004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 71208 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "E" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "F" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "G" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "H" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "I" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "J" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "K" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "L" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "M" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "N" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "O" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "P" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "Q" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 212} Chain: "R" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1616 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "J" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "K" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "L" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 33.16, per 1000 atoms: 0.47 Number of scatterers: 71208 At special positions: 0 Unit cell: (373.43, 209.72, 173.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 300 16.00 O 14004 8.00 N 11820 7.00 C 45084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=104, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.05 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 91 " distance=2.03 Simple disulfide: pdb=" SG CYS E 140 " - pdb=" SG CYS E 199 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 146 " - pdb=" SG CYS F 202 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 91 " distance=2.03 Simple disulfide: pdb=" SG CYS G 140 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 199 " distance=2.03 Simple disulfide: pdb=" SG CYS J 15 " - pdb=" SG CYS J 136 " distance=2.03 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 166 " distance=2.03 Simple disulfide: pdb=" SG CYS J 291 " - pdb=" SG CYS J 301 " distance=2.03 Simple disulfide: pdb=" SG CYS J 336 " - pdb=" SG CYS J 361 " distance=2.03 Simple disulfide: pdb=" SG CYS J 379 " - pdb=" SG CYS J 432 " distance=2.03 Simple disulfide: pdb=" SG CYS J 391 " - pdb=" SG CYS J 525 " distance=2.03 Simple disulfide: pdb=" SG CYS J 480 " - pdb=" SG CYS J 488 " distance=2.03 Simple disulfide: pdb=" SG CYS J 538 " - pdb=" SG CYS J 590 " distance=2.03 Simple disulfide: pdb=" SG CYS J 662 " - pdb=" SG CYS J 671 " distance=2.03 Simple disulfide: pdb=" SG CYS J 743 " - pdb=" SG CYS J 749 " distance=2.03 Simple disulfide: pdb=" SG CYS J1032 " - pdb=" SG CYS J1043 " distance=2.03 Simple disulfide: pdb=" SG CYS J1082 " - pdb=" SG CYS J1126 " distance=2.03 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 136 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 166 " distance=2.03 Simple disulfide: pdb=" SG CYS K 291 " - pdb=" SG CYS K 301 " distance=2.02 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.03 Simple disulfide: pdb=" SG CYS K 379 " - pdb=" SG CYS K 432 " distance=2.03 Simple disulfide: pdb=" SG CYS K 391 " - pdb=" SG CYS K 525 " distance=2.03 Simple disulfide: pdb=" SG CYS K 480 " - pdb=" SG CYS K 488 " distance=2.03 Simple disulfide: pdb=" SG CYS K 538 " - pdb=" SG CYS K 590 " distance=2.03 Simple disulfide: pdb=" SG CYS K 617 " - pdb=" SG CYS K 649 " distance=2.03 Simple disulfide: pdb=" SG CYS K 662 " - pdb=" SG CYS K 671 " distance=2.03 Simple disulfide: pdb=" SG CYS K 738 " - pdb=" SG CYS K 760 " distance=2.03 Simple disulfide: pdb=" SG CYS K 743 " - pdb=" SG CYS K 749 " distance=2.03 Simple disulfide: pdb=" SG CYS K1032 " - pdb=" SG CYS K1043 " distance=2.03 Simple disulfide: pdb=" SG CYS K1082 " - pdb=" SG CYS K1126 " distance=2.03 Simple disulfide: pdb=" SG CYS L 15 " - pdb=" SG CYS L 136 " distance=2.03 Simple disulfide: pdb=" SG CYS L 131 " - pdb=" SG CYS L 166 " distance=2.03 Simple disulfide: pdb=" SG CYS L 291 " - pdb=" SG CYS L 301 " distance=2.05 Simple disulfide: pdb=" SG CYS L 336 " - pdb=" SG CYS L 361 " distance=2.03 Simple disulfide: pdb=" SG CYS L 379 " - pdb=" SG CYS L 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 391 " - pdb=" SG CYS L 525 " distance=2.03 Simple disulfide: pdb=" SG CYS L 480 " - pdb=" SG CYS L 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 538 " - pdb=" SG CYS L 590 " distance=2.03 Simple disulfide: pdb=" SG CYS L 617 " - pdb=" SG CYS L 649 " distance=2.04 Simple disulfide: pdb=" SG CYS L 662 " - pdb=" SG CYS L 671 " distance=2.03 Simple disulfide: pdb=" SG CYS L 738 " - pdb=" SG CYS L 760 " distance=2.03 Simple disulfide: pdb=" SG CYS L 743 " - pdb=" SG CYS L 749 " distance=2.03 Simple disulfide: pdb=" SG CYS L1032 " - pdb=" SG CYS L1043 " distance=2.03 Simple disulfide: pdb=" SG CYS L1082 " - pdb=" SG CYS L1126 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 146 " - pdb=" SG CYS M 202 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 91 " distance=2.03 Simple disulfide: pdb=" SG CYS N 140 " - pdb=" SG CYS N 199 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 146 " - pdb=" SG CYS O 202 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 91 " distance=2.03 Simple disulfide: pdb=" SG CYS P 140 " - pdb=" SG CYS P 199 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 146 " - pdb=" SG CYS Q 202 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 91 " distance=2.03 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 199 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 282 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 801 " " NAG A1312 " - " ASN A1098 " " NAG A1313 " - " ASN A 17 " " NAG A1314 " - " ASN A 122 " " NAG A1315 " - " ASN A 149 " " NAG B1301 " - " ASN B1134 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B 282 " " NAG B1310 " - " ASN B 165 " " NAG B1311 " - " ASN B 61 " " NAG B1312 " - " ASN B 17 " " NAG B1313 " - " ASN B 149 " " NAG B1314 " - " ASN B 122 " " NAG B1315 " - " ASN B1074 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C 717 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C 17 " " NAG C1312 " - " ASN C 149 " " NAG C1313 " - " ASN C 61 " " NAG C1314 " - " ASN C 122 " " NAG C1315 " - " ASN C 165 " " NAG J1301 " - " ASN J 165 " " NAG J1302 " - " ASN J 331 " " NAG J1303 " - " ASN J 616 " " NAG J1304 " - " ASN J 709 " " NAG J1305 " - " ASN J 717 " " NAG J1306 " - " ASN J1074 " " NAG J1307 " - " ASN J1134 " " NAG J1308 " - " ASN J 282 " " NAG J1309 " - " ASN J 61 " " NAG J1310 " - " ASN J 801 " " NAG J1311 " - " ASN J1098 " " NAG J1312 " - " ASN J 17 " " NAG J1313 " - " ASN J 122 " " NAG J1314 " - " ASN J 149 " " NAG J1315 " - " ASN J 343 " " NAG K1301 " - " ASN K1134 " " NAG K1302 " - " ASN K1098 " " NAG K1303 " - " ASN K 801 " " NAG K1304 " - " ASN K 717 " " NAG K1305 " - " ASN K 709 " " NAG K1306 " - " ASN K 616 " " NAG K1307 " - " ASN K 343 " " NAG K1308 " - " ASN K 331 " " NAG K1309 " - " ASN K 282 " " NAG K1310 " - " ASN K 165 " " NAG K1311 " - " ASN K 61 " " NAG K1312 " - " ASN K 17 " " NAG K1313 " - " ASN K 149 " " NAG K1314 " - " ASN K 122 " " NAG K1315 " - " ASN K1074 " " NAG L1301 " - " ASN L 282 " " NAG L1302 " - " ASN L 331 " " NAG L1303 " - " ASN L 343 " " NAG L1304 " - " ASN L 616 " " NAG L1305 " - " ASN L 709 " " NAG L1306 " - " ASN L 717 " " NAG L1307 " - " ASN L1074 " " NAG L1308 " - " ASN L1134 " " NAG L1309 " - " ASN L 801 " " NAG L1310 " - " ASN L1098 " " NAG L1311 " - " ASN L 17 " " NAG L1312 " - " ASN L 149 " " NAG L1313 " - " ASN L 61 " " NAG L1314 " - " ASN L 122 " " NAG L1315 " - " ASN L 165 " Time building additional restraints: 13.30 Conformation dependent library (CDL) restraints added in 7.1 seconds 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16920 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 166 sheets defined 16.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.74 Creating SS restraints... Processing helix chain 'A' and resid 253 through 257 removed outlier: 4.258A pdb=" N GLY A 257 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.935A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.777A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.589A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 782 removed outlier: 3.641A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.462A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 966 removed outlier: 4.099A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.712A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1034 removed outlier: 3.539A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A1034 " --> pdb=" O SER A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.913A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.763A pdb=" N ASN B 74 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.526A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.825A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.504A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.776A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.705A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 941 removed outlier: 4.475A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.787A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.555A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.513A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.660A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 342 removed outlier: 3.544A pdb=" N VAL C 341 " --> pdb=" O PHE C 338 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 342 " --> pdb=" O GLY C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 338 through 342' Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.210A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 4.101A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 416 through 421' Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.657A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.516A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.534A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.013A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'E' and resid 82 through 86 Processing helix chain 'E' and resid 190 through 194 removed outlier: 3.578A pdb=" N HIS E 194 " --> pdb=" O TRP E 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.557A pdb=" N THR F 91 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 86 removed outlier: 3.546A pdb=" N ASP G 85 " --> pdb=" O LYS G 82 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 82 through 86' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.896A pdb=" N SER I 31 " --> pdb=" O SER I 28 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN I 32 " --> pdb=" O ILE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 82 through 86 removed outlier: 3.616A pdb=" N GLU I 86 " --> pdb=" O THR I 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 257 removed outlier: 4.250A pdb=" N GLY J 257 " --> pdb=" O SER J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 304 Processing helix chain 'J' and resid 337 through 343 removed outlier: 3.928A pdb=" N VAL J 341 " --> pdb=" O PRO J 337 " (cutoff:3.500A) Processing helix chain 'J' and resid 364 through 368 removed outlier: 3.730A pdb=" N VAL J 367 " --> pdb=" O ASP J 364 " (cutoff:3.500A) Processing helix chain 'J' and resid 403 through 407 removed outlier: 3.593A pdb=" N VAL J 407 " --> pdb=" O GLY J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 502 through 506 Processing helix chain 'J' and resid 737 through 743 Processing helix chain 'J' and resid 746 through 754 Processing helix chain 'J' and resid 755 through 757 No H-bonds generated for 'chain 'J' and resid 755 through 757' Processing helix chain 'J' and resid 760 through 782 removed outlier: 3.640A pdb=" N ASN J 764 " --> pdb=" O CYS J 760 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR J 778 " --> pdb=" O GLN J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 816 through 826 Processing helix chain 'J' and resid 866 through 884 Processing helix chain 'J' and resid 897 through 907 Processing helix chain 'J' and resid 912 through 941 removed outlier: 4.450A pdb=" N LEU J 916 " --> pdb=" O THR J 912 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LYS J 921 " --> pdb=" O TYR J 917 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU J 922 " --> pdb=" O GLU J 918 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR J 941 " --> pdb=" O SER J 937 " (cutoff:3.500A) Processing helix chain 'J' and resid 946 through 966 removed outlier: 4.072A pdb=" N VAL J 951 " --> pdb=" O LYS J 947 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL J 952 " --> pdb=" O LEU J 948 " (cutoff:3.500A) Processing helix chain 'J' and resid 976 through 983 removed outlier: 3.720A pdb=" N ILE J 980 " --> pdb=" O VAL J 976 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG J 983 " --> pdb=" O ASP J 979 " (cutoff:3.500A) Processing helix chain 'J' and resid 985 through 1034 removed outlier: 3.530A pdb=" N GLU J1017 " --> pdb=" O ILE J1013 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL J1033 " --> pdb=" O MET J1029 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU J1034 " --> pdb=" O SER J1030 " (cutoff:3.500A) Processing helix chain 'J' and resid 1140 through 1146 removed outlier: 3.908A pdb=" N GLU J1144 " --> pdb=" O PRO J1140 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 74 removed outlier: 3.839A pdb=" N ASN K 74 " --> pdb=" O SER K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 303 Processing helix chain 'K' and resid 338 through 343 removed outlier: 3.544A pdb=" N PHE K 342 " --> pdb=" O PHE K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 364 through 368 removed outlier: 3.804A pdb=" N VAL K 367 " --> pdb=" O ASP K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 390 removed outlier: 3.502A pdb=" N LEU K 387 " --> pdb=" O PRO K 384 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASN K 388 " --> pdb=" O THR K 385 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU K 390 " --> pdb=" O LEU K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 403 through 407 removed outlier: 3.715A pdb=" N GLU K 406 " --> pdb=" O ARG K 403 " (cutoff:3.500A) Processing helix chain 'K' and resid 737 through 743 Processing helix chain 'K' and resid 747 through 754 Processing helix chain 'K' and resid 759 through 782 removed outlier: 3.684A pdb=" N THR K 778 " --> pdb=" O GLN K 774 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 826 Processing helix chain 'K' and resid 866 through 884 Processing helix chain 'K' and resid 897 through 910 Processing helix chain 'K' and resid 912 through 941 removed outlier: 4.506A pdb=" N LEU K 916 " --> pdb=" O THR K 912 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS K 921 " --> pdb=" O TYR K 917 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU K 922 " --> pdb=" O GLU K 918 " (cutoff:3.500A) Processing helix chain 'K' and resid 942 through 944 No H-bonds generated for 'chain 'K' and resid 942 through 944' Processing helix chain 'K' and resid 945 through 966 removed outlier: 3.765A pdb=" N VAL K 952 " --> pdb=" O LEU K 948 " (cutoff:3.500A) Processing helix chain 'K' and resid 976 through 984 removed outlier: 3.573A pdb=" N ILE K 980 " --> pdb=" O VAL K 976 " (cutoff:3.500A) Processing helix chain 'K' and resid 985 through 1033 removed outlier: 3.509A pdb=" N VAL K 991 " --> pdb=" O PRO K 987 " (cutoff:3.500A) Processing helix chain 'K' and resid 1141 through 1146 removed outlier: 3.647A pdb=" N LEU K1145 " --> pdb=" O LEU K1141 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 304 Processing helix chain 'L' and resid 338 through 343 removed outlier: 4.099A pdb=" N PHE L 342 " --> pdb=" O PHE L 338 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN L 343 " --> pdb=" O GLY L 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 338 through 343' Processing helix chain 'L' and resid 383 through 390 removed outlier: 5.084A pdb=" N ASN L 388 " --> pdb=" O THR L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 421 removed outlier: 4.103A pdb=" N ASP L 420 " --> pdb=" O GLY L 416 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR L 421 " --> pdb=" O LYS L 417 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 416 through 421' Processing helix chain 'L' and resid 738 through 743 Processing helix chain 'L' and resid 747 through 754 Processing helix chain 'L' and resid 758 through 782 removed outlier: 3.681A pdb=" N THR L 778 " --> pdb=" O GLN L 774 " (cutoff:3.500A) Processing helix chain 'L' and resid 816 through 826 removed outlier: 3.520A pdb=" N VAL L 826 " --> pdb=" O LEU L 822 " (cutoff:3.500A) Processing helix chain 'L' and resid 866 through 884 Processing helix chain 'L' and resid 897 through 908 Processing helix chain 'L' and resid 915 through 941 removed outlier: 7.300A pdb=" N LYS L 921 " --> pdb=" O TYR L 917 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU L 922 " --> pdb=" O GLU L 918 " (cutoff:3.500A) Processing helix chain 'L' and resid 945 through 965 removed outlier: 3.509A pdb=" N GLN L 949 " --> pdb=" O LEU L 945 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL L 952 " --> pdb=" O LEU L 948 " (cutoff:3.500A) Processing helix chain 'L' and resid 976 through 983 Processing helix chain 'L' and resid 985 through 1033 Processing helix chain 'L' and resid 1140 through 1145 removed outlier: 4.020A pdb=" N GLU L1144 " --> pdb=" O PRO L1140 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 164 No H-bonds generated for 'chain 'M' and resid 162 through 164' Processing helix chain 'N' and resid 82 through 86 Processing helix chain 'N' and resid 190 through 194 removed outlier: 3.585A pdb=" N HIS N 194 " --> pdb=" O TRP N 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.561A pdb=" N THR O 91 " --> pdb=" O ALA O 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 86 removed outlier: 3.540A pdb=" N ASP P 85 " --> pdb=" O LYS P 82 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU P 86 " --> pdb=" O THR P 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 82 through 86' Processing helix chain 'R' and resid 28 through 32 removed outlier: 3.848A pdb=" N SER R 31 " --> pdb=" O SER R 28 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN R 32 " --> pdb=" O ILE R 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 28 through 32' Processing helix chain 'R' and resid 82 through 86 removed outlier: 3.641A pdb=" N GLU R 86 " --> pdb=" O THR R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 194 removed outlier: 3.569A pdb=" N SER R 193 " --> pdb=" O GLN R 190 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS R 194 " --> pdb=" O TRP R 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 190 through 194' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.829A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 202 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 6.597A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 118 removed outlier: 3.818A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 154 through 158 removed outlier: 6.789A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY A 142 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG A 246 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.849A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.527A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.804A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.804A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.217A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.674A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.818A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 722 removed outlier: 3.818A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.190A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.942A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.513A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.546A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.602A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 153 through 157 removed outlier: 6.332A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR B 145 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.564A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 609 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.790A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.536A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 394 through 396 removed outlier: 4.052A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 565 through 566 removed outlier: 7.373A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 664 through 667 removed outlier: 6.489A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.034A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.555A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.732A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722 removed outlier: 3.732A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.715A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.715A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 78 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.944A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 103 through 104 removed outlier: 3.677A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.516A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 327 removed outlier: 7.017A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.286A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 394 through 400 removed outlier: 3.604A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.853A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 712 through 713 removed outlier: 4.214A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AF6, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.531A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.174A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.791A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.875A pdb=" N SER D 7 " --> pdb=" O SER D 21 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.304A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 58 through 60 removed outlier: 3.996A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET D 34 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 97 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR D 108 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 126 through 129 removed outlier: 3.585A pdb=" N LYS D 149 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA D 142 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 126 through 129 removed outlier: 3.585A pdb=" N LYS D 149 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA D 142 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 159 through 160 removed outlier: 4.279A pdb=" N CYS D 202 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS D 215 " --> pdb=" O CYS D 202 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 46 through 49 removed outlier: 6.811A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR E 90 " --> pdb=" O TYR E 37 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER E 93 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL E 102 " --> pdb=" O SER E 93 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 46 through 49 removed outlier: 6.811A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR E 90 " --> pdb=" O TYR E 37 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 63 through 68 removed outlier: 3.539A pdb=" N SER E 66 " --> pdb=" O SER E 75 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER E 75 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 120 through 121 removed outlier: 5.932A pdb=" N TYR E 178 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER E 181 " --> pdb=" O THR E 168 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.455A pdb=" N LYS E 155 " --> pdb=" O SER E 198 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER E 198 " --> pdb=" O LYS E 155 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 3 through 7 removed outlier: 4.088A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU F 18 " --> pdb=" O MET F 83 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET F 83 " --> pdb=" O LEU F 18 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU F 20 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP F 73 " --> pdb=" O SER F 78 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 58 through 60 removed outlier: 3.564A pdb=" N TYR F 59 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET F 34 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 97 " --> pdb=" O SER F 35 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 58 through 60 removed outlier: 3.564A pdb=" N TYR F 59 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET F 34 " --> pdb=" O ASN F 50 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA F 92 " --> pdb=" O VAL F 115 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.772A pdb=" N SER F 186 " --> pdb=" O CYS F 146 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N SER F 185 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE F 172 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL F 187 " --> pdb=" O HIS F 170 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 201 through 202 removed outlier: 3.627A pdb=" N CYS F 202 " --> pdb=" O LYS F 215 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS F 215 " --> pdb=" O CYS F 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AH8, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.131A pdb=" N VAL G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR G 107 " --> pdb=" O TYR G 89 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.131A pdb=" N VAL G 10 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR G 107 " --> pdb=" O TYR G 89 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER G 93 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL G 102 " --> pdb=" O SER G 93 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 18 through 20 removed outlier: 3.800A pdb=" N ILE G 20 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU G 76 " --> pdb=" O ILE G 20 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 152 through 155 Processing sheet with id=AI3, first strand: chain 'H' and resid 5 through 7 removed outlier: 4.061A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 45 through 51 removed outlier: 6.722A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET H 34 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER H 35 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA H 97 " --> pdb=" O SER H 35 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG H 98 " --> pdb=" O TYR H 108 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR H 108 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 126 through 127 removed outlier: 4.271A pdb=" N SER H 126 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS H 149 " --> pdb=" O SER H 126 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 143 through 144 Processing sheet with id=AI7, first strand: chain 'H' and resid 159 through 160 removed outlier: 3.840A pdb=" N SER H 159 " --> pdb=" O ASN H 203 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN H 203 " --> pdb=" O SER H 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.156A pdb=" N VAL I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'I' and resid 20 through 21 Processing sheet with id=AJ1, first strand: chain 'I' and resid 45 through 50 removed outlier: 7.158A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP I 88 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL I 102 " --> pdb=" O SER I 93 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP I 95 " --> pdb=" O ASN I 100 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN I 100 " --> pdb=" O ASP I 95 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'I' and resid 152 through 155 removed outlier: 3.928A pdb=" N TYR I 197 " --> pdb=" O VAL I 212 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'I' and resid 167 through 168 removed outlier: 3.618A pdb=" N SER I 181 " --> pdb=" O THR I 168 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'J' and resid 28 through 29 removed outlier: 3.853A pdb=" N VAL J 267 " --> pdb=" O THR J 63 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR J 265 " --> pdb=" O PHE J 65 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA J 264 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU J 191 " --> pdb=" O LYS J 206 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS J 202 " --> pdb=" O LYS J 195 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU J 229 " --> pdb=" O PHE J 201 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER J 205 " --> pdb=" O PRO J 225 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'J' and resid 48 through 55 removed outlier: 7.283A pdb=" N THR J 274 " --> pdb=" O ASP J 290 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP J 290 " --> pdb=" O THR J 274 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU J 276 " --> pdb=" O ALA J 288 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA J 288 " --> pdb=" O LEU J 276 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYS J 278 " --> pdb=" O THR J 286 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'J' and resid 83 through 85 Processing sheet with id=AJ7, first strand: chain 'J' and resid 117 through 118 removed outlier: 3.560A pdb=" N PHE J 168 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLU J 132 " --> pdb=" O CYS J 166 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N CYS J 166 " --> pdb=" O GLU J 132 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'J' and resid 154 through 158 removed outlier: 7.022A pdb=" N GLU J 154 " --> pdb=" O TYR J 144 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR J 144 " --> pdb=" O GLU J 154 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU J 156 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY J 142 " --> pdb=" O GLU J 156 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG J 158 " --> pdb=" O PHE J 140 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG J 246 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'J' and resid 311 through 319 removed outlier: 6.832A pdb=" N VAL J 595 " --> pdb=" O THR J 315 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN J 317 " --> pdb=" O GLY J 593 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLY J 593 " --> pdb=" O ASN J 317 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY J 594 " --> pdb=" O GLN J 613 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA J 609 " --> pdb=" O ILE J 598 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY J 648 " --> pdb=" O THR J 645 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'J' and resid 325 through 327 removed outlier: 6.482A pdb=" N ILE J 326 " --> pdb=" O ASN J 542 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP J 574 " --> pdb=" O ILE J 587 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA J 575 " --> pdb=" O GLY J 566 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'J' and resid 376 through 379 removed outlier: 3.822A pdb=" N THR J 376 " --> pdb=" O ALA J 435 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA J 435 " --> pdb=" O THR J 376 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS J 378 " --> pdb=" O VAL J 433 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL J 433 " --> pdb=" O LYS J 378 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS J 432 " --> pdb=" O LEU J 513 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'J' and resid 376 through 379 removed outlier: 3.822A pdb=" N THR J 376 " --> pdb=" O ALA J 435 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA J 435 " --> pdb=" O THR J 376 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS J 378 " --> pdb=" O VAL J 433 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL J 433 " --> pdb=" O LYS J 378 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS J 432 " --> pdb=" O LEU J 513 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE J 400 " --> pdb=" O VAL J 510 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'J' and resid 452 through 454 Processing sheet with id=AK5, first strand: chain 'J' and resid 473 through 474 removed outlier: 3.508A pdb=" N TYR J 489 " --> pdb=" O TYR J 473 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'J' and resid 654 through 655 removed outlier: 6.171A pdb=" N GLU J 654 " --> pdb=" O ALA J 694 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR J 696 " --> pdb=" O GLU J 654 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN J 675 " --> pdb=" O SER J 691 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER J 673 " --> pdb=" O ILE J 693 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE J 670 " --> pdb=" O ILE J 666 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'J' and resid 712 through 713 removed outlier: 3.668A pdb=" N ILE J 712 " --> pdb=" O PHE J1075 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR J1076 " --> pdb=" O SER J1097 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'J' and resid 718 through 722 removed outlier: 3.856A pdb=" N SER J 721 " --> pdb=" O THR J1066 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'J' and resid 718 through 722 removed outlier: 3.856A pdb=" N SER J 721 " --> pdb=" O THR J1066 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA J1056 " --> pdb=" O GLY J1059 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR J1067 " --> pdb=" O HIS J1048 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N HIS J1048 " --> pdb=" O TYR J1067 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'J' and resid 733 through 736 removed outlier: 4.147A pdb=" N LYS J 733 " --> pdb=" O LEU J 861 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'J' and resid 788 through 790 removed outlier: 5.994A pdb=" N ILE J 788 " --> pdb=" O ASN L 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL2 Processing sheet with id=AL3, first strand: chain 'J' and resid 1120 through 1122 Processing sheet with id=AL4, first strand: chain 'K' and resid 28 through 30 removed outlier: 7.458A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL K 90 " --> pdb=" O PHE K 194 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU K 96 " --> pdb=" O ASN K 188 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN K 188 " --> pdb=" O GLU K 96 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL K 193 " --> pdb=" O TYR K 204 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR K 204 " --> pdb=" O VAL K 193 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER K 205 " --> pdb=" O GLU K 224 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU K 224 " --> pdb=" O SER K 205 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'K' and resid 50 through 55 removed outlier: 4.102A pdb=" N ASP K 53 " --> pdb=" O ARG K 273 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE K 55 " --> pdb=" O GLN K 271 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN K 271 " --> pdb=" O PHE K 55 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP K 287 " --> pdb=" O LYS K 278 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'K' and resid 84 through 85 removed outlier: 3.702A pdb=" N ILE K 105 " --> pdb=" O GLN K 239 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'K' and resid 153 through 157 removed outlier: 6.285A pdb=" N GLY K 142 " --> pdb=" O SER K 155 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU K 244 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N TYR K 145 " --> pdb=" O ARG K 246 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'K' and resid 311 through 319 removed outlier: 7.071A pdb=" N VAL K 595 " --> pdb=" O THR K 315 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN K 317 " --> pdb=" O GLY K 593 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY K 593 " --> pdb=" O ASN K 317 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY K 594 " --> pdb=" O GLN K 613 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA K 609 " --> pdb=" O ILE K 598 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL K 610 " --> pdb=" O ILE K 651 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE K 651 " --> pdb=" O VAL K 610 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'K' and resid 325 through 327 removed outlier: 3.769A pdb=" N VAL K 539 " --> pdb=" O GLY K 550 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'K' and resid 376 through 379 removed outlier: 3.515A pdb=" N ALA K 435 " --> pdb=" O THR K 376 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS K 378 " --> pdb=" O VAL K 433 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL K 433 " --> pdb=" O LYS K 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP K 436 " --> pdb=" O ARG K 509 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG K 509 " --> pdb=" O TRP K 436 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE K 402 " --> pdb=" O TYR K 508 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'K' and resid 394 through 396 removed outlier: 4.097A pdb=" N ASN K 394 " --> pdb=" O GLU K 516 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU K 516 " --> pdb=" O ASN K 394 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'K' and resid 452 through 454 Processing sheet with id=AM4, first strand: chain 'K' and resid 473 through 474 Processing sheet with id=AM5, first strand: chain 'K' and resid 565 through 566 removed outlier: 7.423A pdb=" N PHE K 565 " --> pdb=" O PHE L 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM5 Processing sheet with id=AM6, first strand: chain 'K' and resid 664 through 667 removed outlier: 6.498A pdb=" N ILE K 670 " --> pdb=" O ILE K 666 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER K 673 " --> pdb=" O ILE K 693 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN K 675 " --> pdb=" O SER K 691 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'K' and resid 701 through 702 removed outlier: 6.023A pdb=" N ALA K 701 " --> pdb=" O ILE L 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM7 Processing sheet with id=AM8, first strand: chain 'K' and resid 712 through 715 removed outlier: 3.618A pdb=" N LYS K1073 " --> pdb=" O ILE K 714 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'K' and resid 718 through 722 removed outlier: 3.756A pdb=" N SER K 721 " --> pdb=" O THR K1066 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'K' and resid 718 through 722 removed outlier: 3.756A pdb=" N SER K 721 " --> pdb=" O THR K1066 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR K1067 " --> pdb=" O HIS K1048 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N HIS K1048 " --> pdb=" O TYR K1067 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'K' and resid 733 through 736 removed outlier: 4.450A pdb=" N LYS K 733 " --> pdb=" O LEU K 861 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'K' and resid 1120 through 1122 Processing sheet with id=AN4, first strand: chain 'K' and resid 1094 through 1097 Processing sheet with id=AN5, first strand: chain 'L' and resid 27 through 30 removed outlier: 3.820A pdb=" N ALA L 27 " --> pdb=" O TRP L 64 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR L 63 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL L 267 " --> pdb=" O THR L 63 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE L 65 " --> pdb=" O TYR L 265 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR L 265 " --> pdb=" O PHE L 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL L 90 " --> pdb=" O PHE L 194 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N PHE L 201 " --> pdb=" O ASP L 228 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP L 228 " --> pdb=" O PHE L 201 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE L 203 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N HIS L 207 " --> pdb=" O ALA L 222 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N ALA L 222 " --> pdb=" O HIS L 207 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL L 36 " --> pdb=" O LEU L 223 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'L' and resid 27 through 30 removed outlier: 3.820A pdb=" N ALA L 27 " --> pdb=" O TRP L 64 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG L 78 " --> pdb=" O ILE L 68 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'L' and resid 50 through 55 removed outlier: 3.924A pdb=" N ASP L 53 " --> pdb=" O ARG L 273 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG L 273 " --> pdb=" O ASP L 53 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP L 287 " --> pdb=" O LYS L 278 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'L' and resid 84 through 85 Processing sheet with id=AN9, first strand: chain 'L' and resid 116 through 121 removed outlier: 3.672A pdb=" N CYS L 131 " --> pdb=" O SER L 116 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL L 120 " --> pdb=" O VAL L 127 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'L' and resid 143 through 144 Processing sheet with id=AO2, first strand: chain 'L' and resid 311 through 319 removed outlier: 3.530A pdb=" N GLY L 311 " --> pdb=" O THR L 599 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL L 595 " --> pdb=" O THR L 315 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASN L 317 " --> pdb=" O GLY L 593 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY L 593 " --> pdb=" O ASN L 317 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE L 598 " --> pdb=" O ALA L 609 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR L 612 " --> pdb=" O CYS L 649 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'L' and resid 325 through 326 removed outlier: 3.657A pdb=" N VAL L 539 " --> pdb=" O GLY L 550 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR L 588 " --> pdb=" O VAL L 551 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'L' and resid 394 through 400 removed outlier: 3.567A pdb=" N ILE L 434 " --> pdb=" O VAL L 511 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'L' and resid 473 through 474 Processing sheet with id=AO6, first strand: chain 'L' and resid 664 through 667 removed outlier: 6.871A pdb=" N ILE L 670 " --> pdb=" O ILE L 666 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN L 675 " --> pdb=" O SER L 691 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'L' and resid 712 through 713 removed outlier: 4.262A pdb=" N THR L1076 " --> pdb=" O SER L1097 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'L' and resid 718 through 719 Processing sheet with id=AO9, first strand: chain 'L' and resid 722 through 728 removed outlier: 3.540A pdb=" N ALA L1056 " --> pdb=" O GLY L1059 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET L1050 " --> pdb=" O VAL L1065 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'L' and resid 733 through 736 removed outlier: 4.175A pdb=" N LYS L 733 " --> pdb=" O LEU L 861 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'L' and resid 1120 through 1125 removed outlier: 4.838A pdb=" N ALA L1087 " --> pdb=" O SER L1123 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'M' and resid 6 through 7 removed outlier: 3.850A pdb=" N SER M 7 " --> pdb=" O SER M 21 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER M 21 " --> pdb=" O SER M 7 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU M 18 " --> pdb=" O MET M 83 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.279A pdb=" N GLY M 10 " --> pdb=" O THR M 116 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'M' and resid 58 through 60 removed outlier: 3.981A pdb=" N ALA M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET M 34 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA M 97 " --> pdb=" O SER M 35 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR M 108 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'M' and resid 126 through 129 removed outlier: 3.511A pdb=" N LYS M 149 " --> pdb=" O SER M 126 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA M 142 " --> pdb=" O VAL M 190 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'M' and resid 126 through 129 removed outlier: 3.511A pdb=" N LYS M 149 " --> pdb=" O SER M 126 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA M 142 " --> pdb=" O VAL M 190 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'M' and resid 159 through 160 removed outlier: 4.279A pdb=" N CYS M 202 " --> pdb=" O LYS M 215 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS M 215 " --> pdb=" O CYS M 202 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'N' and resid 46 through 49 removed outlier: 6.787A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR N 90 " --> pdb=" O TYR N 37 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER N 93 " --> pdb=" O VAL N 102 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL N 102 " --> pdb=" O SER N 93 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'N' and resid 46 through 49 removed outlier: 6.787A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR N 90 " --> pdb=" O TYR N 37 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'N' and resid 63 through 68 removed outlier: 3.735A pdb=" N SER N 75 " --> pdb=" O SER N 66 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'N' and resid 120 through 121 removed outlier: 5.941A pdb=" N TYR N 178 " --> pdb=" O ASP N 144 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER N 181 " --> pdb=" O THR N 168 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'N' and resid 152 through 153 removed outlier: 3.605A pdb=" N GLN N 200 " --> pdb=" O ALA N 153 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'O' and resid 3 through 7 removed outlier: 4.131A pdb=" N GLN O 3 " --> pdb=" O SER O 25 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER O 25 " --> pdb=" O GLN O 3 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL O 5 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU O 18 " --> pdb=" O MET O 83 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET O 83 " --> pdb=" O LEU O 18 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU O 20 " --> pdb=" O LEU O 81 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER O 78 " --> pdb=" O ASP O 73 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP O 73 " --> pdb=" O SER O 78 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'O' and resid 58 through 60 removed outlier: 3.531A pdb=" N TYR O 59 " --> pdb=" O ASN O 50 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N MET O 34 " --> pdb=" O ASN O 50 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA O 97 " --> pdb=" O SER O 35 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL O 37 " --> pdb=" O PHE O 95 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA O 92 " --> pdb=" O VAL O 115 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'O' and resid 127 through 129 removed outlier: 3.814A pdb=" N SER O 186 " --> pdb=" O CYS O 146 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER O 185 " --> pdb=" O PHE O 172 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE O 172 " --> pdb=" O SER O 185 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL O 187 " --> pdb=" O HIS O 170 " (cutoff:3.500A) Processing sheet with id=AQ8, first strand: chain 'O' and resid 201 through 202 removed outlier: 3.582A pdb=" N CYS O 202 " --> pdb=" O LYS O 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS O 215 " --> pdb=" O CYS O 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AQ8 Processing sheet with id=AQ9, first strand: chain 'P' and resid 4 through 5 Processing sheet with id=AR1, first strand: chain 'P' and resid 9 through 12 removed outlier: 6.125A pdb=" N VAL P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR P 107 " --> pdb=" O TYR P 89 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'P' and resid 9 through 12 removed outlier: 6.125A pdb=" N VAL P 10 " --> pdb=" O THR P 110 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR P 107 " --> pdb=" O TYR P 89 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER P 93 " --> pdb=" O VAL P 102 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL P 102 " --> pdb=" O SER P 93 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'P' and resid 18 through 20 removed outlier: 3.776A pdb=" N ILE P 20 " --> pdb=" O LEU P 76 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU P 76 " --> pdb=" O ILE P 20 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'P' and resid 152 through 155 Processing sheet with id=AR5, first strand: chain 'Q' and resid 5 through 7 removed outlier: 4.061A pdb=" N VAL Q 5 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER Q 7 " --> pdb=" O SER Q 21 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER Q 21 " --> pdb=" O SER Q 7 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'Q' and resid 45 through 51 removed outlier: 6.711A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASN Q 50 " --> pdb=" O MET Q 34 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N MET Q 34 " --> pdb=" O ASN Q 50 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER Q 35 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA Q 97 " --> pdb=" O SER Q 35 " (cutoff:3.500A) Processing sheet with id=AR7, first strand: chain 'Q' and resid 126 through 127 removed outlier: 4.188A pdb=" N SER Q 126 " --> pdb=" O LYS Q 149 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS Q 149 " --> pdb=" O SER Q 126 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'Q' and resid 143 through 144 Processing sheet with id=AR9, first strand: chain 'Q' and resid 159 through 160 removed outlier: 3.897A pdb=" N SER Q 159 " --> pdb=" O ASN Q 203 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN Q 203 " --> pdb=" O SER Q 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR9 Processing sheet with id=AS1, first strand: chain 'R' and resid 10 through 11 removed outlier: 7.177A pdb=" N VAL R 10 " --> pdb=" O THR R 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AS1 Processing sheet with id=AS2, first strand: chain 'R' and resid 20 through 21 removed outlier: 3.519A pdb=" N SER R 75 " --> pdb=" O SER R 66 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'R' and resid 45 through 50 removed outlier: 7.182A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR R 37 " --> pdb=" O TYR R 90 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP R 88 " --> pdb=" O GLN R 39 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER R 93 " --> pdb=" O VAL R 102 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL R 102 " --> pdb=" O SER R 93 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP R 95 " --> pdb=" O ASN R 100 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASN R 100 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'R' and resid 152 through 155 removed outlier: 3.974A pdb=" N TYR R 197 " --> pdb=" O VAL R 212 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL R 212 " --> pdb=" O TYR R 197 " (cutoff:3.500A) 1997 hydrogen bonds defined for protein. 5385 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: 45.21 Time building geometry restraints manager: 16.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22716 1.34 - 1.46: 16597 1.46 - 1.58: 33185 1.58 - 1.70: 0 1.70 - 1.83: 378 Bond restraints: 72876 Sorted by residual: bond pdb=" CA ASP B 290 " pdb=" C ASP B 290 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.12e-02 7.97e+03 1.55e+01 bond pdb=" CA ASP J 294 " pdb=" C ASP J 294 " ideal model delta sigma weight residual 1.519 1.553 -0.034 1.01e-02 9.80e+03 1.16e+01 bond pdb=" CA CYS K 291 " pdb=" C CYS K 291 " ideal model delta sigma weight residual 1.527 1.486 0.041 1.20e-02 6.94e+03 1.16e+01 bond pdb=" CA GLN C 613 " pdb=" C GLN C 613 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.35e-02 5.49e+03 7.14e+00 bond pdb=" C1 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.17e+00 ... (remaining 72871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 98147 2.01 - 4.02: 1086 4.02 - 6.03: 69 6.03 - 8.04: 7 8.04 - 10.05: 3 Bond angle restraints: 99312 Sorted by residual: angle pdb=" N LEU B 293 " pdb=" CA LEU B 293 " pdb=" C LEU B 293 " ideal model delta sigma weight residual 114.56 105.09 9.47 1.27e+00 6.20e-01 5.55e+01 angle pdb=" N GLN C 613 " pdb=" CA GLN C 613 " pdb=" C GLN C 613 " ideal model delta sigma weight residual 109.59 117.68 -8.09 1.47e+00 4.63e-01 3.03e+01 angle pdb=" N GLN L 613 " pdb=" CA GLN L 613 " pdb=" C GLN L 613 " ideal model delta sigma weight residual 109.59 116.33 -6.74 1.47e+00 4.63e-01 2.10e+01 angle pdb=" C ASP A 290 " pdb=" CA ASP A 290 " pdb=" CB ASP A 290 " ideal model delta sigma weight residual 113.33 103.28 10.05 2.26e+00 1.96e-01 1.98e+01 angle pdb=" N LEU L 293 " pdb=" CA LEU L 293 " pdb=" C LEU L 293 " ideal model delta sigma weight residual 113.23 107.79 5.44 1.24e+00 6.50e-01 1.92e+01 ... (remaining 99307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.10: 43348 23.10 - 46.21: 962 46.21 - 69.31: 131 69.31 - 92.41: 31 92.41 - 115.51: 42 Dihedral angle restraints: 44514 sinusoidal: 18126 harmonic: 26388 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -123.99 37.99 1 1.00e+01 1.00e-02 2.03e+01 dihedral pdb=" CB CYS J1032 " pdb=" SG CYS J1032 " pdb=" SG CYS J1043 " pdb=" CB CYS J1043 " ideal model delta sinusoidal sigma weight residual -86.00 -122.64 36.64 1 1.00e+01 1.00e-02 1.90e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 128.24 -35.24 1 1.00e+01 1.00e-02 1.76e+01 ... (remaining 44511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 10212 0.069 - 0.137: 1257 0.137 - 0.206: 17 0.206 - 0.274: 4 0.274 - 0.343: 6 Chirality restraints: 11496 Sorted by residual: chirality pdb=" C1 NAG J1315 " pdb=" ND2 ASN J 343 " pdb=" C2 NAG J1315 " pdb=" O5 NAG J1315 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C1 NAG J1306 " pdb=" ND2 ASN J1074 " pdb=" C2 NAG J1306 " pdb=" O5 NAG J1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 11493 not shown) Planarity restraints: 12840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J1315 " -0.071 2.00e-02 2.50e+03 5.88e-02 4.31e+01 pdb=" C7 NAG J1315 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG J1315 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG J1315 " 0.092 2.00e-02 2.50e+03 pdb=" O7 NAG J1315 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU L 560 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO L 561 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO L 561 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 561 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 560 " 0.034 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO C 561 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " 0.029 5.00e-02 4.00e+02 ... (remaining 12837 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 10958 2.77 - 3.30: 65264 3.30 - 3.83: 113693 3.83 - 4.37: 125047 4.37 - 4.90: 224704 Nonbonded interactions: 539666 Sorted by model distance: nonbonded pdb=" OE1 GLN O 177 " pdb=" OG SER O 183 " model vdw 2.234 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.237 3.040 nonbonded pdb=" OE1 GLN F 177 " pdb=" OG SER F 183 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR J 756 " pdb=" OD1 ASP J 994 " model vdw 2.243 3.040 nonbonded pdb=" O GLY K 880 " pdb=" OG SER K 884 " model vdw 2.250 3.040 ... (remaining 539661 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 134.680 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: 0.120 Extract box with map and model: 2.470 Check model and map are aligned: 0.430 Set scattering table: 0.580 Process input model: 149.680 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.600 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 293.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 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 : 0.003 0.050 72876 Z= 0.170 Angle : 0.480 10.052 99312 Z= 0.259 Chirality : 0.042 0.343 11496 Planarity : 0.003 0.059 12750 Dihedral : 9.881 115.514 27282 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.06 % Favored : 93.93 % Rotamer: Outliers : 3.89 % Allowed : 5.85 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.08), residues: 9024 helix: 0.76 (0.14), residues: 1250 sheet: -2.67 (0.10), residues: 1940 loop : -3.40 (0.06), residues: 5834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP O 33 HIS 0.002 0.000 HIS O 206 PHE 0.009 0.001 PHE C 106 TYR 0.013 0.001 TYR J 145 ARG 0.001 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1655 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 1352 time to evaluate : 6.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 HIS cc_start: 0.6453 (p90) cc_final: 0.6063 (p-80) REVERT: A 248 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.6239 (t80) REVERT: A 265 TYR cc_start: 0.8555 (p90) cc_final: 0.7992 (p90) REVERT: A 427 ASP cc_start: 0.7148 (m-30) cc_final: 0.6604 (p0) REVERT: A 433 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8187 (m) REVERT: A 452 LEU cc_start: 0.7753 (mt) cc_final: 0.7415 (mt) REVERT: A 453 TYR cc_start: 0.7606 (p90) cc_final: 0.7114 (p90) REVERT: A 464 PHE cc_start: 0.6820 (m-80) cc_final: 0.6340 (m-80) REVERT: A 675 GLN cc_start: 0.6431 (mt0) cc_final: 0.5976 (mt0) REVERT: A 753 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8679 (tt) REVERT: A 886 TRP cc_start: 0.7521 (p90) cc_final: 0.7210 (p90) REVERT: A 900 MET cc_start: 0.5824 (mtp) cc_final: 0.5590 (mtm) REVERT: A 981 LEU cc_start: 0.8122 (pp) cc_final: 0.7468 (tt) REVERT: A 1050 MET cc_start: 0.5730 (ptt) cc_final: 0.5401 (ptm) REVERT: B 176 LEU cc_start: 0.8033 (tp) cc_final: 0.7789 (pp) REVERT: B 228 ASP cc_start: 0.8102 (t0) cc_final: 0.7753 (t0) REVERT: B 237 ARG cc_start: 0.7875 (mtp-110) cc_final: 0.7661 (mtp85) REVERT: B 317 ASN cc_start: 0.7184 (t0) cc_final: 0.6644 (p0) REVERT: B 417 LYS cc_start: 0.9056 (ttpt) cc_final: 0.8791 (ttpp) REVERT: B 517 LEU cc_start: 0.7597 (mt) cc_final: 0.7187 (pp) REVERT: B 546 LEU cc_start: 0.5089 (OUTLIER) cc_final: 0.4732 (pp) REVERT: B 586 ASP cc_start: 0.8244 (t70) cc_final: 0.7884 (t0) REVERT: B 790 LYS cc_start: 0.7539 (mtmm) cc_final: 0.7195 (tptm) REVERT: B 886 TRP cc_start: 0.6496 (p90) cc_final: 0.6276 (p90) REVERT: B 1019 ARG cc_start: 0.6357 (ttp-110) cc_final: 0.5257 (tpp-160) REVERT: C 137 ASN cc_start: 0.8565 (m-40) cc_final: 0.8318 (t0) REVERT: C 215 ASP cc_start: 0.7732 (m-30) cc_final: 0.7268 (p0) REVERT: C 216 LEU cc_start: 0.6510 (tp) cc_final: 0.6157 (tt) REVERT: C 249 LEU cc_start: 0.7501 (mt) cc_final: 0.7078 (tt) REVERT: C 515 PHE cc_start: 0.7773 (m-80) cc_final: 0.7018 (m-10) REVERT: C 697 MET cc_start: 0.7149 (ptm) cc_final: 0.6907 (ptm) REVERT: C 752 LEU cc_start: 0.8890 (mt) cc_final: 0.8181 (mt) REVERT: C 1019 ARG cc_start: 0.6171 (tmm-80) cc_final: 0.5943 (ttp80) REVERT: C 1038 LYS cc_start: 0.7831 (mmtp) cc_final: 0.7410 (mmmt) REVERT: C 1073 LYS cc_start: 0.7213 (tttm) cc_final: 0.6786 (mtmt) REVERT: D 11 LEU cc_start: 0.7554 (pt) cc_final: 0.7280 (pt) REVERT: D 12 VAL cc_start: 0.6367 (m) cc_final: 0.5877 (p) REVERT: D 34 MET cc_start: 0.6287 (mmt) cc_final: 0.5961 (mmm) REVERT: D 60 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7536 (m-80) REVERT: D 86 VAL cc_start: 0.6829 (OUTLIER) cc_final: 0.6379 (p) REVERT: D 150 ASP cc_start: 0.6268 (m-30) cc_final: 0.6015 (t0) REVERT: E 17 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7647 (m) REVERT: E 32 ASN cc_start: 0.7546 (m-40) cc_final: 0.7176 (m-40) REVERT: E 52 ASP cc_start: 0.7753 (t0) cc_final: 0.7480 (t70) REVERT: E 69 SER cc_start: 0.7831 (t) cc_final: 0.7304 (p) REVERT: E 82 LYS cc_start: 0.8024 (mtmm) cc_final: 0.7793 (mtpp) REVERT: E 98 ASN cc_start: 0.7949 (p0) cc_final: 0.7720 (p0) REVERT: E 183 TYR cc_start: 0.5036 (m-80) cc_final: 0.4496 (m-10) REVERT: E 191 TRP cc_start: 0.2574 (OUTLIER) cc_final: 0.1483 (m100) REVERT: F 77 ASN cc_start: 0.8415 (m110) cc_final: 0.7587 (t0) REVERT: F 123 LYS cc_start: 0.5837 (ptmt) cc_final: 0.5227 (mttp) REVERT: F 146 CYS cc_start: 0.3237 (OUTLIER) cc_final: 0.2688 (p) REVERT: F 207 LYS cc_start: 0.8225 (mmtm) cc_final: 0.7979 (mmtm) REVERT: G 50 TYR cc_start: 0.7770 (p90) cc_final: 0.7406 (p90) REVERT: G 89 TYR cc_start: 0.8007 (m-80) cc_final: 0.7228 (m-80) REVERT: G 130 GLU cc_start: 0.3785 (OUTLIER) cc_final: 0.2903 (pt0) REVERT: G 189 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: G 192 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.6679 (tptp) REVERT: H 34 MET cc_start: 0.7513 (mmt) cc_final: 0.7238 (mmm) REVERT: H 52 ASN cc_start: 0.6381 (OUTLIER) cc_final: 0.5674 (t0) REVERT: H 73 ASP cc_start: 0.7772 (t0) cc_final: 0.7286 (t70) REVERT: H 80 PHE cc_start: 0.7903 (m-80) cc_final: 0.7162 (m-80) REVERT: H 89 GLU cc_start: 0.6378 (pm20) cc_final: 0.5897 (pm20) REVERT: H 136 SER cc_start: 0.0747 (OUTLIER) cc_final: -0.0013 (t) REVERT: H 220 LYS cc_start: -0.1515 (OUTLIER) cc_final: -0.1836 (mttp) REVERT: I 171 SER cc_start: 0.7269 (t) cc_final: 0.7048 (p) REVERT: I 192 LYS cc_start: 0.3933 (OUTLIER) cc_final: 0.2999 (tppt) REVERT: J 105 ILE cc_start: 0.7682 (pt) cc_final: 0.7456 (pt) REVERT: J 129 LYS cc_start: 0.7295 (ptpt) cc_final: 0.7073 (ptpp) REVERT: J 248 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.7156 (t80) REVERT: J 304 LYS cc_start: 0.8527 (mptt) cc_final: 0.8295 (ptmt) REVERT: J 326 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8295 (pt) REVERT: J 408 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7938 (ptp90) REVERT: J 433 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8189 (m) REVERT: J 517 LEU cc_start: 0.8382 (tm) cc_final: 0.7607 (pt) REVERT: J 675 GLN cc_start: 0.6637 (mt0) cc_final: 0.6269 (mt0) REVERT: J 886 TRP cc_start: 0.7795 (p90) cc_final: 0.7474 (p90) REVERT: J 984 LEU cc_start: 0.7116 (tp) cc_final: 0.6644 (tp) REVERT: J 1141 LEU cc_start: 0.8717 (tp) cc_final: 0.8508 (tp) REVERT: K 96 GLU cc_start: 0.6105 (pt0) cc_final: 0.5229 (pt0) REVERT: K 137 ASN cc_start: 0.6505 (m-40) cc_final: 0.6224 (m110) REVERT: K 147 LYS cc_start: 0.4174 (OUTLIER) cc_final: 0.3343 (mmpt) REVERT: K 228 ASP cc_start: 0.7858 (t0) cc_final: 0.7297 (t0) REVERT: K 323 THR cc_start: 0.7936 (p) cc_final: 0.7699 (p) REVERT: K 452 LEU cc_start: 0.8287 (mp) cc_final: 0.8016 (mt) REVERT: K 512 VAL cc_start: 0.7922 (OUTLIER) cc_final: 0.7701 (t) REVERT: K 546 LEU cc_start: 0.5762 (OUTLIER) cc_final: 0.4611 (pp) REVERT: K 712 ILE cc_start: 0.7835 (mm) cc_final: 0.7594 (tt) REVERT: K 886 TRP cc_start: 0.7185 (p90) cc_final: 0.6904 (p90) REVERT: K 933 LYS cc_start: 0.7518 (mttm) cc_final: 0.7180 (mmtm) REVERT: L 133 PHE cc_start: 0.5760 (m-10) cc_final: 0.5489 (m-80) REVERT: L 182 LYS cc_start: 0.6323 (OUTLIER) cc_final: 0.5449 (mttt) REVERT: L 215 ASP cc_start: 0.7714 (m-30) cc_final: 0.7386 (p0) REVERT: L 216 LEU cc_start: 0.7235 (tp) cc_final: 0.6995 (tt) REVERT: L 365 TYR cc_start: 0.6949 (m-80) cc_final: 0.6674 (m-80) REVERT: L 378 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7030 (tptt) REVERT: L 396 TYR cc_start: 0.7465 (m-10) cc_final: 0.7058 (m-10) REVERT: L 423 TYR cc_start: 0.5737 (t80) cc_final: 0.5420 (t80) REVERT: L 436 TRP cc_start: 0.7049 (p90) cc_final: 0.6766 (p90) REVERT: L 451 TYR cc_start: 0.4843 (m-80) cc_final: 0.4106 (m-10) REVERT: L 515 PHE cc_start: 0.7382 (m-80) cc_final: 0.7071 (m-80) REVERT: L 651 ILE cc_start: 0.8227 (mt) cc_final: 0.7991 (mt) REVERT: L 752 LEU cc_start: 0.9109 (mt) cc_final: 0.8400 (mt) REVERT: L 1005 GLN cc_start: 0.7815 (mt0) cc_final: 0.7457 (mm-40) REVERT: L 1019 ARG cc_start: 0.6165 (tmm-80) cc_final: 0.5814 (ttp80) REVERT: L 1038 LYS cc_start: 0.7924 (mmtp) cc_final: 0.7581 (mmmt) REVERT: M 60 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.6790 (m-80) REVERT: N 20 ILE cc_start: 0.6981 (mt) cc_final: 0.6532 (mt) REVERT: N 83 THR cc_start: 0.7986 (t) cc_final: 0.7769 (p) REVERT: N 88 ASP cc_start: 0.7953 (m-30) cc_final: 0.6905 (p0) REVERT: N 109 LEU cc_start: 0.7335 (tp) cc_final: 0.7120 (tp) REVERT: O 62 ASP cc_start: 0.8784 (p0) cc_final: 0.8564 (p0) REVERT: O 77 ASN cc_start: 0.8569 (m110) cc_final: 0.8042 (t0) REVERT: O 146 CYS cc_start: 0.4335 (OUTLIER) cc_final: 0.3703 (p) REVERT: O 212 LYS cc_start: 0.5379 (mmtt) cc_final: 0.4997 (mmtt) REVERT: P 37 TYR cc_start: 0.8425 (m-80) cc_final: 0.8105 (m-80) REVERT: P 55 ARG cc_start: 0.7380 (ttm110) cc_final: 0.6264 (ttm-80) REVERT: P 85 ASP cc_start: 0.7760 (m-30) cc_final: 0.7194 (m-30) REVERT: P 89 TYR cc_start: 0.7912 (m-80) cc_final: 0.7473 (m-80) REVERT: P 144 ASP cc_start: 0.5518 (m-30) cc_final: 0.4947 (t0) REVERT: P 189 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7507 (pm20) REVERT: P 190 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6353 (tt0) REVERT: P 192 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.6282 (tptp) REVERT: P 195 ARG cc_start: 0.7158 (mmm160) cc_final: 0.6841 (mmm160) REVERT: Q 50 ASN cc_start: 0.6359 (OUTLIER) cc_final: 0.4806 (t0) REVERT: Q 51 ILE cc_start: 0.6846 (OUTLIER) cc_final: 0.5749 (tt) REVERT: Q 73 ASP cc_start: 0.8251 (t0) cc_final: 0.7993 (t0) REVERT: Q 80 PHE cc_start: 0.8294 (m-80) cc_final: 0.7466 (m-80) REVERT: Q 83 MET cc_start: 0.7028 (mtt) cc_final: 0.6663 (mpp) REVERT: Q 98 ARG cc_start: 0.7320 (ptt90) cc_final: 0.7107 (tmm-80) REVERT: Q 160 TRP cc_start: 0.6241 (m100) cc_final: 0.5896 (m100) REVERT: Q 212 LYS cc_start: 0.7132 (mmtt) cc_final: 0.6528 (mmtt) REVERT: R 4 MET cc_start: 0.7933 (mmm) cc_final: 0.6991 (mtm) REVERT: R 12 GLU cc_start: 0.7145 (tt0) cc_final: 0.6823 (tm-30) REVERT: R 90 TYR cc_start: 0.7571 (m-80) cc_final: 0.7198 (m-80) REVERT: R 102 VAL cc_start: 0.8153 (t) cc_final: 0.7883 (p) outliers start: 303 outliers final: 51 residues processed: 1570 average time/residue: 0.6940 time to fit residues: 1845.7234 Evaluate side-chains 724 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 641 time to evaluate : 6.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 759 optimal weight: 1.9990 chunk 682 optimal weight: 2.9990 chunk 378 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 460 optimal weight: 1.9990 chunk 364 optimal weight: 0.6980 chunk 705 optimal weight: 9.9990 chunk 272 optimal weight: 0.9990 chunk 428 optimal weight: 6.9990 chunk 525 optimal weight: 0.6980 chunk 817 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 23 GLN A 69 HIS A 115 GLN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 GLN A 185 ASN A 360 ASN A 409 GLN A 439 ASN A 450 ASN A 493 GLN A 607 GLN A 655 HIS A 774 GLN A 872 GLN A 935 GLN A 957 GLN A 992 GLN A1002 GLN A1011 GLN A1048 HIS A1101 HIS B 23 GLN B 49 HIS B 69 HIS B 164 ASN B 183 GLN B 218 GLN B 271 GLN B 280 ASN B 409 GLN B 414 GLN B 439 ASN B 460 ASN B 493 GLN B 498 GLN B 536 ASN B 607 GLN B 907 ASN B1011 GLN B1048 HIS C 23 GLN C 146 HIS C 188 ASN C 218 GLN C 409 GLN C 493 GLN C 580 GLN C 613 GLN C 774 GLN C 872 GLN C 920 GLN C 954 GLN C 965 GLN C 992 GLN C1011 GLN C1048 HIS C1108 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 ASN E 32 ASN E 200 GLN F 177 GLN G 6 GLN G 99 HIS G 100 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 39 GLN H 74 ASN H 84 ASN I 39 GLN I 99 HIS J 14 GLN J 23 GLN J 99 ASN J 148 ASN J 183 GLN J 185 ASN J 360 ASN J 409 GLN J 414 GLN J 439 ASN J 450 ASN J 493 GLN J 655 HIS J 762 GLN J 872 GLN J 913 GLN J 992 GLN J1002 GLN J1011 GLN J1048 HIS J1101 HIS K 23 GLN K 30 ASN K 146 HIS K 218 GLN K 271 GLN K 354 ASN K 360 ASN K 409 GLN K 414 GLN K 439 ASN K 460 ASN K 493 GLN K 498 GLN K 536 ASN ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 901 GLN K 907 ASN K1011 GLN K1048 HIS L 23 GLN L 125 ASN L 218 GLN L 409 GLN L 493 GLN L 580 GLN L 613 GLN L 784 GLN L 872 GLN ** L 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 914 ASN L 920 GLN ** L 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 954 GLN L 965 GLN L 992 GLN L1002 GLN L1011 GLN L1048 HIS ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 ASN M 177 GLN N 190 GLN O 177 GLN ** O 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 99 HIS P 100 ASN P 200 GLN Q 6 GLN Q 77 ASN Q 177 GLN R 38 GLN R 200 GLN Total number of N/Q/H flips: 139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 72876 Z= 0.239 Angle : 0.606 12.043 99312 Z= 0.305 Chirality : 0.049 0.801 11496 Planarity : 0.004 0.058 12750 Dihedral : 7.188 107.375 11652 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.06 % Allowed : 2.72 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.08), residues: 9024 helix: 1.50 (0.15), residues: 1258 sheet: -2.05 (0.11), residues: 2119 loop : -3.01 (0.07), residues: 5647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP J 152 HIS 0.009 0.001 HIS J1064 PHE 0.023 0.002 PHE A 400 TYR 0.024 0.002 TYR J 144 ARG 0.010 0.001 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 859 time to evaluate : 6.270 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 VAL cc_start: 0.8355 (t) cc_final: 0.7887 (p) REVERT: A 145 TYR cc_start: 0.6048 (p90) cc_final: 0.5593 (p90) REVERT: A 146 HIS cc_start: 0.6266 (p90) cc_final: 0.5796 (p-80) REVERT: A 210 ILE cc_start: 0.8123 (tp) cc_final: 0.7911 (tp) REVERT: A 212 LEU cc_start: 0.8462 (mm) cc_final: 0.8094 (mm) REVERT: A 265 TYR cc_start: 0.8169 (p90) cc_final: 0.7491 (p90) REVERT: A 464 PHE cc_start: 0.6732 (m-80) cc_final: 0.6387 (m-80) REVERT: A 738 CYS cc_start: 0.7043 (t) cc_final: 0.6712 (t) REVERT: A 760 CYS cc_start: 0.7757 (p) cc_final: 0.7473 (m) REVERT: A 886 TRP cc_start: 0.7715 (p90) cc_final: 0.7202 (p90) REVERT: A 981 LEU cc_start: 0.8147 (pp) cc_final: 0.7609 (tt) REVERT: B 237 ARG cc_start: 0.8058 (mtp-110) cc_final: 0.7748 (mtp85) REVERT: B 492 LEU cc_start: 0.7433 (mm) cc_final: 0.7139 (tp) REVERT: B 517 LEU cc_start: 0.7634 (mt) cc_final: 0.7194 (pp) REVERT: B 886 TRP cc_start: 0.6457 (p90) cc_final: 0.6210 (p90) REVERT: C 215 ASP cc_start: 0.7920 (m-30) cc_final: 0.7443 (p0) REVERT: C 249 LEU cc_start: 0.7494 (mt) cc_final: 0.7050 (tt) REVERT: C 515 PHE cc_start: 0.7701 (m-80) cc_final: 0.7103 (m-10) REVERT: C 697 MET cc_start: 0.7077 (ptm) cc_final: 0.6768 (ptm) REVERT: C 740 MET cc_start: 0.7445 (mmt) cc_final: 0.7238 (mmp) REVERT: C 1019 ARG cc_start: 0.6298 (tmm-80) cc_final: 0.5812 (ttp80) REVERT: C 1038 LYS cc_start: 0.7761 (mmtp) cc_final: 0.7351 (mmmt) REVERT: C 1073 LYS cc_start: 0.7334 (tttm) cc_final: 0.6921 (mtmt) REVERT: D 11 LEU cc_start: 0.7398 (pt) cc_final: 0.7173 (pt) REVERT: D 12 VAL cc_start: 0.6456 (m) cc_final: 0.6247 (p) REVERT: D 51 ILE cc_start: 0.8964 (tt) cc_final: 0.8745 (tt) REVERT: D 150 ASP cc_start: 0.6348 (m-30) cc_final: 0.5994 (t0) REVERT: D 177 GLN cc_start: 0.7074 (tm-30) cc_final: 0.6400 (tm-30) REVERT: E 12 GLU cc_start: 0.8430 (tt0) cc_final: 0.7890 (tm-30) REVERT: E 82 LYS cc_start: 0.8067 (mtmm) cc_final: 0.7638 (mtmm) REVERT: E 123 LEU cc_start: 0.7886 (tp) cc_final: 0.7635 (tp) REVERT: E 183 TYR cc_start: 0.5029 (m-80) cc_final: 0.4450 (m-80) REVERT: F 77 ASN cc_start: 0.8408 (m110) cc_final: 0.8064 (t0) REVERT: F 82 GLN cc_start: 0.6797 (tt0) cc_final: 0.6515 (pt0) REVERT: F 123 LYS cc_start: 0.5910 (ptmt) cc_final: 0.5398 (mttp) REVERT: G 40 ARG cc_start: 0.7591 (tpp80) cc_final: 0.7012 (mmt90) REVERT: G 72 ASN cc_start: 0.7247 (m-40) cc_final: 0.7005 (m-40) REVERT: G 89 TYR cc_start: 0.7529 (m-80) cc_final: 0.7315 (m-10) REVERT: H 34 MET cc_start: 0.7297 (mmt) cc_final: 0.6614 (mmm) REVERT: H 50 ASN cc_start: 0.8378 (m-40) cc_final: 0.8037 (m110) REVERT: H 73 ASP cc_start: 0.7394 (t0) cc_final: 0.6719 (t70) REVERT: H 80 PHE cc_start: 0.7947 (m-80) cc_final: 0.6910 (m-80) REVERT: H 89 GLU cc_start: 0.6914 (pm20) cc_final: 0.6587 (pp20) REVERT: H 210 ASN cc_start: 0.7451 (t0) cc_final: 0.6967 (t0) REVERT: J 177 MET cc_start: 0.6946 (mtt) cc_final: 0.6149 (mtt) REVERT: J 191 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6318 (mt-10) REVERT: J 886 TRP cc_start: 0.7975 (p90) cc_final: 0.7688 (p90) REVERT: J 983 ARG cc_start: 0.7734 (ppt170) cc_final: 0.7507 (ppt170) REVERT: J 1141 LEU cc_start: 0.8778 (tp) cc_final: 0.8572 (tp) REVERT: K 96 GLU cc_start: 0.6354 (pt0) cc_final: 0.5490 (pt0) REVERT: K 202 LYS cc_start: 0.8604 (mptt) cc_final: 0.8315 (mmmt) REVERT: K 228 ASP cc_start: 0.8046 (t0) cc_final: 0.7462 (t0) REVERT: K 452 LEU cc_start: 0.8228 (mp) cc_final: 0.7997 (mt) REVERT: K 481 ASN cc_start: 0.7105 (t0) cc_final: 0.6898 (t0) REVERT: K 549 THR cc_start: 0.7944 (m) cc_final: 0.7664 (p) REVERT: K 712 ILE cc_start: 0.7731 (mm) cc_final: 0.7432 (tt) REVERT: K 933 LYS cc_start: 0.7612 (mttm) cc_final: 0.7404 (mmtt) REVERT: K 1135 ASN cc_start: 0.8069 (t0) cc_final: 0.7635 (t0) REVERT: L 105 ILE cc_start: 0.9407 (mt) cc_final: 0.9181 (mm) REVERT: L 215 ASP cc_start: 0.7723 (m-30) cc_final: 0.7349 (p0) REVERT: L 216 LEU cc_start: 0.7554 (tp) cc_final: 0.7302 (tt) REVERT: L 227 VAL cc_start: 0.8998 (p) cc_final: 0.8778 (t) REVERT: L 423 TYR cc_start: 0.5739 (t80) cc_final: 0.5377 (t80) REVERT: L 451 TYR cc_start: 0.4412 (m-80) cc_final: 0.3802 (m-10) REVERT: L 505 TYR cc_start: 0.7848 (m-80) cc_final: 0.7632 (m-10) REVERT: L 515 PHE cc_start: 0.7409 (m-80) cc_final: 0.7075 (m-80) REVERT: L 983 ARG cc_start: 0.7458 (tmm160) cc_final: 0.6905 (ttp80) REVERT: L 1005 GLN cc_start: 0.8070 (mt0) cc_final: 0.7654 (mm-40) REVERT: L 1038 LYS cc_start: 0.7788 (mmtp) cc_final: 0.7560 (mmmt) REVERT: M 34 MET cc_start: 0.6574 (mmt) cc_final: 0.6348 (mmp) REVERT: M 57 GLU cc_start: 0.7425 (mp0) cc_final: 0.7178 (mp0) REVERT: M 58 LYS cc_start: 0.8230 (mttt) cc_final: 0.7705 (mptt) REVERT: M 130 LEU cc_start: 0.6744 (tp) cc_final: 0.6101 (mm) REVERT: N 20 ILE cc_start: 0.7166 (mt) cc_final: 0.6660 (mt) REVERT: N 88 ASP cc_start: 0.7670 (m-30) cc_final: 0.6796 (p0) REVERT: N 98 ASN cc_start: 0.8185 (p0) cc_final: 0.7869 (p0) REVERT: N 109 LEU cc_start: 0.7497 (tp) cc_final: 0.7190 (tp) REVERT: N 199 CYS cc_start: 0.5752 (t) cc_final: 0.5166 (p) REVERT: O 77 ASN cc_start: 0.8419 (m110) cc_final: 0.8029 (t0) REVERT: P 37 TYR cc_start: 0.8425 (m-80) cc_final: 0.7773 (m-80) REVERT: P 55 ARG cc_start: 0.7875 (ttm110) cc_final: 0.6637 (ttm110) REVERT: P 62 ARG cc_start: 0.8450 (mtm110) cc_final: 0.8120 (mtm-85) REVERT: P 144 ASP cc_start: 0.5626 (m-30) cc_final: 0.4902 (t0) REVERT: P 178 TYR cc_start: 0.5505 (m-80) cc_final: 0.5228 (m-80) REVERT: P 195 ARG cc_start: 0.7061 (mmm160) cc_final: 0.6668 (mmm160) REVERT: Q 73 ASP cc_start: 0.8061 (t0) cc_final: 0.7776 (t0) REVERT: Q 80 PHE cc_start: 0.8372 (m-80) cc_final: 0.7038 (m-80) REVERT: Q 83 MET cc_start: 0.7358 (mtt) cc_final: 0.6651 (mpp) REVERT: Q 98 ARG cc_start: 0.7952 (ptt90) cc_final: 0.7257 (tmm-80) REVERT: Q 160 TRP cc_start: 0.6634 (m100) cc_final: 0.6243 (m100) REVERT: R 4 MET cc_start: 0.8063 (mmm) cc_final: 0.7229 (mtm) REVERT: R 50 TYR cc_start: 0.7773 (p90) cc_final: 0.7530 (p90) REVERT: R 92 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7158 (tm-30) outliers start: 5 outliers final: 0 residues processed: 863 average time/residue: 0.7258 time to fit residues: 1077.5283 Evaluate side-chains 539 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 539 time to evaluate : 6.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 454 optimal weight: 0.9980 chunk 253 optimal weight: 9.9990 chunk 680 optimal weight: 8.9990 chunk 556 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 818 optimal weight: 9.9990 chunk 884 optimal weight: 8.9990 chunk 729 optimal weight: 4.9990 chunk 811 optimal weight: 9.9990 chunk 279 optimal weight: 4.9990 chunk 656 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A1010 GLN B 49 HIS B 125 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 960 ASN C 49 HIS C 115 GLN C 409 GLN C 774 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 170 HIS ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 177 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN H 205 ASN I 32 ASN ** J 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 245 HIS ** J 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 804 GLN K 69 HIS K 125 ASN K 271 GLN ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 804 GLN ** K 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1088 HIS L 49 HIS L 207 HIS L 245 HIS L 481 ASN L 774 GLN L 784 GLN ** L 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 ASN M 111 GLN M 170 HIS ** M 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 ASN ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 177 GLN P 6 GLN P 38 GLN ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN Q 170 HIS Q 205 ASN R 32 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.4241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 72876 Z= 0.493 Angle : 0.765 15.709 99312 Z= 0.394 Chirality : 0.053 0.714 11496 Planarity : 0.005 0.068 12750 Dihedral : 6.955 104.439 11652 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.23 % Favored : 89.75 % Rotamer: Outliers : 0.22 % Allowed : 4.23 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.08), residues: 9024 helix: 1.01 (0.15), residues: 1256 sheet: -1.98 (0.11), residues: 2140 loop : -2.97 (0.07), residues: 5628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 152 HIS 0.017 0.002 HIS K1064 PHE 0.038 0.003 PHE K 86 TYR 0.027 0.002 TYR B 369 ARG 0.013 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 722 time to evaluate : 6.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 VAL cc_start: 0.8200 (t) cc_final: 0.7899 (p) REVERT: A 145 TYR cc_start: 0.6386 (p90) cc_final: 0.5687 (p90) REVERT: A 212 LEU cc_start: 0.8656 (mm) cc_final: 0.8412 (mm) REVERT: A 244 LEU cc_start: 0.8094 (tp) cc_final: 0.7877 (tp) REVERT: A 464 PHE cc_start: 0.6716 (m-80) cc_final: 0.6239 (m-80) REVERT: A 465 GLU cc_start: 0.6829 (pt0) cc_final: 0.6591 (pt0) REVERT: A 740 MET cc_start: 0.7770 (tpp) cc_final: 0.7538 (tpp) REVERT: A 886 TRP cc_start: 0.7599 (p90) cc_final: 0.6929 (p90) REVERT: A 981 LEU cc_start: 0.7994 (pp) cc_final: 0.7466 (tt) REVERT: B 319 ARG cc_start: 0.7415 (mtt-85) cc_final: 0.6860 (mtt-85) REVERT: B 383 SER cc_start: 0.7649 (m) cc_final: 0.6833 (p) REVERT: B 492 LEU cc_start: 0.7337 (mm) cc_final: 0.6958 (tp) REVERT: B 517 LEU cc_start: 0.7734 (mt) cc_final: 0.7385 (pp) REVERT: B 551 VAL cc_start: 0.8839 (m) cc_final: 0.8586 (p) REVERT: B 950 ASP cc_start: 0.6198 (m-30) cc_final: 0.5939 (m-30) REVERT: B 977 LEU cc_start: 0.7445 (pt) cc_final: 0.7149 (mt) REVERT: B 1097 SER cc_start: 0.7955 (p) cc_final: 0.7745 (p) REVERT: B 1135 ASN cc_start: 0.8165 (t0) cc_final: 0.7663 (t0) REVERT: B 1138 TYR cc_start: 0.7040 (t80) cc_final: 0.6519 (t80) REVERT: C 197 ILE cc_start: 0.9171 (pt) cc_final: 0.8727 (pt) REVERT: C 215 ASP cc_start: 0.8122 (m-30) cc_final: 0.7454 (p0) REVERT: C 233 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7473 (mt) REVERT: C 389 ASP cc_start: 0.8620 (p0) cc_final: 0.8320 (p0) REVERT: C 436 TRP cc_start: 0.8040 (p90) cc_final: 0.7148 (p90) REVERT: C 515 PHE cc_start: 0.7539 (m-80) cc_final: 0.7019 (m-10) REVERT: C 886 TRP cc_start: 0.7934 (p90) cc_final: 0.7603 (p90) REVERT: C 949 GLN cc_start: 0.7497 (tp40) cc_final: 0.7232 (tp40) REVERT: D 12 VAL cc_start: 0.7161 (m) cc_final: 0.6940 (p) REVERT: D 150 ASP cc_start: 0.6184 (m-30) cc_final: 0.5864 (t0) REVERT: D 177 GLN cc_start: 0.7325 (tm-30) cc_final: 0.6665 (tt0) REVERT: D 205 ASN cc_start: 0.7960 (m110) cc_final: 0.7569 (m110) REVERT: E 52 ASP cc_start: 0.7816 (t70) cc_final: 0.7341 (t70) REVERT: E 67 ILE cc_start: 0.8047 (tp) cc_final: 0.7808 (tp) REVERT: E 123 LEU cc_start: 0.8049 (tp) cc_final: 0.7842 (tp) REVERT: E 183 TYR cc_start: 0.5067 (m-80) cc_final: 0.4664 (m-80) REVERT: F 73 ASP cc_start: 0.7575 (t0) cc_final: 0.7362 (t0) REVERT: F 82 GLN cc_start: 0.6452 (tt0) cc_final: 0.6218 (tt0) REVERT: F 83 MET cc_start: 0.7354 (pmm) cc_final: 0.7136 (pmm) REVERT: F 123 LYS cc_start: 0.7057 (ptmt) cc_final: 0.5411 (mmtm) REVERT: G 40 ARG cc_start: 0.7538 (tpp80) cc_final: 0.6881 (mmt90) REVERT: G 89 TYR cc_start: 0.7570 (m-80) cc_final: 0.7188 (m-80) REVERT: G 195 ARG cc_start: 0.6557 (tpt90) cc_final: 0.6126 (mpt90) REVERT: H 34 MET cc_start: 0.7265 (mmt) cc_final: 0.6804 (mmm) REVERT: H 50 ASN cc_start: 0.8441 (m-40) cc_final: 0.8006 (m110) REVERT: H 73 ASP cc_start: 0.7383 (t0) cc_final: 0.6725 (t0) REVERT: H 210 ASN cc_start: 0.7452 (t0) cc_final: 0.6940 (t0) REVERT: J 452 LEU cc_start: 0.7535 (mt) cc_final: 0.7265 (mt) REVERT: J 886 TRP cc_start: 0.8027 (p90) cc_final: 0.7743 (p90) REVERT: J 983 ARG cc_start: 0.7801 (ppt170) cc_final: 0.7443 (ppt170) REVERT: K 191 GLU cc_start: 0.8508 (pt0) cc_final: 0.8068 (pt0) REVERT: K 202 LYS cc_start: 0.8539 (mptt) cc_final: 0.8250 (mmtp) REVERT: K 319 ARG cc_start: 0.7132 (mpp80) cc_final: 0.6537 (mtt-85) REVERT: K 549 THR cc_start: 0.7914 (m) cc_final: 0.7710 (p) REVERT: K 902 MET cc_start: 0.7507 (mmm) cc_final: 0.7280 (tpt) REVERT: K 1135 ASN cc_start: 0.8167 (t0) cc_final: 0.7647 (t0) REVERT: L 105 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9218 (mm) REVERT: L 182 LYS cc_start: 0.7313 (mmmt) cc_final: 0.7067 (mttt) REVERT: L 215 ASP cc_start: 0.7920 (m-30) cc_final: 0.7474 (p0) REVERT: L 396 TYR cc_start: 0.7996 (m-80) cc_final: 0.7660 (m-80) REVERT: L 423 TYR cc_start: 0.5677 (t80) cc_final: 0.5264 (t80) REVERT: L 451 TYR cc_start: 0.4347 (m-80) cc_final: 0.3893 (m-10) REVERT: L 454 ARG cc_start: 0.7241 (mmt180) cc_final: 0.6776 (mmm160) REVERT: L 515 PHE cc_start: 0.7557 (m-80) cc_final: 0.7246 (m-80) REVERT: L 740 MET cc_start: 0.7889 (mmm) cc_final: 0.7483 (tpp) REVERT: L 886 TRP cc_start: 0.8217 (p90) cc_final: 0.7689 (p90) REVERT: L 983 ARG cc_start: 0.7501 (tmm160) cc_final: 0.7075 (ttp80) REVERT: L 1005 GLN cc_start: 0.8023 (mt0) cc_final: 0.7820 (mt0) REVERT: L 1038 LYS cc_start: 0.7699 (mmtp) cc_final: 0.7403 (mmmt) REVERT: M 130 LEU cc_start: 0.6903 (tp) cc_final: 0.6332 (mm) REVERT: M 215 LYS cc_start: 0.7072 (tmmt) cc_final: 0.6632 (tmtt) REVERT: N 52 ASP cc_start: 0.7703 (t0) cc_final: 0.7383 (t0) REVERT: N 88 ASP cc_start: 0.7587 (m-30) cc_final: 0.6883 (p0) REVERT: N 98 ASN cc_start: 0.8299 (p0) cc_final: 0.7907 (p0) REVERT: N 109 LEU cc_start: 0.7346 (tp) cc_final: 0.7109 (tp) REVERT: N 145 PHE cc_start: 0.5521 (p90) cc_final: 0.5108 (p90) REVERT: O 77 ASN cc_start: 0.8480 (m110) cc_final: 0.7673 (t0) REVERT: P 33 TYR cc_start: 0.7792 (m-80) cc_final: 0.7500 (m-80) REVERT: P 55 ARG cc_start: 0.8023 (ttm110) cc_final: 0.7756 (ttp-110) REVERT: P 135 LYS cc_start: 0.5957 (tptt) cc_final: 0.5592 (pttt) REVERT: P 178 TYR cc_start: 0.5803 (m-80) cc_final: 0.5573 (m-80) REVERT: P 195 ARG cc_start: 0.6974 (mmm160) cc_final: 0.6418 (mmm160) REVERT: Q 52 ASN cc_start: 0.5218 (OUTLIER) cc_final: 0.3856 (m110) REVERT: Q 73 ASP cc_start: 0.7707 (t0) cc_final: 0.7438 (t0) REVERT: Q 83 MET cc_start: 0.7573 (mtt) cc_final: 0.7149 (mpp) REVERT: Q 98 ARG cc_start: 0.7868 (ptt90) cc_final: 0.7350 (tmm-80) REVERT: Q 160 TRP cc_start: 0.6869 (m100) cc_final: 0.6340 (m100) REVERT: R 4 MET cc_start: 0.7985 (mmm) cc_final: 0.7308 (mtm) REVERT: R 92 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7148 (tm-30) REVERT: R 142 ILE cc_start: 0.6308 (pt) cc_final: 0.6092 (mt) REVERT: R 183 TYR cc_start: 0.6139 (m-10) cc_final: 0.5895 (m-10) outliers start: 17 outliers final: 12 residues processed: 738 average time/residue: 0.6866 time to fit residues: 869.6113 Evaluate side-chains 517 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 502 time to evaluate : 6.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 808 optimal weight: 6.9990 chunk 615 optimal weight: 2.9990 chunk 424 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 390 optimal weight: 4.9990 chunk 549 optimal weight: 0.9980 chunk 821 optimal weight: 5.9990 chunk 869 optimal weight: 0.8980 chunk 429 optimal weight: 9.9990 chunk 778 optimal weight: 8.9990 chunk 234 optimal weight: 0.0070 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 173 GLN A 414 GLN A 474 GLN A1106 GLN B 69 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 607 GLN B 901 GLN C 675 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN J 239 GLN J 474 GLN J1002 GLN K 69 HIS K 271 GLN ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 955 ASN L 146 HIS L 314 GLN L 564 GLN L 774 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 170 HIS ** M 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 205 ASN ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 74 ASN P 38 GLN ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN Q 77 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 72876 Z= 0.220 Angle : 0.583 13.106 99312 Z= 0.297 Chirality : 0.046 0.516 11496 Planarity : 0.004 0.059 12750 Dihedral : 6.228 99.860 11652 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.05 % Allowed : 2.37 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.08), residues: 9024 helix: 1.65 (0.15), residues: 1252 sheet: -1.85 (0.11), residues: 2162 loop : -2.72 (0.07), residues: 5610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP P 154 HIS 0.015 0.001 HIS H 206 PHE 0.056 0.002 PHE F 152 TYR 0.021 0.001 TYR L 380 ARG 0.007 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 686 time to evaluate : 6.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 VAL cc_start: 0.8234 (t) cc_final: 0.7974 (p) REVERT: A 145 TYR cc_start: 0.6098 (p90) cc_final: 0.5712 (p90) REVERT: A 212 LEU cc_start: 0.8563 (mm) cc_final: 0.8253 (mm) REVERT: A 244 LEU cc_start: 0.8146 (tp) cc_final: 0.7912 (tp) REVERT: A 464 PHE cc_start: 0.6688 (m-80) cc_final: 0.6199 (m-80) REVERT: A 465 GLU cc_start: 0.7073 (pt0) cc_final: 0.6731 (pt0) REVERT: A 886 TRP cc_start: 0.7620 (p90) cc_final: 0.6950 (p90) REVERT: A 981 LEU cc_start: 0.7966 (pp) cc_final: 0.7387 (tt) REVERT: B 153 MET cc_start: 0.6669 (ptp) cc_final: 0.5992 (ppp) REVERT: B 347 PHE cc_start: 0.6346 (m-10) cc_final: 0.6013 (m-80) REVERT: B 492 LEU cc_start: 0.7419 (mm) cc_final: 0.6931 (tp) REVERT: B 517 LEU cc_start: 0.7723 (mt) cc_final: 0.7403 (pp) REVERT: B 702 GLU cc_start: 0.7967 (tp30) cc_final: 0.7719 (tp30) REVERT: B 1029 MET cc_start: 0.6626 (ttm) cc_final: 0.6392 (ttm) REVERT: B 1050 MET cc_start: 0.6348 (ptm) cc_final: 0.6106 (ptp) REVERT: B 1097 SER cc_start: 0.7917 (p) cc_final: 0.7678 (p) REVERT: B 1135 ASN cc_start: 0.8108 (t0) cc_final: 0.7490 (t0) REVERT: B 1138 TYR cc_start: 0.6764 (t80) cc_final: 0.6199 (t80) REVERT: C 111 ASP cc_start: 0.7451 (p0) cc_final: 0.7089 (p0) REVERT: C 215 ASP cc_start: 0.8247 (m-30) cc_final: 0.7481 (p0) REVERT: C 388 ASN cc_start: 0.7742 (m-40) cc_final: 0.7396 (m110) REVERT: C 436 TRP cc_start: 0.8015 (p90) cc_final: 0.7058 (p90) REVERT: C 515 PHE cc_start: 0.7422 (m-80) cc_final: 0.6933 (m-10) REVERT: C 886 TRP cc_start: 0.8060 (p90) cc_final: 0.7618 (p90) REVERT: C 949 GLN cc_start: 0.7170 (tp40) cc_final: 0.6862 (tp40) REVERT: D 150 ASP cc_start: 0.6200 (m-30) cc_final: 0.5967 (t0) REVERT: D 177 GLN cc_start: 0.7475 (tm-30) cc_final: 0.6898 (tm-30) REVERT: D 205 ASN cc_start: 0.8028 (m110) cc_final: 0.7732 (m110) REVERT: E 12 GLU cc_start: 0.8321 (tt0) cc_final: 0.7830 (tm-30) REVERT: E 52 ASP cc_start: 0.7804 (t70) cc_final: 0.7447 (t0) REVERT: E 183 TYR cc_start: 0.4956 (m-80) cc_final: 0.4650 (m-80) REVERT: F 83 MET cc_start: 0.7213 (pmm) cc_final: 0.6940 (pmm) REVERT: F 123 LYS cc_start: 0.5524 (ptmt) cc_final: 0.4941 (mttt) REVERT: G 4 MET cc_start: 0.7599 (mmt) cc_final: 0.7201 (mpp) REVERT: G 40 ARG cc_start: 0.7476 (tpp80) cc_final: 0.6905 (mmt90) REVERT: G 89 TYR cc_start: 0.7534 (m-80) cc_final: 0.7086 (m-80) REVERT: G 195 ARG cc_start: 0.6635 (tpt90) cc_final: 0.6310 (tpp-160) REVERT: H 34 MET cc_start: 0.7235 (mmt) cc_final: 0.6823 (mmm) REVERT: H 50 ASN cc_start: 0.8243 (m-40) cc_final: 0.7995 (m110) REVERT: H 73 ASP cc_start: 0.7422 (t0) cc_final: 0.6724 (t70) REVERT: H 210 ASN cc_start: 0.7583 (t0) cc_final: 0.6985 (t0) REVERT: I 35 GLN cc_start: 0.8015 (mp-120) cc_final: 0.7783 (mm-40) REVERT: J 97 LYS cc_start: 0.7497 (ptmm) cc_final: 0.7261 (tppt) REVERT: J 452 LEU cc_start: 0.7532 (mt) cc_final: 0.7270 (mt) REVERT: J 886 TRP cc_start: 0.7971 (p90) cc_final: 0.7649 (p90) REVERT: J 983 ARG cc_start: 0.7633 (ppt170) cc_final: 0.7336 (ppt170) REVERT: K 191 GLU cc_start: 0.8396 (pt0) cc_final: 0.7861 (pt0) REVERT: K 228 ASP cc_start: 0.8158 (t0) cc_final: 0.7814 (t0) REVERT: K 319 ARG cc_start: 0.7206 (mpp80) cc_final: 0.6628 (mtt-85) REVERT: K 481 ASN cc_start: 0.7552 (t0) cc_final: 0.7328 (t0) REVERT: K 549 THR cc_start: 0.8011 (m) cc_final: 0.7751 (p) REVERT: K 795 LYS cc_start: 0.7870 (mptt) cc_final: 0.7479 (mptt) REVERT: K 1135 ASN cc_start: 0.8263 (t0) cc_final: 0.7798 (t0) REVERT: L 105 ILE cc_start: 0.9387 (mt) cc_final: 0.9166 (mm) REVERT: L 182 LYS cc_start: 0.7352 (mmmt) cc_final: 0.7094 (mttm) REVERT: L 215 ASP cc_start: 0.8083 (m-30) cc_final: 0.7663 (p0) REVERT: L 370 ASN cc_start: 0.8716 (m-40) cc_final: 0.8487 (m-40) REVERT: L 377 PHE cc_start: 0.7224 (m-80) cc_final: 0.6902 (m-80) REVERT: L 396 TYR cc_start: 0.7904 (m-80) cc_final: 0.7576 (m-80) REVERT: L 423 TYR cc_start: 0.5755 (t80) cc_final: 0.5376 (t80) REVERT: L 451 TYR cc_start: 0.4697 (m-80) cc_final: 0.4282 (m-10) REVERT: L 515 PHE cc_start: 0.7518 (m-80) cc_final: 0.7164 (m-80) REVERT: L 740 MET cc_start: 0.7931 (mmm) cc_final: 0.7584 (tpp) REVERT: L 886 TRP cc_start: 0.8212 (p90) cc_final: 0.7691 (p90) REVERT: L 1019 ARG cc_start: 0.6211 (tmm160) cc_final: 0.5825 (ttp80) REVERT: L 1038 LYS cc_start: 0.7769 (mmtp) cc_final: 0.7477 (mmmt) REVERT: M 34 MET cc_start: 0.6546 (mmt) cc_final: 0.6182 (mmp) REVERT: M 215 LYS cc_start: 0.6982 (tmmt) cc_final: 0.6592 (tmtt) REVERT: N 12 GLU cc_start: 0.8275 (tt0) cc_final: 0.7869 (tt0) REVERT: N 54 GLN cc_start: 0.7580 (mp10) cc_final: 0.7324 (mp10) REVERT: N 88 ASP cc_start: 0.7614 (m-30) cc_final: 0.6774 (p0) REVERT: N 98 ASN cc_start: 0.8199 (p0) cc_final: 0.7838 (p0) REVERT: N 109 LEU cc_start: 0.7407 (tp) cc_final: 0.7148 (tp) REVERT: O 77 ASN cc_start: 0.8417 (m110) cc_final: 0.7463 (t0) REVERT: P 135 LYS cc_start: 0.5991 (tptt) cc_final: 0.5617 (pttt) REVERT: P 144 ASP cc_start: 0.5628 (m-30) cc_final: 0.5158 (t0) REVERT: P 178 TYR cc_start: 0.5919 (m-80) cc_final: 0.5682 (m-80) REVERT: Q 83 MET cc_start: 0.7476 (mtt) cc_final: 0.7118 (mtm) REVERT: Q 98 ARG cc_start: 0.7804 (ptt90) cc_final: 0.7461 (ptt90) REVERT: Q 160 TRP cc_start: 0.6691 (m100) cc_final: 0.6153 (m100) REVERT: Q 172 PHE cc_start: 0.5443 (p90) cc_final: 0.5064 (p90) REVERT: Q 210 ASN cc_start: 0.7495 (t0) cc_final: 0.6646 (t0) REVERT: R 4 MET cc_start: 0.8038 (mmm) cc_final: 0.7321 (mtm) REVERT: R 86 GLU cc_start: 0.7593 (mm-30) cc_final: 0.6094 (pp20) REVERT: R 90 TYR cc_start: 0.7722 (m-10) cc_final: 0.7272 (m-10) REVERT: R 92 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7315 (tm-30) REVERT: R 175 ASN cc_start: 0.7682 (m-40) cc_final: 0.7072 (m-40) outliers start: 4 outliers final: 0 residues processed: 689 average time/residue: 0.7002 time to fit residues: 830.0829 Evaluate side-chains 512 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 512 time to evaluate : 6.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 724 optimal weight: 1.9990 chunk 493 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 647 optimal weight: 8.9990 chunk 358 optimal weight: 10.0000 chunk 742 optimal weight: 4.9990 chunk 601 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 444 optimal weight: 9.9990 chunk 780 optimal weight: 7.9990 chunk 219 optimal weight: 0.0170 overall best weight: 1.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A1106 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 607 GLN B 856 ASN B 901 GLN C 675 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN F 206 HIS ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN H 111 GLN J 239 GLN J1002 GLN K 271 GLN K 354 ASN ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 774 GLN ** L 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1002 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 GLN ** M 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 74 ASN ** O 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 200 GLN Q 6 GLN Q 77 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 72876 Z= 0.299 Angle : 0.611 12.487 99312 Z= 0.311 Chirality : 0.047 0.497 11496 Planarity : 0.004 0.065 12750 Dihedral : 6.120 99.618 11652 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.04 % Allowed : 2.49 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.08), residues: 9024 helix: 1.63 (0.15), residues: 1254 sheet: -1.77 (0.11), residues: 2162 loop : -2.66 (0.07), residues: 5608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP L 152 HIS 0.009 0.001 HIS J1064 PHE 0.035 0.002 PHE F 152 TYR 0.026 0.002 TYR D 59 ARG 0.010 0.001 ARG P 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 670 time to evaluate : 6.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 VAL cc_start: 0.8171 (t) cc_final: 0.7675 (p) REVERT: A 145 TYR cc_start: 0.6110 (p90) cc_final: 0.5680 (p90) REVERT: A 464 PHE cc_start: 0.6697 (m-80) cc_final: 0.6191 (m-80) REVERT: A 886 TRP cc_start: 0.7600 (p90) cc_final: 0.6934 (p90) REVERT: A 981 LEU cc_start: 0.7875 (pp) cc_final: 0.7381 (tt) REVERT: B 153 MET cc_start: 0.6845 (ptp) cc_final: 0.5906 (ppp) REVERT: B 228 ASP cc_start: 0.8062 (t0) cc_final: 0.7811 (t0) REVERT: B 383 SER cc_start: 0.7731 (m) cc_final: 0.7048 (p) REVERT: B 429 PHE cc_start: 0.6242 (t80) cc_final: 0.5999 (t80) REVERT: B 517 LEU cc_start: 0.7744 (mt) cc_final: 0.7335 (pp) REVERT: B 551 VAL cc_start: 0.8764 (m) cc_final: 0.8494 (p) REVERT: B 977 LEU cc_start: 0.7455 (pt) cc_final: 0.7034 (mt) REVERT: B 1097 SER cc_start: 0.7868 (p) cc_final: 0.7653 (p) REVERT: B 1107 ARG cc_start: 0.6722 (ptt-90) cc_final: 0.6512 (ptt-90) REVERT: B 1135 ASN cc_start: 0.8135 (t0) cc_final: 0.7520 (t0) REVERT: B 1138 TYR cc_start: 0.6829 (t80) cc_final: 0.6320 (t80) REVERT: C 215 ASP cc_start: 0.8327 (m-30) cc_final: 0.7565 (p0) REVERT: C 436 TRP cc_start: 0.8062 (p90) cc_final: 0.6878 (p90) REVERT: C 515 PHE cc_start: 0.7595 (m-80) cc_final: 0.6999 (m-10) REVERT: C 547 THR cc_start: 0.8575 (p) cc_final: 0.8332 (p) REVERT: C 886 TRP cc_start: 0.7961 (p90) cc_final: 0.7521 (p90) REVERT: C 949 GLN cc_start: 0.7265 (tp40) cc_final: 0.6936 (tp40) REVERT: D 150 ASP cc_start: 0.6275 (m-30) cc_final: 0.5926 (t0) REVERT: D 177 GLN cc_start: 0.7543 (tm-30) cc_final: 0.6794 (tt0) REVERT: D 205 ASN cc_start: 0.8118 (m110) cc_final: 0.7771 (m110) REVERT: E 54 GLN cc_start: 0.7925 (mp10) cc_final: 0.7724 (mp10) REVERT: E 183 TYR cc_start: 0.5174 (m-80) cc_final: 0.4920 (m-80) REVERT: F 83 MET cc_start: 0.7093 (pmm) cc_final: 0.6761 (pmm) REVERT: F 123 LYS cc_start: 0.5835 (ptmt) cc_final: 0.5545 (mttt) REVERT: G 38 GLN cc_start: 0.7939 (tp40) cc_final: 0.7547 (tp40) REVERT: G 40 ARG cc_start: 0.7479 (tpp80) cc_final: 0.6933 (mmt90) REVERT: G 85 ASP cc_start: 0.7273 (m-30) cc_final: 0.7039 (m-30) REVERT: H 34 MET cc_start: 0.7205 (mmt) cc_final: 0.6855 (mmm) REVERT: H 50 ASN cc_start: 0.8241 (m-40) cc_final: 0.7936 (m110) REVERT: H 73 ASP cc_start: 0.7529 (t0) cc_final: 0.6815 (t70) REVERT: H 210 ASN cc_start: 0.7633 (t0) cc_final: 0.7073 (t0) REVERT: I 35 GLN cc_start: 0.8012 (mp-120) cc_final: 0.7649 (mm-40) REVERT: I 186 LEU cc_start: 0.3334 (mp) cc_final: 0.2675 (tp) REVERT: J 97 LYS cc_start: 0.7533 (ptmm) cc_final: 0.7272 (tppt) REVERT: J 153 MET cc_start: 0.6855 (tmm) cc_final: 0.6440 (tmm) REVERT: J 177 MET cc_start: 0.7137 (mtt) cc_final: 0.6017 (mtt) REVERT: J 182 LYS cc_start: 0.4459 (mtmm) cc_final: 0.4168 (mtmm) REVERT: J 239 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6477 (tp-100) REVERT: J 452 LEU cc_start: 0.7544 (mt) cc_final: 0.7284 (mt) REVERT: J 572 THR cc_start: 0.8835 (m) cc_final: 0.8589 (p) REVERT: J 886 TRP cc_start: 0.8001 (p90) cc_final: 0.7663 (p90) REVERT: J 983 ARG cc_start: 0.7652 (ppt170) cc_final: 0.7350 (ppt170) REVERT: J 1050 MET cc_start: 0.6047 (ptp) cc_final: 0.5824 (ptp) REVERT: K 191 GLU cc_start: 0.8428 (pt0) cc_final: 0.7951 (pt0) REVERT: K 1135 ASN cc_start: 0.8215 (t0) cc_final: 0.7698 (t0) REVERT: L 105 ILE cc_start: 0.9395 (mt) cc_final: 0.9188 (mm) REVERT: L 182 LYS cc_start: 0.7620 (mmmt) cc_final: 0.7397 (mttm) REVERT: L 215 ASP cc_start: 0.8102 (m-30) cc_final: 0.7546 (p0) REVERT: L 377 PHE cc_start: 0.7371 (m-80) cc_final: 0.6897 (m-80) REVERT: L 396 TYR cc_start: 0.7802 (m-80) cc_final: 0.7028 (m-80) REVERT: L 423 TYR cc_start: 0.5588 (t80) cc_final: 0.5160 (t80) REVERT: L 451 TYR cc_start: 0.4832 (m-80) cc_final: 0.4452 (m-10) REVERT: L 515 PHE cc_start: 0.7398 (m-80) cc_final: 0.7136 (m-80) REVERT: L 886 TRP cc_start: 0.8145 (p90) cc_final: 0.7609 (p90) REVERT: L 1038 LYS cc_start: 0.7740 (mmtp) cc_final: 0.7405 (mmmt) REVERT: M 34 MET cc_start: 0.6670 (mmt) cc_final: 0.6357 (mmp) REVERT: M 215 LYS cc_start: 0.7180 (tmmt) cc_final: 0.6854 (tmtt) REVERT: N 12 GLU cc_start: 0.8291 (tt0) cc_final: 0.7956 (tt0) REVERT: N 52 ASP cc_start: 0.7831 (t70) cc_final: 0.7592 (t0) REVERT: N 54 GLN cc_start: 0.7822 (mp10) cc_final: 0.7557 (mp10) REVERT: N 88 ASP cc_start: 0.7590 (m-30) cc_final: 0.6763 (p0) REVERT: N 98 ASN cc_start: 0.8224 (p0) cc_final: 0.7850 (p0) REVERT: N 109 LEU cc_start: 0.7413 (tp) cc_final: 0.7205 (tp) REVERT: N 145 PHE cc_start: 0.5577 (p90) cc_final: 0.5153 (p90) REVERT: P 135 LYS cc_start: 0.5939 (tptt) cc_final: 0.5554 (pttt) REVERT: P 178 TYR cc_start: 0.5872 (m-80) cc_final: 0.5617 (m-80) REVERT: P 195 ARG cc_start: 0.6907 (mmm160) cc_final: 0.6126 (mmm160) REVERT: Q 73 ASP cc_start: 0.7512 (t0) cc_final: 0.7295 (t0) REVERT: Q 83 MET cc_start: 0.7484 (mtt) cc_final: 0.7152 (mtm) REVERT: Q 98 ARG cc_start: 0.7832 (ptt90) cc_final: 0.7375 (tmm-80) REVERT: Q 160 TRP cc_start: 0.6775 (m100) cc_final: 0.6236 (m100) REVERT: Q 172 PHE cc_start: 0.5534 (p90) cc_final: 0.5088 (p90) REVERT: Q 210 ASN cc_start: 0.7536 (t0) cc_final: 0.6625 (t0) REVERT: R 4 MET cc_start: 0.7924 (mmm) cc_final: 0.7216 (mtm) REVERT: R 40 ARG cc_start: 0.7224 (tpp80) cc_final: 0.7015 (tpp80) REVERT: R 86 GLU cc_start: 0.7633 (mm-30) cc_final: 0.6155 (pp20) REVERT: R 92 GLN cc_start: 0.7945 (tm-30) cc_final: 0.7215 (tm-30) REVERT: R 175 ASN cc_start: 0.7573 (m-40) cc_final: 0.7053 (m-40) outliers start: 3 outliers final: 0 residues processed: 672 average time/residue: 0.6868 time to fit residues: 795.7595 Evaluate side-chains 517 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 516 time to evaluate : 6.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 292 optimal weight: 5.9990 chunk 783 optimal weight: 6.9990 chunk 171 optimal weight: 0.0870 chunk 510 optimal weight: 5.9990 chunk 214 optimal weight: 8.9990 chunk 870 optimal weight: 5.9990 chunk 722 optimal weight: 4.9990 chunk 403 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 288 optimal weight: 0.6980 chunk 457 optimal weight: 3.9990 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 146 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 271 GLN B 439 ASN B 607 GLN C 388 ASN C 675 GLN C 774 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 HIS J 66 HIS J 907 ASN J1002 GLN K 87 ASN K 271 GLN ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 GLN L 388 ASN L 774 GLN ** L 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1002 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 GLN ** M 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 74 ASN O 82 GLN ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN Q 77 ASN R 100 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 72876 Z= 0.397 Angle : 0.677 13.295 99312 Z= 0.347 Chirality : 0.049 0.474 11496 Planarity : 0.005 0.067 12750 Dihedral : 6.439 102.771 11652 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.01 % Allowed : 10.57 % Favored : 89.42 % Rotamer: Outliers : 0.03 % Allowed : 2.01 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.08), residues: 9024 helix: 1.19 (0.15), residues: 1284 sheet: -1.82 (0.11), residues: 2216 loop : -2.68 (0.07), residues: 5524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 154 HIS 0.012 0.002 HIS Q 206 PHE 0.054 0.002 PHE J 906 TYR 0.022 0.002 TYR L 380 ARG 0.015 0.001 ARG O 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 659 time to evaluate : 6.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TYR cc_start: 0.5851 (t80) cc_final: 0.5428 (t80) REVERT: A 145 TYR cc_start: 0.6118 (p90) cc_final: 0.5784 (p90) REVERT: A 464 PHE cc_start: 0.6537 (m-80) cc_final: 0.6206 (m-80) REVERT: A 886 TRP cc_start: 0.7599 (p90) cc_final: 0.6936 (p90) REVERT: A 981 LEU cc_start: 0.7785 (pp) cc_final: 0.7274 (tt) REVERT: A 1050 MET cc_start: 0.5994 (ptm) cc_final: 0.5725 (ptm) REVERT: B 153 MET cc_start: 0.6853 (ptp) cc_final: 0.6577 (mtp) REVERT: B 177 MET cc_start: 0.6267 (ttt) cc_final: 0.5791 (ttp) REVERT: B 228 ASP cc_start: 0.8115 (t0) cc_final: 0.7902 (t0) REVERT: B 383 SER cc_start: 0.8174 (m) cc_final: 0.7860 (t) REVERT: B 517 LEU cc_start: 0.7663 (mt) cc_final: 0.7254 (pp) REVERT: B 551 VAL cc_start: 0.8773 (m) cc_final: 0.8532 (p) REVERT: B 950 ASP cc_start: 0.6345 (m-30) cc_final: 0.6121 (m-30) REVERT: B 977 LEU cc_start: 0.7488 (pt) cc_final: 0.7092 (mt) REVERT: B 1029 MET cc_start: 0.6831 (ttm) cc_final: 0.6195 (ttm) REVERT: B 1135 ASN cc_start: 0.8105 (t0) cc_final: 0.7477 (t0) REVERT: B 1138 TYR cc_start: 0.6851 (t80) cc_final: 0.6540 (t80) REVERT: C 215 ASP cc_start: 0.8463 (m-30) cc_final: 0.7581 (p0) REVERT: C 436 TRP cc_start: 0.7993 (p90) cc_final: 0.6651 (p90) REVERT: C 515 PHE cc_start: 0.7560 (m-80) cc_final: 0.6950 (m-10) REVERT: C 740 MET cc_start: 0.7621 (tpp) cc_final: 0.7296 (tpp) REVERT: D 87 ARG cc_start: 0.8214 (mmt90) cc_final: 0.7458 (mmt90) REVERT: D 150 ASP cc_start: 0.6294 (m-30) cc_final: 0.5980 (t0) REVERT: D 177 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7160 (tt0) REVERT: D 205 ASN cc_start: 0.8093 (m110) cc_final: 0.7784 (m110) REVERT: E 12 GLU cc_start: 0.7997 (tt0) cc_final: 0.7451 (tm-30) REVERT: E 29 ILE cc_start: 0.8051 (tp) cc_final: 0.7807 (tp) REVERT: E 54 GLN cc_start: 0.7803 (mp10) cc_final: 0.7521 (mp10) REVERT: E 81 LEU cc_start: 0.6935 (tt) cc_final: 0.6553 (mt) REVERT: E 183 TYR cc_start: 0.5383 (m-80) cc_final: 0.5173 (m-80) REVERT: E 210 LYS cc_start: 0.6464 (ptpp) cc_final: 0.5996 (ptmt) REVERT: F 83 MET cc_start: 0.6845 (pmm) cc_final: 0.6470 (pmm) REVERT: F 123 LYS cc_start: 0.6800 (ptmt) cc_final: 0.6342 (mtmt) REVERT: G 40 ARG cc_start: 0.7333 (tpp80) cc_final: 0.6588 (mmt90) REVERT: G 195 ARG cc_start: 0.7393 (tpm170) cc_final: 0.6933 (tpp-160) REVERT: H 34 MET cc_start: 0.7270 (mmt) cc_final: 0.6818 (mmm) REVERT: H 50 ASN cc_start: 0.8282 (m-40) cc_final: 0.8033 (m110) REVERT: H 73 ASP cc_start: 0.7440 (t0) cc_final: 0.7032 (t70) REVERT: H 87 ARG cc_start: 0.7015 (mtp-110) cc_final: 0.6006 (mtp85) REVERT: H 210 ASN cc_start: 0.7609 (t0) cc_final: 0.7020 (t0) REVERT: I 35 GLN cc_start: 0.8110 (mp-120) cc_final: 0.7658 (mm-40) REVERT: I 176 ASN cc_start: 0.6214 (m-40) cc_final: 0.5567 (p0) REVERT: I 183 TYR cc_start: 0.6988 (t80) cc_final: 0.6770 (t80) REVERT: J 177 MET cc_start: 0.7013 (mtt) cc_final: 0.5804 (mtt) REVERT: J 212 LEU cc_start: 0.7914 (tp) cc_final: 0.7657 (tt) REVERT: J 452 LEU cc_start: 0.7653 (mt) cc_final: 0.7415 (mt) REVERT: J 572 THR cc_start: 0.8842 (m) cc_final: 0.8612 (p) REVERT: J 886 TRP cc_start: 0.8003 (p90) cc_final: 0.7673 (p90) REVERT: J 981 LEU cc_start: 0.7919 (pp) cc_final: 0.7662 (tp) REVERT: J 983 ARG cc_start: 0.7614 (ppt170) cc_final: 0.7387 (ppt170) REVERT: J 1050 MET cc_start: 0.6233 (ptp) cc_final: 0.5960 (ptp) REVERT: K 191 GLU cc_start: 0.8546 (pt0) cc_final: 0.8117 (pt0) REVERT: K 383 SER cc_start: 0.8139 (m) cc_final: 0.7639 (p) REVERT: K 1135 ASN cc_start: 0.8187 (t0) cc_final: 0.7649 (t0) REVERT: L 215 ASP cc_start: 0.8366 (m-30) cc_final: 0.7617 (p0) REVERT: L 377 PHE cc_start: 0.7220 (m-80) cc_final: 0.6599 (m-80) REVERT: L 451 TYR cc_start: 0.4850 (m-80) cc_final: 0.4610 (m-10) REVERT: L 515 PHE cc_start: 0.7323 (m-80) cc_final: 0.7120 (m-80) REVERT: L 740 MET cc_start: 0.7801 (tpp) cc_final: 0.7448 (tpp) REVERT: L 1038 LYS cc_start: 0.7533 (mmtp) cc_final: 0.7132 (mmmt) REVERT: M 34 MET cc_start: 0.6583 (mmt) cc_final: 0.6250 (mmp) REVERT: M 202 CYS cc_start: 0.4139 (t) cc_final: 0.3538 (t) REVERT: N 12 GLU cc_start: 0.8313 (tt0) cc_final: 0.8073 (tt0) REVERT: N 52 ASP cc_start: 0.7940 (t70) cc_final: 0.7725 (t0) REVERT: N 88 ASP cc_start: 0.7698 (m-30) cc_final: 0.6894 (p0) REVERT: N 98 ASN cc_start: 0.8138 (p0) cc_final: 0.7739 (p0) REVERT: O 77 ASN cc_start: 0.8464 (m110) cc_final: 0.7715 (t0) REVERT: O 83 MET cc_start: 0.6552 (pmm) cc_final: 0.6292 (pmm) REVERT: P 81 LEU cc_start: 0.6846 (tp) cc_final: 0.6615 (tp) REVERT: P 135 LYS cc_start: 0.6170 (tptt) cc_final: 0.5741 (pttt) REVERT: P 178 TYR cc_start: 0.5889 (m-80) cc_final: 0.5616 (m-80) REVERT: Q 83 MET cc_start: 0.7498 (mtt) cc_final: 0.7197 (mtm) REVERT: Q 98 ARG cc_start: 0.7901 (ptt90) cc_final: 0.7485 (tmm-80) REVERT: Q 160 TRP cc_start: 0.6901 (m100) cc_final: 0.6366 (m100) REVERT: Q 172 PHE cc_start: 0.5966 (p90) cc_final: 0.5406 (p90) REVERT: Q 210 ASN cc_start: 0.7500 (t0) cc_final: 0.6533 (t0) REVERT: R 4 MET cc_start: 0.7965 (mmm) cc_final: 0.7223 (mtm) REVERT: R 86 GLU cc_start: 0.7639 (mm-30) cc_final: 0.6142 (pp20) REVERT: R 92 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7245 (tm-30) REVERT: R 98 ASN cc_start: 0.8576 (p0) cc_final: 0.8145 (t0) REVERT: R 109 LEU cc_start: 0.7894 (tt) cc_final: 0.7682 (tp) REVERT: R 175 ASN cc_start: 0.7635 (m-40) cc_final: 0.7087 (m-40) REVERT: R 195 ARG cc_start: 0.4461 (mmm160) cc_final: 0.3743 (mmm160) outliers start: 2 outliers final: 0 residues processed: 661 average time/residue: 0.6814 time to fit residues: 774.8036 Evaluate side-chains 493 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 493 time to evaluate : 6.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 839 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 496 optimal weight: 0.3980 chunk 635 optimal weight: 5.9990 chunk 492 optimal weight: 4.9990 chunk 733 optimal weight: 3.9990 chunk 486 optimal weight: 0.5980 chunk 867 optimal weight: 5.9990 chunk 542 optimal weight: 0.8980 chunk 528 optimal weight: 4.9990 chunk 400 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 146 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 607 GLN C 314 GLN C 774 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 74 ASN H 177 GLN I 99 HIS J 239 GLN J1002 GLN K 271 GLN ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 774 GLN ** L 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 203 ASN N 38 GLN ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 74 ASN ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN Q 77 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 72876 Z= 0.196 Angle : 0.579 11.105 99312 Z= 0.294 Chirality : 0.046 0.727 11496 Planarity : 0.004 0.063 12750 Dihedral : 5.998 103.348 11652 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 0.01 % Allowed : 1.08 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.09), residues: 9024 helix: 1.78 (0.15), residues: 1266 sheet: -1.60 (0.11), residues: 2162 loop : -2.53 (0.08), residues: 5596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 152 HIS 0.011 0.001 HIS Q 206 PHE 0.029 0.001 PHE F 152 TYR 0.020 0.001 TYR G 50 ARG 0.009 0.000 ARG O 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 652 time to evaluate : 6.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.6151 (p90) cc_final: 0.5704 (p90) REVERT: A 177 MET cc_start: 0.5162 (ptp) cc_final: 0.4824 (ptp) REVERT: A 423 TYR cc_start: 0.7010 (t80) cc_final: 0.6807 (t80) REVERT: A 464 PHE cc_start: 0.6883 (m-80) cc_final: 0.6532 (m-80) REVERT: A 886 TRP cc_start: 0.7628 (p90) cc_final: 0.6997 (p90) REVERT: A 981 LEU cc_start: 0.7913 (pp) cc_final: 0.7374 (tt) REVERT: B 153 MET cc_start: 0.6833 (ptp) cc_final: 0.5896 (ppp) REVERT: B 228 ASP cc_start: 0.8005 (t0) cc_final: 0.7788 (t0) REVERT: B 229 LEU cc_start: 0.7946 (mm) cc_final: 0.7742 (mm) REVERT: B 383 SER cc_start: 0.8002 (m) cc_final: 0.7712 (t) REVERT: B 517 LEU cc_start: 0.7694 (mt) cc_final: 0.7296 (pp) REVERT: B 551 VAL cc_start: 0.8771 (m) cc_final: 0.8551 (p) REVERT: B 1097 SER cc_start: 0.7858 (p) cc_final: 0.7649 (p) REVERT: B 1135 ASN cc_start: 0.8145 (t0) cc_final: 0.7558 (t0) REVERT: B 1138 TYR cc_start: 0.6817 (t80) cc_final: 0.6423 (t80) REVERT: C 111 ASP cc_start: 0.7462 (p0) cc_final: 0.7236 (p0) REVERT: C 215 ASP cc_start: 0.8436 (m-30) cc_final: 0.7608 (p0) REVERT: C 436 TRP cc_start: 0.7943 (p90) cc_final: 0.6722 (p90) REVERT: C 451 TYR cc_start: 0.3947 (m-80) cc_final: 0.3746 (m-80) REVERT: C 515 PHE cc_start: 0.7547 (m-80) cc_final: 0.7014 (m-10) REVERT: C 547 THR cc_start: 0.8710 (p) cc_final: 0.8488 (p) REVERT: C 740 MET cc_start: 0.7597 (tpp) cc_final: 0.7332 (tpp) REVERT: C 774 GLN cc_start: 0.5652 (mm-40) cc_final: 0.5436 (mm110) REVERT: C 949 GLN cc_start: 0.7001 (tp40) cc_final: 0.6543 (tp-100) REVERT: C 1019 ARG cc_start: 0.6028 (ttp-170) cc_final: 0.5660 (ttp80) REVERT: D 6 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6534 (pm20) REVERT: D 87 ARG cc_start: 0.8183 (mmt90) cc_final: 0.7406 (mmt90) REVERT: D 150 ASP cc_start: 0.6113 (m-30) cc_final: 0.5801 (t0) REVERT: D 177 GLN cc_start: 0.7549 (tm-30) cc_final: 0.6938 (tt0) REVERT: D 205 ASN cc_start: 0.8157 (m110) cc_final: 0.7889 (m110) REVERT: E 12 GLU cc_start: 0.7946 (tt0) cc_final: 0.7255 (tm-30) REVERT: E 29 ILE cc_start: 0.8033 (tp) cc_final: 0.7747 (tp) REVERT: E 54 GLN cc_start: 0.7807 (mp10) cc_final: 0.7507 (mp10) REVERT: E 210 LYS cc_start: 0.6407 (ptpp) cc_final: 0.5840 (ptmt) REVERT: F 82 GLN cc_start: 0.6623 (tt0) cc_final: 0.5794 (mm-40) REVERT: F 83 MET cc_start: 0.6766 (pmm) cc_final: 0.6329 (pmm) REVERT: F 123 LYS cc_start: 0.6739 (ptmt) cc_final: 0.6254 (mttp) REVERT: G 38 GLN cc_start: 0.7926 (tp40) cc_final: 0.7510 (tp40) REVERT: G 40 ARG cc_start: 0.7298 (tpp80) cc_final: 0.6852 (mmt90) REVERT: G 195 ARG cc_start: 0.7209 (tpm170) cc_final: 0.6569 (tpp-160) REVERT: H 34 MET cc_start: 0.7126 (mmt) cc_final: 0.6758 (mmm) REVERT: H 73 ASP cc_start: 0.7546 (t0) cc_final: 0.7137 (t70) REVERT: H 87 ARG cc_start: 0.6922 (mtp-110) cc_final: 0.6615 (mtm110) REVERT: H 210 ASN cc_start: 0.7514 (t0) cc_final: 0.6957 (t0) REVERT: I 35 GLN cc_start: 0.7967 (mp-120) cc_final: 0.7589 (mm-40) REVERT: I 176 ASN cc_start: 0.6409 (m-40) cc_final: 0.5820 (p0) REVERT: I 183 TYR cc_start: 0.6865 (t80) cc_final: 0.6589 (t80) REVERT: J 212 LEU cc_start: 0.8025 (tp) cc_final: 0.7763 (tt) REVERT: J 452 LEU cc_start: 0.7664 (mt) cc_final: 0.7367 (mt) REVERT: J 572 THR cc_start: 0.8882 (m) cc_final: 0.8659 (p) REVERT: J 886 TRP cc_start: 0.8013 (p90) cc_final: 0.7724 (p90) REVERT: J 981 LEU cc_start: 0.8198 (pp) cc_final: 0.7875 (tp) REVERT: J 983 ARG cc_start: 0.7540 (ppt170) cc_final: 0.7331 (ppt170) REVERT: K 177 MET cc_start: 0.6758 (ttp) cc_final: 0.5248 (tpp) REVERT: K 191 GLU cc_start: 0.8423 (pt0) cc_final: 0.7921 (pt0) REVERT: K 481 ASN cc_start: 0.7818 (t0) cc_final: 0.7606 (t0) REVERT: K 1135 ASN cc_start: 0.8112 (t0) cc_final: 0.7656 (t0) REVERT: L 215 ASP cc_start: 0.8386 (m-30) cc_final: 0.7597 (p0) REVERT: L 370 ASN cc_start: 0.8751 (m-40) cc_final: 0.8544 (m-40) REVERT: L 396 TYR cc_start: 0.7488 (m-80) cc_final: 0.6990 (m-80) REVERT: L 515 PHE cc_start: 0.7275 (m-80) cc_final: 0.7033 (m-80) REVERT: L 731 MET cc_start: 0.7348 (ptm) cc_final: 0.7006 (ptm) REVERT: L 1038 LYS cc_start: 0.7547 (mmtp) cc_final: 0.7164 (mmmt) REVERT: M 34 MET cc_start: 0.6514 (mmt) cc_final: 0.6201 (mmp) REVERT: N 12 GLU cc_start: 0.8307 (tt0) cc_final: 0.8064 (tt0) REVERT: N 52 ASP cc_start: 0.7950 (t70) cc_final: 0.7731 (t0) REVERT: N 88 ASP cc_start: 0.7614 (m-30) cc_final: 0.6744 (p0) REVERT: N 98 ASN cc_start: 0.8193 (p0) cc_final: 0.7888 (p0) REVERT: N 150 VAL cc_start: 0.8517 (t) cc_final: 0.8290 (m) REVERT: O 77 ASN cc_start: 0.8372 (m110) cc_final: 0.7691 (t0) REVERT: O 83 MET cc_start: 0.6412 (pmm) cc_final: 0.6211 (pmm) REVERT: P 81 LEU cc_start: 0.6583 (tp) cc_final: 0.6340 (tp) REVERT: P 82 LYS cc_start: 0.7674 (mtmm) cc_final: 0.7309 (mtmt) REVERT: P 135 LYS cc_start: 0.6232 (tptt) cc_final: 0.5749 (pttt) REVERT: P 178 TYR cc_start: 0.5932 (m-80) cc_final: 0.5664 (m-80) REVERT: Q 57 GLU cc_start: 0.6756 (pm20) cc_final: 0.5772 (mp0) REVERT: Q 73 ASP cc_start: 0.7662 (t0) cc_final: 0.7431 (t0) REVERT: Q 160 TRP cc_start: 0.6712 (m100) cc_final: 0.6183 (m100) REVERT: Q 172 PHE cc_start: 0.5794 (p90) cc_final: 0.5271 (p90) REVERT: Q 210 ASN cc_start: 0.7543 (t0) cc_final: 0.6624 (t0) REVERT: R 4 MET cc_start: 0.7945 (mmm) cc_final: 0.7230 (mtm) REVERT: R 40 ARG cc_start: 0.7298 (tpp80) cc_final: 0.7039 (tpp80) REVERT: R 86 GLU cc_start: 0.7417 (mm-30) cc_final: 0.5991 (pp20) REVERT: R 92 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7333 (tm-30) REVERT: R 98 ASN cc_start: 0.8621 (p0) cc_final: 0.8232 (t0) REVERT: R 141 LEU cc_start: 0.4956 (pp) cc_final: 0.4520 (tp) REVERT: R 175 ASN cc_start: 0.7616 (m-40) cc_final: 0.7074 (m-40) outliers start: 1 outliers final: 0 residues processed: 653 average time/residue: 0.6764 time to fit residues: 759.4058 Evaluate side-chains 499 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 498 time to evaluate : 6.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 536 optimal weight: 1.9990 chunk 346 optimal weight: 0.7980 chunk 518 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 chunk 168 optimal weight: 0.9980 chunk 551 optimal weight: 4.9990 chunk 590 optimal weight: 5.9990 chunk 428 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 681 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 146 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 439 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 HIS J 239 GLN J1002 GLN K 271 GLN ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 774 GLN ** L 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 74 ASN ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN Q 77 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 72876 Z= 0.214 Angle : 0.579 10.808 99312 Z= 0.293 Chirality : 0.046 0.673 11496 Planarity : 0.004 0.062 12750 Dihedral : 5.869 101.724 11652 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.09), residues: 9024 helix: 1.84 (0.15), residues: 1268 sheet: -1.52 (0.11), residues: 2192 loop : -2.45 (0.08), residues: 5564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP C 152 HIS 0.010 0.001 HIS Q 206 PHE 0.029 0.001 PHE F 152 TYR 0.019 0.001 TYR L 380 ARG 0.008 0.001 ARG R 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 622 time to evaluate : 6.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.6204 (p90) cc_final: 0.5751 (p90) REVERT: A 464 PHE cc_start: 0.6644 (m-80) cc_final: 0.6340 (m-80) REVERT: A 886 TRP cc_start: 0.7648 (p90) cc_final: 0.7000 (p90) REVERT: A 981 LEU cc_start: 0.7898 (pp) cc_final: 0.7367 (tt) REVERT: B 153 MET cc_start: 0.6838 (ptp) cc_final: 0.5895 (ppp) REVERT: B 177 MET cc_start: 0.6191 (ttt) cc_final: 0.5904 (ttp) REVERT: B 228 ASP cc_start: 0.8016 (t0) cc_final: 0.7787 (t0) REVERT: B 229 LEU cc_start: 0.7979 (mm) cc_final: 0.7755 (mm) REVERT: B 383 SER cc_start: 0.7982 (m) cc_final: 0.7719 (t) REVERT: B 517 LEU cc_start: 0.7598 (mt) cc_final: 0.7223 (pp) REVERT: B 551 VAL cc_start: 0.8778 (m) cc_final: 0.8569 (p) REVERT: B 795 LYS cc_start: 0.7397 (mptt) cc_final: 0.6983 (mptt) REVERT: B 1097 SER cc_start: 0.7869 (p) cc_final: 0.7645 (p) REVERT: B 1107 ARG cc_start: 0.6747 (mtm-85) cc_final: 0.5947 (mtm180) REVERT: B 1135 ASN cc_start: 0.8125 (t0) cc_final: 0.7563 (t0) REVERT: B 1138 TYR cc_start: 0.6807 (t80) cc_final: 0.6587 (t80) REVERT: C 111 ASP cc_start: 0.7456 (p0) cc_final: 0.7243 (p0) REVERT: C 215 ASP cc_start: 0.8393 (m-30) cc_final: 0.7582 (p0) REVERT: C 515 PHE cc_start: 0.7567 (m-80) cc_final: 0.7047 (m-10) REVERT: C 547 THR cc_start: 0.8719 (p) cc_final: 0.8498 (p) REVERT: C 1019 ARG cc_start: 0.6034 (ttp-170) cc_final: 0.5589 (ttp80) REVERT: D 87 ARG cc_start: 0.8242 (mmt90) cc_final: 0.7514 (mmt90) REVERT: D 150 ASP cc_start: 0.6175 (m-30) cc_final: 0.5874 (t0) REVERT: D 177 GLN cc_start: 0.7472 (tm-30) cc_final: 0.7054 (tt0) REVERT: D 205 ASN cc_start: 0.8126 (m110) cc_final: 0.7853 (m110) REVERT: E 54 GLN cc_start: 0.7788 (mp10) cc_final: 0.7452 (mp10) REVERT: E 123 LEU cc_start: 0.8003 (tp) cc_final: 0.7769 (tp) REVERT: E 210 LYS cc_start: 0.6240 (ptpp) cc_final: 0.5807 (ptmt) REVERT: F 73 ASP cc_start: 0.7870 (t70) cc_final: 0.7488 (t0) REVERT: F 82 GLN cc_start: 0.6643 (tt0) cc_final: 0.5804 (mm-40) REVERT: F 83 MET cc_start: 0.6718 (pmm) cc_final: 0.6263 (pmm) REVERT: F 123 LYS cc_start: 0.6754 (ptmt) cc_final: 0.6253 (mtmt) REVERT: G 4 MET cc_start: 0.7401 (mmt) cc_final: 0.7152 (mmt) REVERT: G 38 GLN cc_start: 0.7924 (tp40) cc_final: 0.7452 (tp40) REVERT: G 40 ARG cc_start: 0.7452 (tpp80) cc_final: 0.6912 (mmt90) REVERT: G 195 ARG cc_start: 0.7225 (tpm170) cc_final: 0.6595 (tpp-160) REVERT: H 34 MET cc_start: 0.7155 (mmt) cc_final: 0.6834 (mmm) REVERT: H 73 ASP cc_start: 0.7545 (t0) cc_final: 0.7130 (t70) REVERT: H 210 ASN cc_start: 0.7565 (t0) cc_final: 0.7020 (t0) REVERT: I 35 GLN cc_start: 0.7921 (mp-120) cc_final: 0.7599 (mm-40) REVERT: I 176 ASN cc_start: 0.6418 (m-40) cc_final: 0.5804 (p0) REVERT: I 183 TYR cc_start: 0.6938 (t80) cc_final: 0.6647 (t80) REVERT: J 212 LEU cc_start: 0.8069 (tp) cc_final: 0.7806 (tt) REVERT: J 452 LEU cc_start: 0.7700 (mt) cc_final: 0.7435 (mt) REVERT: J 572 THR cc_start: 0.8900 (m) cc_final: 0.8664 (p) REVERT: J 886 TRP cc_start: 0.7995 (p90) cc_final: 0.7704 (p90) REVERT: J 981 LEU cc_start: 0.8187 (pp) cc_final: 0.7865 (tp) REVERT: K 177 MET cc_start: 0.6901 (ttp) cc_final: 0.5329 (tpp) REVERT: K 191 GLU cc_start: 0.8422 (pt0) cc_final: 0.7944 (pt0) REVERT: K 383 SER cc_start: 0.8071 (m) cc_final: 0.7595 (p) REVERT: K 472 ILE cc_start: 0.7519 (mm) cc_final: 0.7306 (mm) REVERT: K 1135 ASN cc_start: 0.8120 (t0) cc_final: 0.7658 (t0) REVERT: L 215 ASP cc_start: 0.8340 (m-30) cc_final: 0.7580 (p0) REVERT: L 370 ASN cc_start: 0.8774 (m-40) cc_final: 0.8554 (m-40) REVERT: L 515 PHE cc_start: 0.7299 (m-80) cc_final: 0.7023 (m-80) REVERT: L 546 LEU cc_start: 0.8145 (mm) cc_final: 0.7720 (mm) REVERT: L 731 MET cc_start: 0.7356 (ptm) cc_final: 0.7029 (ptm) REVERT: L 949 GLN cc_start: 0.7235 (tp40) cc_final: 0.6980 (tp40) REVERT: L 1038 LYS cc_start: 0.7596 (mmtp) cc_final: 0.7224 (mmmt) REVERT: M 34 MET cc_start: 0.6515 (mmt) cc_final: 0.6182 (mmp) REVERT: N 52 ASP cc_start: 0.7963 (t70) cc_final: 0.7723 (t0) REVERT: N 88 ASP cc_start: 0.7581 (m-30) cc_final: 0.6734 (p0) REVERT: N 98 ASN cc_start: 0.8193 (p0) cc_final: 0.7895 (p0) REVERT: N 145 PHE cc_start: 0.5466 (p90) cc_final: 0.5084 (p90) REVERT: O 77 ASN cc_start: 0.8392 (m110) cc_final: 0.7676 (t0) REVERT: O 83 MET cc_start: 0.6289 (pmm) cc_final: 0.6083 (pmm) REVERT: P 81 LEU cc_start: 0.6636 (tp) cc_final: 0.6218 (tp) REVERT: P 135 LYS cc_start: 0.6165 (tptt) cc_final: 0.5693 (pttt) REVERT: P 178 TYR cc_start: 0.5910 (m-80) cc_final: 0.5645 (m-80) REVERT: Q 73 ASP cc_start: 0.7689 (t0) cc_final: 0.7455 (t0) REVERT: Q 83 MET cc_start: 0.7363 (mtt) cc_final: 0.6943 (mpp) REVERT: Q 160 TRP cc_start: 0.6716 (m100) cc_final: 0.6236 (m100) REVERT: Q 172 PHE cc_start: 0.5923 (p90) cc_final: 0.5313 (p90) REVERT: Q 210 ASN cc_start: 0.7489 (t0) cc_final: 0.6591 (t0) REVERT: Q 215 LYS cc_start: 0.6056 (tptt) cc_final: 0.5773 (tptm) REVERT: R 4 MET cc_start: 0.7940 (mmm) cc_final: 0.7236 (mtm) REVERT: R 40 ARG cc_start: 0.7367 (tpp80) cc_final: 0.7082 (tpp80) REVERT: R 86 GLU cc_start: 0.7457 (mm-30) cc_final: 0.5969 (pp20) REVERT: R 90 TYR cc_start: 0.7297 (m-80) cc_final: 0.7004 (m-10) REVERT: R 92 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7316 (tm-30) REVERT: R 98 ASN cc_start: 0.8645 (p0) cc_final: 0.8299 (t0) REVERT: R 141 LEU cc_start: 0.4950 (pp) cc_final: 0.4478 (tp) REVERT: R 175 ASN cc_start: 0.7431 (m-40) cc_final: 0.6928 (m-40) outliers start: 0 outliers final: 0 residues processed: 622 average time/residue: 0.6943 time to fit residues: 747.4838 Evaluate side-chains 498 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 6.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 789 optimal weight: 4.9990 chunk 831 optimal weight: 2.9990 chunk 758 optimal weight: 1.9990 chunk 808 optimal weight: 5.9990 chunk 830 optimal weight: 0.0040 chunk 486 optimal weight: 3.9990 chunk 352 optimal weight: 5.9990 chunk 634 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 730 optimal weight: 2.9990 chunk 764 optimal weight: 1.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 146 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 439 ASN B 607 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 949 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 74 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN I 99 HIS J1002 GLN K 271 GLN ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 784 GLN ** L 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 GLN ** M 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 74 ASN ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN Q 77 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 72876 Z= 0.295 Angle : 0.624 11.416 99312 Z= 0.317 Chirality : 0.047 0.610 11496 Planarity : 0.004 0.062 12750 Dihedral : 6.085 98.999 11652 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.09), residues: 9024 helix: 1.62 (0.15), residues: 1278 sheet: -1.51 (0.11), residues: 2254 loop : -2.50 (0.08), residues: 5492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 152 HIS 0.010 0.001 HIS Q 206 PHE 0.043 0.002 PHE A 906 TYR 0.048 0.002 TYR C 904 ARG 0.009 0.001 ARG Q 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 606 time to evaluate : 6.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.6001 (p90) cc_final: 0.5631 (p90) REVERT: A 464 PHE cc_start: 0.6602 (m-80) cc_final: 0.6212 (m-80) REVERT: A 886 TRP cc_start: 0.7616 (p90) cc_final: 0.6979 (p90) REVERT: A 981 LEU cc_start: 0.7926 (pp) cc_final: 0.7488 (tp) REVERT: B 153 MET cc_start: 0.6904 (ptp) cc_final: 0.5935 (ppp) REVERT: B 177 MET cc_start: 0.6294 (ttt) cc_final: 0.5553 (ttp) REVERT: B 228 ASP cc_start: 0.8067 (t0) cc_final: 0.7831 (t0) REVERT: B 383 SER cc_start: 0.8137 (m) cc_final: 0.7811 (t) REVERT: B 464 PHE cc_start: 0.8105 (m-80) cc_final: 0.7897 (m-80) REVERT: B 517 LEU cc_start: 0.7675 (mt) cc_final: 0.7282 (pp) REVERT: B 551 VAL cc_start: 0.8812 (m) cc_final: 0.8561 (p) REVERT: B 977 LEU cc_start: 0.7500 (pt) cc_final: 0.7026 (mt) REVERT: B 995 ARG cc_start: 0.6766 (mtm110) cc_final: 0.6559 (mtm110) REVERT: B 1097 SER cc_start: 0.7883 (p) cc_final: 0.7674 (p) REVERT: B 1135 ASN cc_start: 0.8202 (t0) cc_final: 0.7616 (t0) REVERT: B 1138 TYR cc_start: 0.6792 (t80) cc_final: 0.6527 (t80) REVERT: C 215 ASP cc_start: 0.8411 (m-30) cc_final: 0.7710 (p0) REVERT: C 436 TRP cc_start: 0.7843 (p90) cc_final: 0.7119 (p90) REVERT: C 515 PHE cc_start: 0.7605 (m-80) cc_final: 0.7062 (m-10) REVERT: C 740 MET cc_start: 0.7478 (tpp) cc_final: 0.7194 (tpp) REVERT: C 1019 ARG cc_start: 0.5997 (ttp-170) cc_final: 0.5732 (ttp80) REVERT: D 87 ARG cc_start: 0.8251 (mmt90) cc_final: 0.7502 (mmt90) REVERT: D 150 ASP cc_start: 0.6253 (m-30) cc_final: 0.5994 (t0) REVERT: D 205 ASN cc_start: 0.8104 (m110) cc_final: 0.7853 (m110) REVERT: E 12 GLU cc_start: 0.8202 (tt0) cc_final: 0.7758 (tt0) REVERT: E 54 GLN cc_start: 0.7790 (mp10) cc_final: 0.7456 (mp10) REVERT: E 123 LEU cc_start: 0.8142 (tp) cc_final: 0.7869 (tp) REVERT: E 210 LYS cc_start: 0.6271 (ptpp) cc_final: 0.5815 (ptmt) REVERT: F 73 ASP cc_start: 0.7883 (t70) cc_final: 0.7620 (t70) REVERT: F 82 GLN cc_start: 0.6667 (tt0) cc_final: 0.5683 (tm-30) REVERT: F 123 LYS cc_start: 0.6733 (ptmt) cc_final: 0.6467 (mttp) REVERT: G 4 MET cc_start: 0.7472 (mmt) cc_final: 0.7242 (mmt) REVERT: G 33 TYR cc_start: 0.7758 (m-80) cc_final: 0.7206 (m-80) REVERT: G 38 GLN cc_start: 0.7908 (tp40) cc_final: 0.7378 (tp40) REVERT: G 40 ARG cc_start: 0.7424 (tpp80) cc_final: 0.6689 (mmt90) REVERT: G 195 ARG cc_start: 0.7088 (tpm170) cc_final: 0.6269 (mmm160) REVERT: H 34 MET cc_start: 0.7275 (mmt) cc_final: 0.6934 (mmm) REVERT: H 73 ASP cc_start: 0.7483 (t0) cc_final: 0.7093 (t70) REVERT: H 210 ASN cc_start: 0.7610 (t0) cc_final: 0.7058 (t0) REVERT: I 35 GLN cc_start: 0.7994 (mp-120) cc_final: 0.7592 (mm-40) REVERT: I 176 ASN cc_start: 0.6366 (m-40) cc_final: 0.5714 (p0) REVERT: I 183 TYR cc_start: 0.6895 (t80) cc_final: 0.6618 (t80) REVERT: J 177 MET cc_start: 0.6849 (mtt) cc_final: 0.5656 (mtt) REVERT: J 212 LEU cc_start: 0.8208 (tp) cc_final: 0.7952 (tt) REVERT: J 452 LEU cc_start: 0.7719 (mt) cc_final: 0.7461 (mt) REVERT: J 572 THR cc_start: 0.8900 (m) cc_final: 0.8657 (p) REVERT: J 740 MET cc_start: 0.7162 (ttm) cc_final: 0.6873 (ttm) REVERT: J 886 TRP cc_start: 0.8005 (p90) cc_final: 0.7725 (p90) REVERT: J 981 LEU cc_start: 0.8175 (pp) cc_final: 0.7900 (tp) REVERT: K 177 MET cc_start: 0.7174 (ttp) cc_final: 0.5561 (tpp) REVERT: K 191 GLU cc_start: 0.8455 (pt0) cc_final: 0.8009 (pt0) REVERT: K 228 ASP cc_start: 0.8199 (t0) cc_final: 0.7808 (t0) REVERT: K 383 SER cc_start: 0.8239 (m) cc_final: 0.7728 (p) REVERT: K 1135 ASN cc_start: 0.8116 (t0) cc_final: 0.7657 (t0) REVERT: L 215 ASP cc_start: 0.8394 (m-30) cc_final: 0.7629 (p0) REVERT: L 515 PHE cc_start: 0.7449 (m-80) cc_final: 0.7135 (m-80) REVERT: L 731 MET cc_start: 0.7306 (ptm) cc_final: 0.7038 (ptm) REVERT: L 949 GLN cc_start: 0.7384 (tp40) cc_final: 0.7145 (tp40) REVERT: L 1038 LYS cc_start: 0.7584 (mmtp) cc_final: 0.7228 (mmmt) REVERT: M 34 MET cc_start: 0.6636 (mmt) cc_final: 0.6316 (mmp) REVERT: N 52 ASP cc_start: 0.7946 (t70) cc_final: 0.7690 (t0) REVERT: N 88 ASP cc_start: 0.7624 (m-30) cc_final: 0.6790 (p0) REVERT: N 98 ASN cc_start: 0.8170 (p0) cc_final: 0.7872 (p0) REVERT: N 145 PHE cc_start: 0.5367 (p90) cc_final: 0.4983 (p90) REVERT: O 34 MET cc_start: 0.7876 (mmm) cc_final: 0.7587 (mmm) REVERT: O 77 ASN cc_start: 0.8470 (m110) cc_final: 0.7749 (t0) REVERT: O 83 MET cc_start: 0.6263 (pmm) cc_final: 0.6013 (pmm) REVERT: P 81 LEU cc_start: 0.6662 (tp) cc_final: 0.6305 (tp) REVERT: P 89 TYR cc_start: 0.7763 (m-80) cc_final: 0.7545 (m-10) REVERT: P 135 LYS cc_start: 0.6252 (tptt) cc_final: 0.5789 (pttt) REVERT: Q 50 ASN cc_start: 0.7061 (t0) cc_final: 0.6770 (m-40) REVERT: Q 73 ASP cc_start: 0.7671 (t0) cc_final: 0.7428 (t0) REVERT: Q 83 MET cc_start: 0.7382 (mtt) cc_final: 0.6905 (mpp) REVERT: Q 160 TRP cc_start: 0.6770 (m100) cc_final: 0.6319 (m100) REVERT: Q 172 PHE cc_start: 0.5944 (p90) cc_final: 0.5308 (p90) REVERT: Q 210 ASN cc_start: 0.7514 (t0) cc_final: 0.6659 (t0) REVERT: R 4 MET cc_start: 0.7929 (mmm) cc_final: 0.7172 (mtm) REVERT: R 40 ARG cc_start: 0.7448 (tpp80) cc_final: 0.7176 (tpp80) REVERT: R 86 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6008 (pp20) REVERT: R 90 TYR cc_start: 0.7204 (m-80) cc_final: 0.6923 (m-10) REVERT: R 92 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7237 (tm-30) REVERT: R 98 ASN cc_start: 0.8669 (p0) cc_final: 0.8358 (t0) REVERT: R 141 LEU cc_start: 0.5130 (pp) cc_final: 0.4592 (tp) REVERT: R 175 ASN cc_start: 0.7186 (m-40) cc_final: 0.6756 (m-40) outliers start: 0 outliers final: 0 residues processed: 606 average time/residue: 0.6935 time to fit residues: 729.7217 Evaluate side-chains 481 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 481 time to evaluate : 6.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 805 optimal weight: 0.9980 chunk 530 optimal weight: 1.9990 chunk 854 optimal weight: 7.9990 chunk 521 optimal weight: 3.9990 chunk 405 optimal weight: 0.2980 chunk 594 optimal weight: 0.8980 chunk 896 optimal weight: 4.9990 chunk 825 optimal weight: 9.9990 chunk 713 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 551 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 146 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 439 ASN B 607 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1002 GLN K 271 GLN ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 774 GLN L 784 GLN ** L 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 74 ASN P 6 GLN ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN Q 77 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 72876 Z= 0.222 Angle : 0.592 10.716 99312 Z= 0.299 Chirality : 0.046 0.580 11496 Planarity : 0.004 0.095 12750 Dihedral : 5.901 98.925 11652 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.09), residues: 9024 helix: 1.74 (0.15), residues: 1280 sheet: -1.39 (0.11), residues: 2180 loop : -2.40 (0.08), residues: 5564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 152 HIS 0.007 0.001 HIS Q 206 PHE 0.036 0.001 PHE B 429 TYR 0.036 0.001 TYR C 904 ARG 0.009 0.001 ARG Q 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18048 Ramachandran restraints generated. 9024 Oldfield, 0 Emsley, 9024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 593 time to evaluate : 6.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 TYR cc_start: 0.5868 (p90) cc_final: 0.5547 (p90) REVERT: A 464 PHE cc_start: 0.6637 (m-80) cc_final: 0.6364 (m-80) REVERT: A 773 GLU cc_start: 0.5400 (tt0) cc_final: 0.5158 (tt0) REVERT: A 886 TRP cc_start: 0.7625 (p90) cc_final: 0.6988 (p90) REVERT: A 981 LEU cc_start: 0.8175 (pp) cc_final: 0.7691 (tp) REVERT: A 1050 MET cc_start: 0.5834 (ptm) cc_final: 0.5554 (ptm) REVERT: B 153 MET cc_start: 0.6871 (ptp) cc_final: 0.5913 (ppp) REVERT: B 177 MET cc_start: 0.6279 (ttt) cc_final: 0.5806 (ttp) REVERT: B 228 ASP cc_start: 0.8023 (t0) cc_final: 0.7810 (t0) REVERT: B 383 SER cc_start: 0.8092 (m) cc_final: 0.7769 (t) REVERT: B 464 PHE cc_start: 0.8082 (m-80) cc_final: 0.7870 (m-80) REVERT: B 517 LEU cc_start: 0.7727 (mt) cc_final: 0.7319 (pp) REVERT: B 551 VAL cc_start: 0.8800 (m) cc_final: 0.8563 (p) REVERT: B 795 LYS cc_start: 0.7407 (mptt) cc_final: 0.7102 (mptt) REVERT: B 977 LEU cc_start: 0.7453 (pt) cc_final: 0.7051 (mt) REVERT: B 1135 ASN cc_start: 0.8166 (t0) cc_final: 0.7616 (t0) REVERT: B 1138 TYR cc_start: 0.6699 (t80) cc_final: 0.6402 (t80) REVERT: C 111 ASP cc_start: 0.7435 (p0) cc_final: 0.7203 (p0) REVERT: C 215 ASP cc_start: 0.8441 (m-30) cc_final: 0.7729 (p0) REVERT: C 436 TRP cc_start: 0.7807 (p90) cc_final: 0.7088 (p90) REVERT: C 515 PHE cc_start: 0.7573 (m-80) cc_final: 0.7048 (m-10) REVERT: C 547 THR cc_start: 0.8741 (p) cc_final: 0.8538 (p) REVERT: C 740 MET cc_start: 0.7479 (tpp) cc_final: 0.7180 (tpp) REVERT: C 774 GLN cc_start: 0.5584 (mm-40) cc_final: 0.5375 (mm110) REVERT: C 1019 ARG cc_start: 0.6118 (ttp-170) cc_final: 0.5665 (ttp80) REVERT: D 87 ARG cc_start: 0.8274 (mmt90) cc_final: 0.7572 (mmt90) REVERT: D 150 ASP cc_start: 0.6162 (m-30) cc_final: 0.5910 (t0) REVERT: D 177 GLN cc_start: 0.7076 (tm-30) cc_final: 0.6767 (tm-30) REVERT: D 205 ASN cc_start: 0.8145 (m110) cc_final: 0.7895 (m110) REVERT: E 12 GLU cc_start: 0.8223 (tt0) cc_final: 0.7824 (tt0) REVERT: E 52 ASP cc_start: 0.7290 (t0) cc_final: 0.6823 (t0) REVERT: E 54 GLN cc_start: 0.7654 (mp10) cc_final: 0.7410 (mp10) REVERT: E 123 LEU cc_start: 0.8099 (tp) cc_final: 0.7824 (tp) REVERT: E 210 LYS cc_start: 0.6242 (ptpp) cc_final: 0.5789 (ptmt) REVERT: F 73 ASP cc_start: 0.7896 (t70) cc_final: 0.7661 (t70) REVERT: F 82 GLN cc_start: 0.6561 (tt0) cc_final: 0.5808 (mm-40) REVERT: F 111 GLN cc_start: 0.8167 (pm20) cc_final: 0.7891 (pm20) REVERT: F 123 LYS cc_start: 0.6706 (ptmt) cc_final: 0.6157 (mtmt) REVERT: G 4 MET cc_start: 0.7397 (mmt) cc_final: 0.7193 (mmt) REVERT: G 33 TYR cc_start: 0.7709 (m-80) cc_final: 0.7278 (m-80) REVERT: G 38 GLN cc_start: 0.7974 (tp40) cc_final: 0.7514 (tp40) REVERT: G 40 ARG cc_start: 0.7441 (tpp80) cc_final: 0.6905 (mmt90) REVERT: G 195 ARG cc_start: 0.7025 (tpm170) cc_final: 0.6222 (mmm160) REVERT: H 34 MET cc_start: 0.7167 (mmt) cc_final: 0.6853 (mmm) REVERT: H 73 ASP cc_start: 0.7460 (t0) cc_final: 0.7003 (t70) REVERT: I 35 GLN cc_start: 0.8012 (mp-120) cc_final: 0.7594 (mm-40) REVERT: I 40 ARG cc_start: 0.7226 (mmm160) cc_final: 0.6746 (mmm-85) REVERT: I 176 ASN cc_start: 0.6315 (m-40) cc_final: 0.5707 (p0) REVERT: I 183 TYR cc_start: 0.6917 (t80) cc_final: 0.6595 (t80) REVERT: J 177 MET cc_start: 0.6855 (mtt) cc_final: 0.5654 (mtt) REVERT: J 212 LEU cc_start: 0.8198 (tp) cc_final: 0.7938 (tt) REVERT: J 452 LEU cc_start: 0.7729 (mt) cc_final: 0.7441 (mt) REVERT: J 572 THR cc_start: 0.8933 (m) cc_final: 0.8665 (p) REVERT: J 740 MET cc_start: 0.7190 (ttm) cc_final: 0.6812 (ttm) REVERT: J 886 TRP cc_start: 0.8008 (p90) cc_final: 0.7722 (p90) REVERT: J 981 LEU cc_start: 0.8178 (pp) cc_final: 0.7883 (tp) REVERT: K 177 MET cc_start: 0.7101 (ttp) cc_final: 0.5576 (tpp) REVERT: K 191 GLU cc_start: 0.8387 (pt0) cc_final: 0.7887 (pt0) REVERT: K 228 ASP cc_start: 0.8215 (t0) cc_final: 0.7771 (t0) REVERT: K 383 SER cc_start: 0.8199 (m) cc_final: 0.7694 (p) REVERT: K 390 LEU cc_start: 0.8389 (tp) cc_final: 0.8161 (tp) REVERT: K 1135 ASN cc_start: 0.8231 (t0) cc_final: 0.7768 (t0) REVERT: L 215 ASP cc_start: 0.8402 (m-30) cc_final: 0.7699 (p0) REVERT: L 451 TYR cc_start: 0.4031 (m-10) cc_final: 0.3828 (m-10) REVERT: L 515 PHE cc_start: 0.7368 (m-80) cc_final: 0.7059 (m-80) REVERT: L 731 MET cc_start: 0.7379 (ptm) cc_final: 0.6998 (ptm) REVERT: L 740 MET cc_start: 0.7372 (tpp) cc_final: 0.7151 (tpp) REVERT: L 773 GLU cc_start: 0.6550 (tp30) cc_final: 0.6281 (tt0) REVERT: L 949 GLN cc_start: 0.7285 (tp40) cc_final: 0.7011 (tp40) REVERT: L 1038 LYS cc_start: 0.7595 (mmtp) cc_final: 0.7234 (mmmt) REVERT: M 34 MET cc_start: 0.6588 (mmt) cc_final: 0.6252 (mmp) REVERT: N 52 ASP cc_start: 0.7953 (t70) cc_final: 0.7653 (t0) REVERT: N 88 ASP cc_start: 0.7614 (m-30) cc_final: 0.6768 (p0) REVERT: N 98 ASN cc_start: 0.8197 (p0) cc_final: 0.7900 (p0) REVERT: N 145 PHE cc_start: 0.5464 (p90) cc_final: 0.5144 (p90) REVERT: P 81 LEU cc_start: 0.6547 (tp) cc_final: 0.6323 (tp) REVERT: P 135 LYS cc_start: 0.6163 (tptt) cc_final: 0.5718 (pttt) REVERT: Q 50 ASN cc_start: 0.7033 (t0) cc_final: 0.6777 (m-40) REVERT: Q 73 ASP cc_start: 0.7638 (t0) cc_final: 0.7406 (t0) REVERT: Q 83 MET cc_start: 0.7350 (mtt) cc_final: 0.6856 (mpp) REVERT: Q 160 TRP cc_start: 0.6761 (m100) cc_final: 0.6353 (m100) REVERT: Q 172 PHE cc_start: 0.6038 (p90) cc_final: 0.5425 (p90) REVERT: R 4 MET cc_start: 0.7953 (mmm) cc_final: 0.7125 (mtm) REVERT: R 86 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7146 (pm20) REVERT: R 90 TYR cc_start: 0.7164 (m-80) cc_final: 0.6910 (m-10) REVERT: R 92 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7261 (tm-30) REVERT: R 98 ASN cc_start: 0.8699 (p0) cc_final: 0.8405 (t0) REVERT: R 141 LEU cc_start: 0.5101 (pp) cc_final: 0.4537 (tp) REVERT: R 175 ASN cc_start: 0.7199 (m-40) cc_final: 0.6767 (m-40) outliers start: 0 outliers final: 0 residues processed: 593 average time/residue: 0.6722 time to fit residues: 689.3317 Evaluate side-chains 479 residues out of total 7896 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 479 time to evaluate : 6.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 900 random chunks: chunk 437 optimal weight: 10.0000 chunk 567 optimal weight: 1.9990 chunk 760 optimal weight: 0.9980 chunk 218 optimal weight: 0.6980 chunk 658 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 chunk 715 optimal weight: 10.0000 chunk 299 optimal weight: 2.9990 chunk 734 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 146 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 GLN B 360 ASN B 439 ASN B 607 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 74 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN K 271 GLN ** K 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1002 GLN ** L 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 74 ASN ** P 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 176 ASN Q 6 GLN Q 77 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.078139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.064309 restraints weight = 258382.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.063300 restraints weight = 531451.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.063488 restraints weight = 490519.412| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 72876 Z= 0.212 Angle : 0.583 10.246 99312 Z= 0.295 Chirality : 0.046 0.559 11496 Planarity : 0.004 0.061 12750 Dihedral : 5.787 97.770 11652 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.09), residues: 9024 helix: 1.79 (0.15), residues: 1280 sheet: -1.33 (0.11), residues: 2168 loop : -2.36 (0.08), residues: 5576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 152 HIS 0.009 0.001 HIS Q 206 PHE 0.036 0.001 PHE B 429 TYR 0.031 0.001 TYR C 904 ARG 0.015 0.001 ARG A1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15470.21 seconds wall clock time: 269 minutes 36.75 seconds (16176.75 seconds total)