Starting phenix.real_space_refine on Sat Dec 9 18:04:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns6_12561/12_2023/7ns6_12561.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns6_12561/12_2023/7ns6_12561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns6_12561/12_2023/7ns6_12561.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns6_12561/12_2023/7ns6_12561.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns6_12561/12_2023/7ns6_12561.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns6_12561/12_2023/7ns6_12561.pdb" } resolution = 3.18 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8656 atoms to isotropic. 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 243 5.16 5 C 35593 2.51 5 N 9216 2.21 5 O 10847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 55899 Number of models: 1 Model: "" Number of chains: 20 Chain: "G" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1021 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "S" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1021 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1021 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "T" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1021 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "O" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1021 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "U" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1021 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 5, 'TRANS': 127} Chain: "I" Number of atoms: 8115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8115 Classifications: {'peptide': 1044} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 55, 'TRANS': 988} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "K" Number of atoms: 8248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8248 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 55, 'TRANS': 1006} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "M" Number of atoms: 8098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8098 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 52, 'TRANS': 989} Chain breaks: 9 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 8160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 8160 Classifications: {'peptide': 1049} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 55, 'TRANS': 993} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 8222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8222 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 55, 'TRANS': 1002} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "N" Number of atoms: 8208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8208 Classifications: {'peptide': 1056} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 54, 'TRANS': 1001} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "M" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "J" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "L" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 22.08, per 1000 atoms: 0.39 Number of scatterers: 55899 At special positions: 0 Unit cell: (166.65, 160.59, 344.41, 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 243 16.00 O 10847 8.00 N 9216 7.00 C 35593 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=82, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 166 " distance=2.03 Simple disulfide: pdb=" SG CYS I 291 " - pdb=" SG CYS I 301 " distance=2.03 Simple disulfide: pdb=" SG CYS I 336 " - pdb=" SG CYS I 361 " distance=2.02 Simple disulfide: pdb=" SG CYS I 379 " - pdb=" SG CYS I 432 " distance=2.03 Simple disulfide: pdb=" SG CYS I 391 " - pdb=" SG CYS I 525 " distance=2.06 Simple disulfide: pdb=" SG CYS I 480 " - pdb=" SG CYS I 488 " distance=2.03 Simple disulfide: pdb=" SG CYS I 538 " - pdb=" SG CYS I 590 " distance=2.04 Simple disulfide: pdb=" SG CYS I 617 " - pdb=" SG CYS I 649 " distance=2.03 Simple disulfide: pdb=" SG CYS I 662 " - pdb=" SG CYS I 671 " distance=2.02 Simple disulfide: pdb=" SG CYS I 743 " - pdb=" SG CYS I 749 " distance=2.03 Simple disulfide: pdb=" SG CYS I1032 " - pdb=" SG CYS I1043 " distance=2.02 Simple disulfide: pdb=" SG CYS I1082 " - pdb=" SG CYS I1126 " 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=2.03 Simple disulfide: pdb=" SG CYS K 336 " - pdb=" SG CYS K 361 " distance=2.05 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=2.06 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=2.04 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 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 M 15 " - pdb=" SG CYS M 136 " distance=2.03 Simple disulfide: pdb=" SG CYS M 131 " - pdb=" SG CYS M 166 " distance=2.03 Simple disulfide: pdb=" SG CYS M 291 " - pdb=" SG CYS M 301 " distance=2.03 Simple disulfide: pdb=" SG CYS M 336 " - pdb=" SG CYS M 361 " distance=2.04 Simple disulfide: pdb=" SG CYS M 379 " - pdb=" SG CYS M 432 " distance=2.03 Simple disulfide: pdb=" SG CYS M 391 " - pdb=" SG CYS M 525 " distance=2.04 Simple disulfide: pdb=" SG CYS M 480 " - pdb=" SG CYS M 488 " distance=2.03 Simple disulfide: pdb=" SG CYS M 538 " - pdb=" SG CYS M 590 " distance=2.04 Simple disulfide: pdb=" SG CYS M 617 " - pdb=" SG CYS M 649 " distance=2.02 Simple disulfide: pdb=" SG CYS M 662 " - pdb=" SG CYS M 671 " distance=2.02 Simple disulfide: pdb=" SG CYS M 743 " - pdb=" SG CYS M 749 " distance=2.03 Simple disulfide: pdb=" SG CYS M1032 " - pdb=" SG CYS M1043 " distance=2.03 Simple disulfide: pdb=" SG CYS M1082 " - pdb=" SG CYS M1126 " 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS J 617 " - pdb=" SG CYS J 649 " distance=2.03 Simple disulfide: pdb=" SG CYS J 662 " - pdb=" SG CYS J 671 " distance=2.02 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 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=2.03 Simple disulfide: pdb=" SG CYS L 336 " - pdb=" SG CYS L 361 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS L 617 " - pdb=" SG CYS L 649 " distance=2.03 Simple disulfide: pdb=" SG CYS L 662 " - pdb=" SG CYS L 671 " 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 N 15 " - pdb=" SG CYS N 136 " distance=2.03 Simple disulfide: pdb=" SG CYS N 131 " - pdb=" SG CYS N 166 " distance=2.03 Simple disulfide: pdb=" SG CYS N 291 " - pdb=" SG CYS N 301 " distance=2.03 Simple disulfide: pdb=" SG CYS N 336 " - pdb=" SG CYS N 361 " distance=2.03 Simple disulfide: pdb=" SG CYS N 379 " - pdb=" SG CYS N 432 " distance=2.03 Simple disulfide: pdb=" SG CYS N 391 " - pdb=" SG CYS N 525 " distance=2.04 Simple disulfide: pdb=" SG CYS N 480 " - pdb=" SG CYS N 488 " distance=2.03 Simple disulfide: pdb=" SG CYS N 538 " - pdb=" SG CYS N 590 " distance=2.04 Simple disulfide: pdb=" SG CYS N 617 " - pdb=" SG CYS N 649 " distance=2.03 Simple disulfide: pdb=" SG CYS N 662 " - pdb=" SG CYS N 671 " distance=2.02 Simple disulfide: pdb=" SG CYS N 743 " - pdb=" SG CYS N 749 " distance=2.03 Simple disulfide: pdb=" SG CYS N1032 " - pdb=" SG CYS N1043 " distance=2.03 Simple disulfide: pdb=" SG CYS N1082 " - pdb=" SG CYS N1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 1 " - " ASN I 331 " " NAG B 1 " - " ASN K 343 " " NAG I1301 " - " ASN I 717 " " NAG I1302 " - " ASN I 709 " " NAG I1303 " - " ASN I1134 " " NAG I1304 " - " ASN I 801 " " NAG I1305 " - " ASN I 343 " " NAG I1306 " - " ASN I1074 " " NAG I1307 " - " ASN I 616 " " NAG I1308 " - " ASN I1098 " " NAG J1301 " - " ASN J 801 " " NAG J1302 " - " ASN J 343 " " NAG J1303 " - " ASN J1098 " " NAG J1304 " - " ASN J1134 " " NAG J1305 " - " ASN J 331 " " NAG J1306 " - " ASN J 717 " " NAG J1307 " - " ASN J 709 " " NAG J1308 " - " ASN J1074 " " NAG K1301 " - " ASN K 717 " " NAG K1302 " - " ASN K1134 " " NAG K1303 " - " ASN K 709 " " NAG K1304 " - " ASN K 331 " " NAG K1305 " - " ASN K 801 " " NAG K1306 " - " ASN K1098 " " NAG K1307 " - " ASN K 616 " " NAG L1301 " - " ASN L 709 " " NAG L1302 " - " ASN L1098 " " NAG L1303 " - " ASN L1134 " " NAG L1304 " - " ASN L 717 " " NAG L1305 " - " ASN L 928 " " NAG M1301 " - " ASN M1134 " " NAG M1302 " - " ASN M 709 " " NAG M1303 " - " ASN M 801 " " NAG M1304 " - " ASN M 717 " " NAG M1305 " - " ASN M1074 " " NAG M1306 " - " ASN M 331 " " NAG M1307 " - " ASN M 343 " " NAG M1308 " - " ASN M 282 " " NAG M1309 " - " ASN M1098 " " NAG M1310 " - " ASN M 616 " " NAG N1301 " - " ASN N 801 " " NAG N1302 " - " ASN N 717 " " NAG N1303 " - " ASN N1134 " " NAG N1304 " - " ASN N 616 " " NAG N1305 " - " ASN N 331 " " NAG N1306 " - " ASN N 343 " " NAG N1307 " - " ASN N 709 " " NAG N1308 " - " ASN N1098 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.08 Conformation dependent library (CDL) restraints added in 7.9 seconds 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13212 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 115 sheets defined 23.2% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.25 Creating SS restraints... Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'G' and resid 102 through 106 Processing helix chain 'G' and resid 114 through 118 Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 102 through 106 Processing helix chain 'S' and resid 114 through 118 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 102 through 106 Processing helix chain 'H' and resid 114 through 118 Processing helix chain 'T' and resid 102 through 106 Processing helix chain 'T' and resid 114 through 118 Processing helix chain 'O' and resid 102 through 106 Processing helix chain 'O' and resid 114 through 118 Processing helix chain 'U' and resid 62 through 65 Processing helix chain 'U' and resid 102 through 106 Processing helix chain 'U' and resid 114 through 118 Processing helix chain 'I' and resid 294 through 304 Processing helix chain 'I' and resid 337 through 343 Processing helix chain 'I' and resid 364 through 371 removed outlier: 3.739A pdb=" N LEU I 368 " --> pdb=" O ASP I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 390 removed outlier: 3.839A pdb=" N ASP I 389 " --> pdb=" O THR I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 410 removed outlier: 4.023A pdb=" N ARG I 408 " --> pdb=" O GLY I 404 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN I 409 " --> pdb=" O ASP I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 422 Processing helix chain 'I' and resid 616 through 620 removed outlier: 4.470A pdb=" N GLU I 619 " --> pdb=" O ASN I 616 " (cutoff:3.500A) Processing helix chain 'I' and resid 737 through 743 Processing helix chain 'I' and resid 746 through 756 removed outlier: 3.624A pdb=" N GLN I 755 " --> pdb=" O ASN I 751 " (cutoff:3.500A) Processing helix chain 'I' and resid 758 through 783 Processing helix chain 'I' and resid 816 through 826 Processing helix chain 'I' and resid 866 through 885 Processing helix chain 'I' and resid 886 through 890 Processing helix chain 'I' and resid 897 through 909 Processing helix chain 'I' and resid 912 through 919 removed outlier: 4.272A pdb=" N LEU I 916 " --> pdb=" O THR I 912 " (cutoff:3.500A) Processing helix chain 'I' and resid 919 through 941 Processing helix chain 'I' and resid 945 through 967 removed outlier: 3.748A pdb=" N SER I 967 " --> pdb=" O VAL I 963 " (cutoff:3.500A) Processing helix chain 'I' and resid 976 through 984 removed outlier: 3.589A pdb=" N ILE I 980 " --> pdb=" O VAL I 976 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 1033 Processing helix chain 'I' and resid 1141 through 1146 Processing helix chain 'K' and resid 294 through 304 Processing helix chain 'K' and resid 337 through 343 Processing helix chain 'K' and resid 364 through 371 removed outlier: 3.920A pdb=" N LEU K 368 " --> pdb=" O ASP K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 390 removed outlier: 3.842A pdb=" N ASP K 389 " --> pdb=" O THR K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 410 removed outlier: 4.071A pdb=" N ARG K 408 " --> pdb=" O GLY K 404 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN K 409 " --> pdb=" O ASP K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 422 Processing helix chain 'K' and resid 737 through 743 Processing helix chain 'K' and resid 746 through 756 removed outlier: 3.584A pdb=" N GLN K 755 " --> pdb=" O ASN K 751 " (cutoff:3.500A) Processing helix chain 'K' and resid 758 through 783 Processing helix chain 'K' and resid 802 through 806 Processing helix chain 'K' and resid 816 through 826 Processing helix chain 'K' and resid 866 through 885 Processing helix chain 'K' and resid 886 through 890 Processing helix chain 'K' and resid 897 through 909 Processing helix chain 'K' and resid 912 through 919 removed outlier: 4.263A pdb=" N LEU K 916 " --> pdb=" O THR K 912 " (cutoff:3.500A) Processing helix chain 'K' and resid 919 through 941 Processing helix chain 'K' and resid 945 through 966 Processing helix chain 'K' and resid 976 through 984 removed outlier: 3.560A pdb=" N ILE K 980 " --> pdb=" O VAL K 976 " (cutoff:3.500A) Processing helix chain 'K' and resid 985 through 1033 Processing helix chain 'K' and resid 1141 through 1146 Processing helix chain 'M' and resid 294 through 304 Processing helix chain 'M' and resid 337 through 343 Processing helix chain 'M' and resid 364 through 371 removed outlier: 4.007A pdb=" N LEU M 368 " --> pdb=" O ASP M 364 " (cutoff:3.500A) Processing helix chain 'M' and resid 383 through 390 removed outlier: 3.789A pdb=" N ASP M 389 " --> pdb=" O THR M 385 " (cutoff:3.500A) Processing helix chain 'M' and resid 404 through 410 removed outlier: 4.037A pdb=" N ARG M 408 " --> pdb=" O GLY M 404 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLN M 409 " --> pdb=" O ASP M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 422 Processing helix chain 'M' and resid 737 through 743 Processing helix chain 'M' and resid 746 through 756 removed outlier: 3.590A pdb=" N GLN M 755 " --> pdb=" O ASN M 751 " (cutoff:3.500A) Processing helix chain 'M' and resid 758 through 783 Processing helix chain 'M' and resid 816 through 826 Processing helix chain 'M' and resid 866 through 885 Processing helix chain 'M' and resid 886 through 890 Processing helix chain 'M' and resid 897 through 909 Processing helix chain 'M' and resid 912 through 919 removed outlier: 4.265A pdb=" N LEU M 916 " --> pdb=" O THR M 912 " (cutoff:3.500A) Processing helix chain 'M' and resid 919 through 941 Processing helix chain 'M' and resid 945 through 967 removed outlier: 3.745A pdb=" N SER M 967 " --> pdb=" O VAL M 963 " (cutoff:3.500A) Processing helix chain 'M' and resid 976 through 984 Processing helix chain 'M' and resid 985 through 1033 Processing helix chain 'M' and resid 1141 through 1146 Processing helix chain 'J' and resid 294 through 304 Processing helix chain 'J' and resid 337 through 343 Processing helix chain 'J' and resid 364 through 371 removed outlier: 3.688A pdb=" N LEU J 368 " --> pdb=" O ASP J 364 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 390 removed outlier: 3.798A pdb=" N ASP J 389 " --> pdb=" O THR J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 404 through 410 removed outlier: 4.024A pdb=" N ARG J 408 " --> pdb=" O GLY J 404 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN J 409 " --> pdb=" O ASP J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 422 Processing helix chain 'J' and resid 616 through 620 removed outlier: 4.083A pdb=" N GLU J 619 " --> pdb=" O ASN J 616 " (cutoff:3.500A) Processing helix chain 'J' and resid 737 through 743 Processing helix chain 'J' and resid 746 through 756 removed outlier: 3.597A pdb=" N GLN J 755 " --> pdb=" O ASN J 751 " (cutoff:3.500A) Processing helix chain 'J' and resid 758 through 783 Processing helix chain 'J' and resid 816 through 826 Processing helix chain 'J' and resid 866 through 885 Processing helix chain 'J' and resid 886 through 890 Processing helix chain 'J' and resid 897 through 909 Processing helix chain 'J' and resid 912 through 919 removed outlier: 4.273A pdb=" N LEU J 916 " --> pdb=" O THR J 912 " (cutoff:3.500A) Processing helix chain 'J' and resid 919 through 941 Processing helix chain 'J' and resid 945 through 967 removed outlier: 3.768A pdb=" N SER J 967 " --> pdb=" O VAL J 963 " (cutoff:3.500A) Processing helix chain 'J' and resid 976 through 984 removed outlier: 3.544A pdb=" N ILE J 980 " --> pdb=" O VAL J 976 " (cutoff:3.500A) Processing helix chain 'J' and resid 985 through 1033 Processing helix chain 'J' and resid 1141 through 1146 Processing helix chain 'L' and resid 294 through 304 Processing helix chain 'L' and resid 337 through 343 Processing helix chain 'L' and resid 364 through 371 removed outlier: 3.942A pdb=" N LEU L 368 " --> pdb=" O ASP L 364 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 390 removed outlier: 3.810A pdb=" N ASP L 389 " --> pdb=" O THR L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 404 through 410 removed outlier: 4.035A pdb=" N ARG L 408 " --> pdb=" O GLY L 404 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN L 409 " --> pdb=" O ASP L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 422 Processing helix chain 'L' and resid 616 through 620 removed outlier: 4.134A pdb=" N GLU L 619 " --> pdb=" O ASN L 616 " (cutoff:3.500A) Processing helix chain 'L' and resid 737 through 743 Processing helix chain 'L' and resid 746 through 756 removed outlier: 3.593A pdb=" N GLN L 755 " --> pdb=" O ASN L 751 " (cutoff:3.500A) Processing helix chain 'L' and resid 758 through 783 Processing helix chain 'L' and resid 816 through 826 Processing helix chain 'L' and resid 866 through 885 Processing helix chain 'L' and resid 886 through 891 removed outlier: 3.618A pdb=" N GLY L 891 " --> pdb=" O PHE L 888 " (cutoff:3.500A) Processing helix chain 'L' and resid 897 through 909 Processing helix chain 'L' and resid 912 through 919 removed outlier: 4.291A pdb=" N LEU L 916 " --> pdb=" O THR L 912 " (cutoff:3.500A) Processing helix chain 'L' and resid 919 through 941 Processing helix chain 'L' and resid 945 through 967 removed outlier: 3.750A pdb=" N SER L 967 " --> pdb=" O VAL L 963 " (cutoff:3.500A) Processing helix chain 'L' and resid 976 through 984 removed outlier: 3.512A pdb=" N ILE L 980 " --> pdb=" O VAL L 976 " (cutoff:3.500A) Processing helix chain 'L' and resid 985 through 1033 Processing helix chain 'L' and resid 1141 through 1146 Processing helix chain 'N' and resid 294 through 304 Processing helix chain 'N' and resid 337 through 343 Processing helix chain 'N' and resid 364 through 371 removed outlier: 3.977A pdb=" N LEU N 368 " --> pdb=" O ASP N 364 " (cutoff:3.500A) Processing helix chain 'N' and resid 383 through 390 removed outlier: 3.810A pdb=" N ASP N 389 " --> pdb=" O THR N 385 " (cutoff:3.500A) Processing helix chain 'N' and resid 404 through 410 removed outlier: 4.032A pdb=" N ARG N 408 " --> pdb=" O GLY N 404 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN N 409 " --> pdb=" O ASP N 405 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 422 Processing helix chain 'N' and resid 737 through 743 Processing helix chain 'N' and resid 746 through 756 removed outlier: 3.590A pdb=" N GLN N 755 " --> pdb=" O ASN N 751 " (cutoff:3.500A) Processing helix chain 'N' and resid 758 through 783 Processing helix chain 'N' and resid 816 through 826 Processing helix chain 'N' and resid 866 through 885 Processing helix chain 'N' and resid 886 through 890 Processing helix chain 'N' and resid 897 through 909 Processing helix chain 'N' and resid 912 through 919 removed outlier: 4.281A pdb=" N LEU N 916 " --> pdb=" O THR N 912 " (cutoff:3.500A) Processing helix chain 'N' and resid 919 through 941 Processing helix chain 'N' and resid 945 through 967 removed outlier: 3.768A pdb=" N SER N 967 " --> pdb=" O VAL N 963 " (cutoff:3.500A) Processing helix chain 'N' and resid 976 through 984 removed outlier: 3.563A pdb=" N ILE N 980 " --> pdb=" O VAL N 976 " (cutoff:3.500A) Processing helix chain 'N' and resid 985 through 1033 Processing helix chain 'N' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.773A pdb=" N ALA G 33 " --> pdb=" O GLY G 99 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE G 34 " --> pdb=" O PHE G 50 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N PHE G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AA4, first strand: chain 'G' and resid 109 through 112 removed outlier: 4.005A pdb=" N TYR G 109 " --> pdb=" O CYS L 379 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ALA L 348 " --> pdb=" O VAL L 401 " (cutoff:3.500A) removed outlier: 9.972A pdb=" N ARG L 403 " --> pdb=" O ALA L 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 109 through 112 removed outlier: 4.005A pdb=" N TYR G 109 " --> pdb=" O CYS L 379 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN L 354 " --> pdb=" O SER L 399 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.809A pdb=" N ALA S 33 " --> pdb=" O GLY S 99 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE S 34 " --> pdb=" O PHE S 50 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE S 50 " --> pdb=" O ILE S 34 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 10 through 12 Processing sheet with id=AA9, first strand: chain 'S' and resid 107 through 112 removed outlier: 3.613A pdb=" N TYR S 109 " --> pdb=" O CYS M 379 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG S 111 " --> pdb=" O PHE M 377 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN M 354 " --> pdb=" O SER M 399 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.819A pdb=" N ALA H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N PHE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'H' and resid 107 through 109 removed outlier: 4.060A pdb=" N TYR H 109 " --> pdb=" O CYS J 379 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA J 348 " --> pdb=" O VAL J 401 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N ARG J 403 " --> pdb=" O ALA J 348 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 107 through 109 removed outlier: 4.060A pdb=" N TYR H 109 " --> pdb=" O CYS J 379 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN J 354 " --> pdb=" O SER J 399 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 3 through 7 removed outlier: 3.505A pdb=" N GLN T 3 " --> pdb=" O SER T 25 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'T' and resid 10 through 12 removed outlier: 3.828A pdb=" N ALA T 33 " --> pdb=" O GLY T 99 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE T 34 " --> pdb=" O PHE T 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE T 50 " --> pdb=" O ILE T 34 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP T 36 " --> pdb=" O VAL T 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'T' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'T' and resid 109 through 112 removed outlier: 3.530A pdb=" N TYR T 109 " --> pdb=" O CYS I 379 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA I 348 " --> pdb=" O VAL I 401 " (cutoff:3.500A) removed outlier: 9.943A pdb=" N ARG I 403 " --> pdb=" O ALA I 348 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'T' and resid 109 through 112 removed outlier: 3.530A pdb=" N TYR T 109 " --> pdb=" O CYS I 379 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN I 354 " --> pdb=" O SER I 399 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AC3, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.811A pdb=" N ALA O 33 " --> pdb=" O GLY O 99 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE O 34 " --> pdb=" O PHE O 50 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 10 through 12 Processing sheet with id=AC5, first strand: chain 'O' and resid 107 through 112 removed outlier: 3.511A pdb=" N ARG O 111 " --> pdb=" O PHE N 377 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ALA N 348 " --> pdb=" O VAL N 401 " (cutoff:3.500A) removed outlier: 10.010A pdb=" N ARG N 403 " --> pdb=" O ALA N 348 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 107 through 112 removed outlier: 3.511A pdb=" N ARG O 111 " --> pdb=" O PHE N 377 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN N 354 " --> pdb=" O SER N 399 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 3 through 7 removed outlier: 3.522A pdb=" N GLN U 3 " --> pdb=" O SER U 25 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.816A pdb=" N ALA U 33 " --> pdb=" O GLY U 99 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE U 34 " --> pdb=" O PHE U 50 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE U 50 " --> pdb=" O ILE U 34 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 10 through 12 Processing sheet with id=AD1, first strand: chain 'U' and resid 107 through 109 removed outlier: 7.542A pdb=" N ALA K 348 " --> pdb=" O VAL K 401 " (cutoff:3.500A) removed outlier: 9.977A pdb=" N ARG K 403 " --> pdb=" O ALA K 348 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'U' and resid 107 through 109 removed outlier: 3.616A pdb=" N ASN K 354 " --> pdb=" O SER K 399 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 27 through 31 removed outlier: 3.885A pdb=" N ALA I 27 " --> pdb=" O TRP I 64 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ASN I 61 " --> pdb=" O TYR I 269 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR I 269 " --> pdb=" O ASN I 61 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE I 201 " --> pdb=" O ASP I 228 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP I 228 " --> pdb=" O PHE I 201 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE I 203 " --> pdb=" O LEU I 226 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N HIS I 207 " --> pdb=" O ALA I 222 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N ALA I 222 " --> pdb=" O HIS I 207 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL I 36 " --> pdb=" O LEU I 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 47 through 55 removed outlier: 3.737A pdb=" N ASP I 287 " --> pdb=" O LYS I 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 84 through 85 removed outlier: 5.821A pdb=" N TYR I 144 " --> pdb=" O GLU I 154 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLU I 154 " --> pdb=" O TYR I 144 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 84 through 85 removed outlier: 3.870A pdb=" N GLY I 103 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ALA I 243 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ILE I 101 " --> pdb=" O ALA I 243 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ARG I 102 " --> pdb=" O ASN I 121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 311 through 319 removed outlier: 5.351A pdb=" N ILE I 312 " --> pdb=" O THR I 599 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR I 599 " --> pdb=" O ILE I 312 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN I 314 " --> pdb=" O VAL I 597 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL I 597 " --> pdb=" O GLN I 314 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY I 594 " --> pdb=" O GLN I 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 326 through 328 removed outlier: 3.770A pdb=" N GLU I 583 " --> pdb=" O ASP I 578 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP I 574 " --> pdb=" O ILE I 587 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA I 575 " --> pdb=" O GLY I 566 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N PHE I 565 " --> pdb=" O PHE K 43 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'I' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'I' and resid 654 through 655 removed outlier: 6.183A pdb=" N GLU I 654 " --> pdb=" O ALA I 694 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N THR I 696 " --> pdb=" O GLU I 654 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA I 672 " --> pdb=" O PRO I 665 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 701 through 702 removed outlier: 6.431A pdb=" N ALA I 701 " --> pdb=" O ILE K 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'I' and resid 711 through 728 removed outlier: 6.768A pdb=" N GLN I1071 " --> pdb=" O THR I 716 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE I 718 " --> pdb=" O PRO I1069 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE I 720 " --> pdb=" O TYR I1067 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR I1067 " --> pdb=" O ILE I 720 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL I 722 " --> pdb=" O VAL I1065 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL I1065 " --> pdb=" O VAL I 722 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR I 724 " --> pdb=" O LEU I1063 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU I1063 " --> pdb=" O THR I 724 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE I 726 " --> pdb=" O VAL I1061 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL I1061 " --> pdb=" O ILE I 726 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY I1059 " --> pdb=" O PRO I 728 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY I1059 " --> pdb=" O ALA I1056 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TYR I1067 " --> pdb=" O HIS I1048 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS I1048 " --> pdb=" O TYR I1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 711 through 728 removed outlier: 6.768A pdb=" N GLN I1071 " --> pdb=" O THR I 716 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE I 718 " --> pdb=" O PRO I1069 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE I 720 " --> pdb=" O TYR I1067 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TYR I1067 " --> pdb=" O ILE I 720 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL I 722 " --> pdb=" O VAL I1065 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL I1065 " --> pdb=" O VAL I 722 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR I 724 " --> pdb=" O LEU I1063 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU I1063 " --> pdb=" O THR I 724 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE I 726 " --> pdb=" O VAL I1061 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL I1061 " --> pdb=" O ILE I 726 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY I1059 " --> pdb=" O PRO I 728 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR I1076 " --> pdb=" O SER I1097 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 733 through 736 removed outlier: 4.371A pdb=" N LYS I 733 " --> pdb=" O LEU I 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 787 through 788 Processing sheet with id=AE8, first strand: chain 'I' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'I' and resid 1104 through 1106 removed outlier: 4.722A pdb=" N GLN I1106 " --> pdb=" O GLU I1111 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLU I1111 " --> pdb=" O GLN I1106 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 27 through 31 removed outlier: 3.842A pdb=" N ALA K 27 " --> pdb=" O TRP K 64 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ASN K 61 " --> pdb=" O TYR K 269 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR K 269 " --> pdb=" O ASN K 61 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N PHE K 201 " --> pdb=" O ASP K 228 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP K 228 " --> pdb=" O PHE K 201 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE K 203 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N HIS K 207 " --> pdb=" O ALA K 222 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ALA K 222 " --> pdb=" O HIS K 207 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL K 36 " --> pdb=" O LEU K 223 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 47 through 55 removed outlier: 3.693A pdb=" N ASP K 287 " --> pdb=" O LYS K 278 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 84 through 85 removed outlier: 7.009A pdb=" N PHE K 140 " --> pdb=" O PHE K 157 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N PHE K 157 " --> pdb=" O PHE K 140 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY K 142 " --> pdb=" O SER K 155 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET K 153 " --> pdb=" O TYR K 144 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 84 through 85 removed outlier: 3.879A pdb=" N GLY K 103 " --> pdb=" O LEU K 241 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA K 243 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE K 101 " --> pdb=" O ALA K 243 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 311 through 319 removed outlier: 5.310A pdb=" N ILE K 312 " --> pdb=" O THR K 599 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR K 599 " --> pdb=" O ILE K 312 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLN K 314 " --> pdb=" O VAL K 597 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL K 597 " --> pdb=" O GLN K 314 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY K 594 " --> pdb=" O GLN K 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 326 through 328 removed outlier: 5.048A pdb=" N ASP K 574 " --> pdb=" O ILE K 587 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA K 575 " --> pdb=" O GLY K 566 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'K' and resid 473 through 474 Processing sheet with id=AF9, first strand: chain 'K' and resid 654 through 655 removed outlier: 6.170A pdb=" N GLU K 654 " --> pdb=" O ALA K 694 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR K 696 " --> pdb=" O GLU K 654 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA K 672 " --> pdb=" O PRO K 665 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 701 through 702 removed outlier: 6.748A pdb=" N ALA K 701 " --> pdb=" O ILE M 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'K' and resid 712 through 728 removed outlier: 6.612A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR K1067 " --> pdb=" O HIS K1048 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N HIS K1048 " --> pdb=" O TYR K1067 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 712 through 728 removed outlier: 6.612A pdb=" N ALA K 713 " --> pdb=" O ASN K1074 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN K1074 " --> pdb=" O ALA K 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU K1072 " --> pdb=" O PRO K 715 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR K1076 " --> pdb=" O SER K1097 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLN K1106 " --> pdb=" O GLU K1111 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLU K1111 " --> pdb=" O GLN K1106 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 733 through 736 removed outlier: 4.323A pdb=" N LYS K 733 " --> pdb=" O LEU K 861 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 1120 through 1122 Processing sheet with id=AG6, first strand: chain 'M' and resid 28 through 31 removed outlier: 8.518A pdb=" N ASN M 61 " --> pdb=" O TYR M 269 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR M 269 " --> pdb=" O ASN M 61 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE M 201 " --> pdb=" O ASP M 228 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP M 228 " --> pdb=" O PHE M 201 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE M 203 " --> pdb=" O LEU M 226 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N HIS M 207 " --> pdb=" O ALA M 222 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ALA M 222 " --> pdb=" O HIS M 207 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL M 36 " --> pdb=" O LEU M 223 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 49 through 55 removed outlier: 3.835A pdb=" N ASP M 287 " --> pdb=" O LYS M 278 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 84 through 85 removed outlier: 5.830A pdb=" N TYR M 144 " --> pdb=" O GLU M 154 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU M 154 " --> pdb=" O TYR M 144 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'M' and resid 84 through 85 removed outlier: 3.843A pdb=" N GLY M 103 " --> pdb=" O LEU M 241 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ALA M 243 " --> pdb=" O ILE M 101 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE M 101 " --> pdb=" O ALA M 243 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ARG M 102 " --> pdb=" O ASN M 121 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 311 through 319 removed outlier: 6.812A pdb=" N VAL M 595 " --> pdb=" O THR M 315 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASN M 317 " --> pdb=" O GLY M 593 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY M 593 " --> pdb=" O ASN M 317 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY M 594 " --> pdb=" O GLN M 613 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR M 645 " --> pdb=" O GLY M 648 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 326 through 328 removed outlier: 5.012A pdb=" N ASP M 574 " --> pdb=" O ILE M 587 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA M 575 " --> pdb=" O GLY M 566 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 452 through 454 Processing sheet with id=AH4, first strand: chain 'M' and resid 473 through 474 Processing sheet with id=AH5, first strand: chain 'M' and resid 654 through 655 removed outlier: 6.113A pdb=" N GLU M 654 " --> pdb=" O ALA M 694 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N THR M 696 " --> pdb=" O GLU M 654 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA M 672 " --> pdb=" O PRO M 665 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'M' and resid 711 through 728 removed outlier: 6.263A pdb=" N SER M 711 " --> pdb=" O THR M1076 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR M1076 " --> pdb=" O SER M 711 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA M 713 " --> pdb=" O ASN M1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN M1074 " --> pdb=" O ALA M 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU M1072 " --> pdb=" O PRO M 715 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N TYR M1067 " --> pdb=" O HIS M1048 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N HIS M1048 " --> pdb=" O TYR M1067 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'M' and resid 711 through 728 removed outlier: 6.263A pdb=" N SER M 711 " --> pdb=" O THR M1076 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR M1076 " --> pdb=" O SER M 711 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA M 713 " --> pdb=" O ASN M1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN M1074 " --> pdb=" O ALA M 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU M1072 " --> pdb=" O PRO M 715 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR M1076 " --> pdb=" O SER M1097 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 733 through 736 removed outlier: 4.315A pdb=" N LYS M 733 " --> pdb=" O LEU M 861 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'M' and resid 1120 through 1122 Processing sheet with id=AI1, first strand: chain 'J' and resid 27 through 31 removed outlier: 3.862A pdb=" N ALA J 27 " --> pdb=" O TRP J 64 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASN J 61 " --> pdb=" O TYR J 269 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N TYR J 269 " --> pdb=" O ASN J 61 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N PHE J 201 " --> pdb=" O ASP J 228 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASP J 228 " --> pdb=" O PHE J 201 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE J 203 " --> pdb=" O LEU J 226 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N HIS J 207 " --> pdb=" O ALA J 222 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ALA J 222 " --> pdb=" O HIS J 207 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL J 36 " --> pdb=" O LEU J 223 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 42 through 43 removed outlier: 3.777A pdb=" N ALA N 575 " --> pdb=" O GLY N 566 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ASP N 574 " --> pdb=" O ILE N 587 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 47 through 55 removed outlier: 3.728A pdb=" N ASP J 287 " --> pdb=" O LYS J 278 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 84 through 85 removed outlier: 5.758A pdb=" N TYR J 144 " --> pdb=" O GLU J 154 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLU J 154 " --> pdb=" O TYR J 144 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 84 through 85 removed outlier: 3.854A pdb=" N GLY J 103 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ALA J 243 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE J 101 " --> pdb=" O ALA J 243 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ARG J 102 " --> pdb=" O ASN J 121 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 311 through 319 removed outlier: 5.360A pdb=" N ILE J 312 " --> pdb=" O THR J 599 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N THR J 599 " --> pdb=" O ILE J 312 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLN J 314 " --> pdb=" O VAL J 597 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL J 597 " --> pdb=" O GLN J 314 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLY J 594 " --> pdb=" O GLN J 613 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 326 through 328 Processing sheet with id=AI8, first strand: chain 'J' and resid 452 through 454 Processing sheet with id=AI9, first strand: chain 'J' and resid 473 through 474 Processing sheet with id=AJ1, first strand: chain 'J' and resid 573 through 576 removed outlier: 3.972A pdb=" N ALA J 575 " --> pdb=" O GLY J 566 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N PHE J 565 " --> pdb=" O PHE L 43 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'J' and resid 654 through 655 removed outlier: 6.157A pdb=" N GLU J 654 " --> pdb=" O ALA J 694 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N THR J 696 " --> pdb=" O GLU J 654 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA J 672 " --> pdb=" O PRO J 665 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'J' and resid 701 through 702 removed outlier: 6.669A pdb=" N ALA J 701 " --> pdb=" O ILE L 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'J' and resid 711 through 728 removed outlier: 6.839A pdb=" N GLN J1071 " --> pdb=" O THR J 716 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE J 718 " --> pdb=" O PRO J1069 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE J 720 " --> pdb=" O TYR J1067 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR J1067 " --> pdb=" O ILE J 720 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL J 722 " --> pdb=" O VAL J1065 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL J1065 " --> pdb=" O VAL J 722 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR J 724 " --> pdb=" O LEU J1063 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU J1063 " --> pdb=" O THR J 724 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE J 726 " --> pdb=" O VAL J1061 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL J1061 " --> pdb=" O ILE J 726 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY J1059 " --> pdb=" O PRO J 728 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR J1067 " --> pdb=" O HIS J1048 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N HIS J1048 " --> pdb=" O TYR J1067 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'J' and resid 711 through 728 removed outlier: 6.839A pdb=" N GLN J1071 " --> pdb=" O THR J 716 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE J 718 " --> pdb=" O PRO J1069 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE J 720 " --> pdb=" O TYR J1067 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR J1067 " --> pdb=" O ILE J 720 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL J 722 " --> pdb=" O VAL J1065 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL J1065 " --> pdb=" O VAL J 722 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR J 724 " --> pdb=" O LEU J1063 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LEU J1063 " --> pdb=" O THR J 724 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE J 726 " --> pdb=" O VAL J1061 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL J1061 " --> pdb=" O ILE J 726 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY J1059 " --> pdb=" O PRO J 728 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR J1076 " --> pdb=" O SER J1097 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'J' and resid 733 through 736 removed outlier: 4.381A pdb=" N LYS J 733 " --> pdb=" O LEU J 861 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'J' and resid 787 through 788 Processing sheet with id=AJ8, first strand: chain 'J' and resid 1120 through 1122 Processing sheet with id=AJ9, first strand: chain 'L' and resid 27 through 31 removed outlier: 3.892A pdb=" N ALA L 27 " --> pdb=" O TRP L 64 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ASN L 61 " --> pdb=" O TYR L 269 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR L 269 " --> pdb=" O ASN L 61 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N PHE L 201 " --> pdb=" O ASP L 228 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP L 228 " --> pdb=" O PHE L 201 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE L 203 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N HIS L 207 " --> pdb=" O ALA L 222 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ALA L 222 " --> pdb=" O HIS L 207 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL L 36 " --> pdb=" O LEU L 223 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'L' and resid 47 through 55 removed outlier: 3.723A pdb=" N ASP L 287 " --> pdb=" O LYS L 278 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'L' and resid 84 through 85 removed outlier: 5.780A pdb=" N TYR L 144 " --> pdb=" O GLU L 154 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N GLU L 154 " --> pdb=" O TYR L 144 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'L' and resid 84 through 85 removed outlier: 3.853A pdb=" N GLY L 103 " --> pdb=" O LEU L 241 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ALA L 243 " --> pdb=" O ILE L 101 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE L 101 " --> pdb=" O ALA L 243 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG L 102 " --> pdb=" O ASN L 121 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'L' and resid 311 through 319 removed outlier: 5.361A pdb=" N ILE L 312 " --> pdb=" O THR L 599 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N THR L 599 " --> pdb=" O ILE L 312 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN L 314 " --> pdb=" O VAL L 597 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL L 597 " --> pdb=" O GLN L 314 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY L 594 " --> pdb=" O GLN L 613 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'L' and resid 326 through 328 removed outlier: 5.056A pdb=" N ASP L 574 " --> pdb=" O ILE L 587 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA L 575 " --> pdb=" O GLY L 566 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE L 565 " --> pdb=" O PHE N 43 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'L' and resid 452 through 454 Processing sheet with id=AK7, first strand: chain 'L' and resid 473 through 474 Processing sheet with id=AK8, first strand: chain 'L' and resid 654 through 655 removed outlier: 6.185A pdb=" N GLU L 654 " --> pdb=" O ALA L 694 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR L 696 " --> pdb=" O GLU L 654 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ALA L 672 " --> pdb=" O PRO L 665 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'L' and resid 701 through 702 removed outlier: 7.206A pdb=" N ALA L 701 " --> pdb=" O ILE N 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK9 Processing sheet with id=AL1, first strand: chain 'L' and resid 711 through 728 removed outlier: 6.607A pdb=" N SER L 711 " --> pdb=" O THR L1076 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR L1076 " --> pdb=" O SER L 711 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA L 713 " --> pdb=" O ASN L1074 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN L1074 " --> pdb=" O ALA L 713 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU L1072 " --> pdb=" O PRO L 715 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY L1059 " --> pdb=" O ALA L1056 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N TYR L1067 " --> pdb=" O HIS L1048 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N HIS L1048 " --> pdb=" O TYR L1067 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'L' and resid 733 through 736 removed outlier: 4.354A pdb=" N LYS L 733 " --> pdb=" O LEU L 861 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'L' and resid 1120 through 1122 Processing sheet with id=AL4, first strand: chain 'L' and resid 1094 through 1096 removed outlier: 4.560A pdb=" N GLN L1106 " --> pdb=" O GLU L1111 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLU L1111 " --> pdb=" O GLN L1106 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'N' and resid 27 through 31 removed outlier: 3.894A pdb=" N ALA N 27 " --> pdb=" O TRP N 64 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ASN N 61 " --> pdb=" O TYR N 269 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR N 269 " --> pdb=" O ASN N 61 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE N 201 " --> pdb=" O ASP N 228 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASP N 228 " --> pdb=" O PHE N 201 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE N 203 " --> pdb=" O LEU N 226 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N HIS N 207 " --> pdb=" O ALA N 222 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N ALA N 222 " --> pdb=" O HIS N 207 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL N 36 " --> pdb=" O LEU N 223 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'N' and resid 47 through 55 removed outlier: 3.712A pdb=" N ASP N 287 " --> pdb=" O LYS N 278 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'N' and resid 84 through 85 removed outlier: 5.816A pdb=" N TYR N 144 " --> pdb=" O GLU N 154 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLU N 154 " --> pdb=" O TYR N 144 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'N' and resid 84 through 85 removed outlier: 3.847A pdb=" N GLY N 103 " --> pdb=" O LEU N 241 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ALA N 243 " --> pdb=" O ILE N 101 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE N 101 " --> pdb=" O ALA N 243 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ARG N 102 " --> pdb=" O ASN N 121 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'N' and resid 311 through 319 removed outlier: 5.324A pdb=" N ILE N 312 " --> pdb=" O THR N 599 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR N 599 " --> pdb=" O ILE N 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN N 314 " --> pdb=" O VAL N 597 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL N 597 " --> pdb=" O GLN N 314 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY N 594 " --> pdb=" O GLN N 613 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'N' and resid 452 through 454 Processing sheet with id=AM2, first strand: chain 'N' and resid 473 through 474 Processing sheet with id=AM3, first strand: chain 'N' and resid 654 through 655 removed outlier: 6.155A pdb=" N GLU N 654 " --> pdb=" O ALA N 694 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N THR N 696 " --> pdb=" O GLU N 654 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA N 672 " --> pdb=" O PRO N 665 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'N' and resid 711 through 728 removed outlier: 6.475A pdb=" N SER N 711 " --> pdb=" O THR N1076 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR N1076 " --> pdb=" O SER N 711 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA N 713 " --> pdb=" O ASN N1074 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN N1074 " --> pdb=" O ALA N 713 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU N1072 " --> pdb=" O PRO N 715 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY N1059 " --> pdb=" O ALA N1056 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N TYR N1067 " --> pdb=" O HIS N1048 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N HIS N1048 " --> pdb=" O TYR N1067 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'N' and resid 711 through 728 removed outlier: 6.475A pdb=" N SER N 711 " --> pdb=" O THR N1076 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR N1076 " --> pdb=" O SER N 711 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA N 713 " --> pdb=" O ASN N1074 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN N1074 " --> pdb=" O ALA N 713 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLU N1072 " --> pdb=" O PRO N 715 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN N1106 " --> pdb=" O GLU N1111 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLU N1111 " --> pdb=" O GLN N1106 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'N' and resid 733 through 736 removed outlier: 4.392A pdb=" N LYS N 733 " --> pdb=" O LEU N 861 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'N' and resid 1120 through 1122 2668 hydrogen bonds defined for protein. 7191 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: 26.76 Time building geometry restraints manager: 18.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 17948 1.34 - 1.49: 15929 1.49 - 1.64: 23008 1.64 - 1.79: 128 1.79 - 1.94: 182 Bond restraints: 57195 Sorted by residual: bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.668 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" C1 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sigma weight residual 1.410 1.523 -0.113 2.00e-02 2.50e+03 3.20e+01 bond pdb=" CA ASN J 343 " pdb=" CB ASN J 343 " ideal model delta sigma weight residual 1.536 1.707 -0.171 4.10e-02 5.95e+02 1.75e+01 bond pdb=" CB CYS I 391 " pdb=" SG CYS I 391 " ideal model delta sigma weight residual 1.808 1.944 -0.136 3.30e-02 9.18e+02 1.70e+01 bond pdb=" CB CYS I 525 " pdb=" SG CYS I 525 " ideal model delta sigma weight residual 1.808 1.686 0.122 3.30e-02 9.18e+02 1.36e+01 ... (remaining 57190 not shown) Histogram of bond angle deviations from ideal: 94.03 - 104.27: 862 104.27 - 114.51: 33658 114.51 - 124.75: 42506 124.75 - 134.99: 820 134.99 - 145.23: 5 Bond angle restraints: 77851 Sorted by residual: angle pdb=" CB ARG L 214 " pdb=" CG ARG L 214 " pdb=" CD ARG L 214 " ideal model delta sigma weight residual 111.30 145.23 -33.93 2.30e+00 1.89e-01 2.18e+02 angle pdb=" CA ARG L 214 " pdb=" CB ARG L 214 " pdb=" CG ARG L 214 " ideal model delta sigma weight residual 114.10 137.46 -23.36 2.00e+00 2.50e-01 1.36e+02 angle pdb=" CA ARG I 214 " pdb=" CB ARG I 214 " pdb=" CG ARG I 214 " ideal model delta sigma weight residual 114.10 136.77 -22.67 2.00e+00 2.50e-01 1.28e+02 angle pdb=" CA CYS K 525 " pdb=" CB CYS K 525 " pdb=" SG CYS K 525 " ideal model delta sigma weight residual 114.40 138.09 -23.69 2.30e+00 1.89e-01 1.06e+02 angle pdb=" CA ARG M 214 " pdb=" CB ARG M 214 " pdb=" CG ARG M 214 " ideal model delta sigma weight residual 114.10 134.69 -20.59 2.00e+00 2.50e-01 1.06e+02 ... (remaining 77846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 31336 18.00 - 36.00: 2575 36.00 - 54.00: 449 54.00 - 72.00: 78 72.00 - 90.00: 37 Dihedral angle restraints: 34475 sinusoidal: 13862 harmonic: 20613 Sorted by residual: dihedral pdb=" CB CYS I 391 " pdb=" SG CYS I 391 " pdb=" SG CYS I 525 " pdb=" CB CYS I 525 " ideal model delta sinusoidal sigma weight residual 93.00 26.11 66.89 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS M 15 " pdb=" SG CYS M 15 " pdb=" SG CYS M 136 " pdb=" CB CYS M 136 " ideal model delta sinusoidal sigma weight residual -86.00 -148.09 62.09 1 1.00e+01 1.00e-02 5.11e+01 dihedral pdb=" CB CYS K 391 " pdb=" SG CYS K 391 " pdb=" SG CYS K 525 " pdb=" CB CYS K 525 " ideal model delta sinusoidal sigma weight residual 93.00 31.25 61.75 1 1.00e+01 1.00e-02 5.06e+01 ... (remaining 34472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.289: 8860 0.289 - 0.579: 30 0.579 - 0.868: 1 0.868 - 1.157: 5 1.157 - 1.446: 2 Chirality restraints: 8898 Sorted by residual: chirality pdb=" C1 NAG N1304 " pdb=" ND2 ASN N 616 " pdb=" C2 NAG N1304 " pdb=" O5 NAG N1304 " both_signs ideal model delta sigma weight residual False -2.40 -0.95 -1.45 2.00e-01 2.50e+01 5.23e+01 chirality pdb=" C1 NAG J1308 " pdb=" ND2 ASN J1074 " pdb=" C2 NAG J1308 " pdb=" O5 NAG J1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.21 -1.19 2.00e-01 2.50e+01 3.53e+01 chirality pdb=" C1 NAG J1303 " pdb=" ND2 ASN J1098 " pdb=" C2 NAG J1303 " pdb=" O5 NAG J1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.62e+01 ... (remaining 8895 not shown) Planarity restraints: 10088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN J 801 " 0.106 2.00e-02 2.50e+03 1.04e-01 1.36e+02 pdb=" CG ASN J 801 " -0.150 2.00e-02 2.50e+03 pdb=" OD1 ASN J 801 " 0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN J 801 " -0.097 2.00e-02 2.50e+03 pdb=" C1 NAG J1301 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 717 " 0.103 2.00e-02 2.50e+03 9.51e-02 1.13e+02 pdb=" CG ASN J 717 " -0.133 2.00e-02 2.50e+03 pdb=" OD1 ASN J 717 " 0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN J 717 " -0.089 2.00e-02 2.50e+03 pdb=" C1 NAG J1306 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN M 616 " 0.081 2.00e-02 2.50e+03 7.96e-02 7.92e+01 pdb=" CG ASN M 616 " -0.107 2.00e-02 2.50e+03 pdb=" OD1 ASN M 616 " 0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN M 616 " -0.083 2.00e-02 2.50e+03 pdb=" C1 NAG M1310 " 0.075 2.00e-02 2.50e+03 ... (remaining 10085 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 486 2.58 - 3.16: 46541 3.16 - 3.74: 86881 3.74 - 4.32: 123201 4.32 - 4.90: 204326 Nonbonded interactions: 461435 Sorted by model distance: nonbonded pdb=" OD1 ASN M1098 " pdb=" OG1 THR M1100 " model vdw 2.006 2.440 nonbonded pdb=" O PHE N 329 " pdb=" O7 NAG N1305 " model vdw 2.029 2.432 nonbonded pdb=" OG SER I 708 " pdb=" O7 NAG I1302 " model vdw 2.084 2.440 nonbonded pdb=" OG SER S 53 " pdb=" OD1 ASP S 55 " model vdw 2.113 2.440 nonbonded pdb=" OG SER U 53 " pdb=" OD1 ASP U 55 " model vdw 2.113 2.440 ... (remaining 461430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = (chain 'I' and (resid 23 or resid 27 through 175 or resid 186 through 439 or res \ id 441 through 528 or (resid 529 and (name N or name CA or name C or name O or n \ ame CB )) or resid 530 through 577 or resid 584 through 1146 or resid 1301 throu \ gh 1305)) selection = (chain 'J' and (resid 23 or resid 27 through 175 or resid 186 through 439 or res \ id 441 through 527 or (resid 528 through 529 and (name N or name CA or name C or \ name O or name CB )) or resid 530 through 577 or resid 584 through 1146 or resi \ d 1301 through 1305)) selection = (chain 'K' and (resid 23 or resid 27 through 175 or resid 186 through 439 or res \ id 441 through 577 or resid 584 through 1146 or resid 1301 through 1305)) selection = (chain 'L' and (resid 23 or resid 27 through 175 or resid 186 through 439 or res \ id 441 through 527 or (resid 528 through 529 and (name N or name CA or name C or \ name O or name CB )) or resid 530 through 577 or resid 584 through 1146 or resi \ d 1301 through 1305)) selection = (chain 'M' and (resid 14 or resid 27 through 175 or resid 186 through 528 or (re \ sid 529 and (name N or name CA or name C or name O or name CB )) or resid 530 th \ rough 1146 or resid 1301 through 1305)) selection = (chain 'N' and (resid 23 or resid 27 through 175 or resid 186 through 439 or res \ id 441 through 527 or (resid 528 through 529 and (name N or name CA or name C or \ name O or name CB )) or resid 530 through 1146 or resid 1301 through 1305)) } 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 individual isotropic 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: 9.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.030 Extract box with map and model: 42.140 Check model and map are aligned: 0.720 Set scattering table: 0.400 Process input model: 122.770 Find NCS groups from input model: 3.900 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 57195 Z= 0.278 Angle : 0.849 33.926 77851 Z= 0.458 Chirality : 0.063 1.446 8898 Planarity : 0.005 0.073 10040 Dihedral : 13.262 89.998 21017 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.34 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.10), residues: 7009 helix: 3.32 (0.13), residues: 1384 sheet: 0.75 (0.12), residues: 1702 loop : -0.74 (0.09), residues: 3923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 64 HIS 0.043 0.001 HIS N1101 PHE 0.079 0.002 PHE I 817 TYR 0.029 0.002 TYR J1067 ARG 0.046 0.001 ARG M 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 5.541 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.5749 time to fit residues: 137.6706 Evaluate side-chains 95 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 4.950 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.5001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 596 optimal weight: 9.9990 chunk 535 optimal weight: 8.9990 chunk 296 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 360 optimal weight: 0.1980 chunk 285 optimal weight: 5.9990 chunk 553 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 336 optimal weight: 9.9990 chunk 411 optimal weight: 0.5980 chunk 641 optimal weight: 10.0000 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 239 GLN I 282 ASN ** I 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 185 ASN ** M 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 ASN ** J1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 641 ASN ** N1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 57195 Z= 0.311 Angle : 0.637 12.609 77851 Z= 0.327 Chirality : 0.047 0.466 8898 Planarity : 0.004 0.082 10040 Dihedral : 6.506 78.235 8688 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.91 % Favored : 97.03 % Rotamer: Outliers : 0.43 % Allowed : 8.72 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.10), residues: 7009 helix: 2.67 (0.14), residues: 1423 sheet: 0.52 (0.12), residues: 1779 loop : -0.82 (0.09), residues: 3807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 121 HIS 0.005 0.001 HIS M 66 PHE 0.043 0.002 PHE M 817 TYR 0.034 0.002 TYR G 120 ARG 0.030 0.001 ARG M 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 5.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 8 residues processed: 125 average time/residue: 0.5539 time to fit residues: 126.9580 Evaluate side-chains 102 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 4.967 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4417 time to fit residues: 13.5820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 356 optimal weight: 1.9990 chunk 198 optimal weight: 20.0000 chunk 533 optimal weight: 6.9990 chunk 436 optimal weight: 7.9990 chunk 176 optimal weight: 0.0470 chunk 642 optimal weight: 9.9990 chunk 693 optimal weight: 3.9990 chunk 572 optimal weight: 4.9990 chunk 636 optimal weight: 0.6980 chunk 218 optimal weight: 8.9990 chunk 515 optimal weight: 9.9990 overall best weight: 2.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 126 GLN I 282 ASN ** I 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 HIS K 901 GLN ** K1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 641 ASN ** N1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N1011 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 57195 Z= 0.302 Angle : 0.598 22.600 77851 Z= 0.307 Chirality : 0.045 0.452 8898 Planarity : 0.004 0.064 10040 Dihedral : 6.091 57.586 8688 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.09 % Allowed : 11.39 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.10), residues: 7009 helix: 2.60 (0.14), residues: 1425 sheet: 0.48 (0.12), residues: 1783 loop : -0.81 (0.09), residues: 3801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 64 HIS 0.007 0.001 HIS I 66 PHE 0.026 0.001 PHE K 817 TYR 0.023 0.001 TYR K1067 ARG 0.018 0.000 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 93 time to evaluate : 5.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 24 residues processed: 154 average time/residue: 0.5074 time to fit residues: 144.2322 Evaluate side-chains 112 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 4.919 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.4000 time to fit residues: 24.9296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 634 optimal weight: 20.0000 chunk 482 optimal weight: 4.9990 chunk 333 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 306 optimal weight: 0.4980 chunk 431 optimal weight: 10.0000 chunk 644 optimal weight: 5.9990 chunk 682 optimal weight: 2.9990 chunk 336 optimal weight: 0.9980 chunk 610 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 1 GLN ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 ASN ** I 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 901 GLN ** L1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1011 GLN ** N1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 57195 Z= 0.250 Angle : 0.550 14.681 77851 Z= 0.280 Chirality : 0.044 0.488 8898 Planarity : 0.003 0.041 10040 Dihedral : 6.016 59.286 8688 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.57 % Allowed : 12.48 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.10), residues: 7009 helix: 2.52 (0.14), residues: 1432 sheet: 0.43 (0.12), residues: 1807 loop : -0.80 (0.10), residues: 3770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 121 HIS 0.006 0.001 HIS M 66 PHE 0.023 0.001 PHE K 817 TYR 0.021 0.001 TYR K1067 ARG 0.005 0.000 ARG M 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 90 time to evaluate : 4.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 30 residues processed: 178 average time/residue: 0.5310 time to fit residues: 177.0997 Evaluate side-chains 117 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 87 time to evaluate : 6.435 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.4669 time to fit residues: 34.0386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 568 optimal weight: 3.9990 chunk 387 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 508 optimal weight: 8.9990 chunk 281 optimal weight: 1.9990 chunk 582 optimal weight: 0.8980 chunk 471 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 348 optimal weight: 0.7980 chunk 612 optimal weight: 0.9990 chunk 172 optimal weight: 0.5980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 126 GLN I 239 GLN ** I 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 901 GLN ** I1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1002 GLN ** K1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 57195 Z= 0.145 Angle : 0.519 12.024 77851 Z= 0.261 Chirality : 0.045 1.027 8898 Planarity : 0.003 0.039 10040 Dihedral : 5.760 58.693 8688 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.86 % Allowed : 13.30 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.10), residues: 7009 helix: 2.49 (0.14), residues: 1438 sheet: 0.42 (0.12), residues: 1830 loop : -0.76 (0.10), residues: 3741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 436 HIS 0.004 0.001 HIS I 66 PHE 0.016 0.001 PHE K 486 TYR 0.019 0.001 TYR M1067 ARG 0.003 0.000 ARG I 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 94 time to evaluate : 4.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 17 residues processed: 143 average time/residue: 0.5308 time to fit residues: 138.4044 Evaluate side-chains 106 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 4.884 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4101 time to fit residues: 19.7920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 229 optimal weight: 7.9990 chunk 614 optimal weight: 20.0000 chunk 134 optimal weight: 0.3980 chunk 400 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 683 optimal weight: 6.9990 chunk 567 optimal weight: 4.9990 chunk 316 optimal weight: 4.9990 chunk 56 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 126 GLN I 207 HIS ** I 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1106 GLN ** K 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 HIS ** M 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 955 ASN ** J1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 360 ASN ** L 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 955 ASN ** L1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 146 HIS N 282 ASN ** N1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 57195 Z= 0.424 Angle : 0.659 11.504 77851 Z= 0.334 Chirality : 0.046 0.748 8898 Planarity : 0.004 0.044 10040 Dihedral : 6.152 59.573 8688 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.68 % Allowed : 13.47 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.10), residues: 7009 helix: 2.30 (0.14), residues: 1428 sheet: 0.20 (0.12), residues: 1871 loop : -0.86 (0.10), residues: 3710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I1102 HIS 0.006 0.001 HIS J1064 PHE 0.033 0.002 PHE I 906 TYR 0.022 0.002 TYR K1067 ARG 0.008 0.001 ARG U 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 89 time to evaluate : 4.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 39 residues processed: 184 average time/residue: 0.4983 time to fit residues: 169.6157 Evaluate side-chains 127 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 88 time to evaluate : 4.887 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.4367 time to fit residues: 38.3991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 658 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 389 optimal weight: 1.9990 chunk 498 optimal weight: 7.9990 chunk 386 optimal weight: 0.7980 chunk 575 optimal weight: 4.9990 chunk 381 optimal weight: 3.9990 chunk 680 optimal weight: 0.9990 chunk 425 optimal weight: 9.9990 chunk 414 optimal weight: 50.0000 chunk 314 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 317 ASN ** I 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1106 GLN ** M 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 57195 Z= 0.215 Angle : 0.548 10.838 77851 Z= 0.277 Chirality : 0.044 0.698 8898 Planarity : 0.003 0.044 10040 Dihedral : 5.888 59.656 8688 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.51 % Allowed : 14.34 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.10), residues: 7009 helix: 2.43 (0.14), residues: 1432 sheet: 0.27 (0.12), residues: 1830 loop : -0.79 (0.10), residues: 3747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 121 HIS 0.003 0.001 HIS N 519 PHE 0.016 0.001 PHE K 817 TYR 0.020 0.001 TYR K1067 ARG 0.010 0.000 ARG M 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 5.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 7 residues processed: 120 average time/residue: 0.5614 time to fit residues: 121.9218 Evaluate side-chains 92 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 85 time to evaluate : 5.339 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.5334 time to fit residues: 13.0893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 420 optimal weight: 4.9990 chunk 271 optimal weight: 3.9990 chunk 406 optimal weight: 7.9990 chunk 204 optimal weight: 10.0000 chunk 133 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 432 optimal weight: 0.2980 chunk 463 optimal weight: 4.9990 chunk 336 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 534 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 317 ASN ** I 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 955 ASN ** L 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 801 ASN ** L1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 57195 Z= 0.210 Angle : 0.537 9.712 77851 Z= 0.272 Chirality : 0.044 0.583 8898 Planarity : 0.003 0.048 10040 Dihedral : 5.774 58.617 8688 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.58 % Allowed : 14.44 % Favored : 84.98 % 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: 0.29 (0.10), residues: 7009 helix: 2.47 (0.14), residues: 1429 sheet: 0.28 (0.12), residues: 1820 loop : -0.77 (0.10), residues: 3760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 258 HIS 0.004 0.001 HIS M 66 PHE 0.018 0.001 PHE M 817 TYR 0.020 0.001 TYR K1067 ARG 0.009 0.000 ARG M 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 89 time to evaluate : 4.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 17 residues processed: 118 average time/residue: 0.5118 time to fit residues: 113.1304 Evaluate side-chains 102 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 4.870 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.4084 time to fit residues: 19.8207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 618 optimal weight: 9.9990 chunk 651 optimal weight: 0.7980 chunk 594 optimal weight: 10.0000 chunk 634 optimal weight: 5.9990 chunk 381 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 497 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 573 optimal weight: 0.0070 chunk 599 optimal weight: 4.9990 chunk 631 optimal weight: 6.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 955 ASN ** K1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 57195 Z= 0.281 Angle : 0.564 9.760 77851 Z= 0.285 Chirality : 0.044 0.506 8898 Planarity : 0.003 0.051 10040 Dihedral : 5.846 58.518 8688 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.46 % Allowed : 14.54 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.10), residues: 7009 helix: 2.41 (0.14), residues: 1433 sheet: 0.22 (0.12), residues: 1812 loop : -0.79 (0.10), residues: 3764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I1102 HIS 0.008 0.001 HIS L 519 PHE 0.031 0.001 PHE K 140 TYR 0.021 0.001 TYR K1067 ARG 0.009 0.000 ARG M 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 87 time to evaluate : 4.878 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 11 residues processed: 109 average time/residue: 0.5227 time to fit residues: 107.6289 Evaluate side-chains 96 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 4.913 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.4227 time to fit residues: 15.3466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 416 optimal weight: 10.0000 chunk 670 optimal weight: 6.9990 chunk 409 optimal weight: 9.9990 chunk 318 optimal weight: 5.9990 chunk 466 optimal weight: 0.9990 chunk 703 optimal weight: 8.9990 chunk 647 optimal weight: 9.9990 chunk 560 optimal weight: 0.4980 chunk 58 optimal weight: 0.0870 chunk 432 optimal weight: 8.9990 chunk 343 optimal weight: 2.9990 overall best weight: 2.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 57195 Z= 0.267 Angle : 0.553 9.585 77851 Z= 0.280 Chirality : 0.044 0.467 8898 Planarity : 0.003 0.050 10040 Dihedral : 5.826 58.794 8688 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.23 % Allowed : 14.64 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.10), residues: 7009 helix: 2.39 (0.14), residues: 1432 sheet: 0.21 (0.12), residues: 1836 loop : -0.84 (0.10), residues: 3741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 152 HIS 0.004 0.001 HIS L 519 PHE 0.023 0.001 PHE L 106 TYR 0.020 0.001 TYR K1067 ARG 0.008 0.000 ARG M 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14018 Ramachandran restraints generated. 7009 Oldfield, 0 Emsley, 7009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 5.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 97 average time/residue: 0.5576 time to fit residues: 102.1477 Evaluate side-chains 91 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 4.994 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 7 average time/residue: 0.4395 time to fit residues: 12.3810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 444 optimal weight: 0.7980 chunk 596 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 516 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 560 optimal weight: 2.9990 chunk 234 optimal weight: 0.6980 chunk 576 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 103 optimal weight: 0.0030 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 1 GLN H 126 GLN T 1 GLN ** I 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 644 GLN ** L1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 282 ASN ** N 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.047202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.033379 restraints weight = 443805.826| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 4.31 r_work: 0.2955 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 57195 Z= 0.141 Angle : 0.521 9.636 77851 Z= 0.261 Chirality : 0.043 0.420 8898 Planarity : 0.003 0.056 10040 Dihedral : 5.625 59.210 8688 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.18 % Allowed : 14.85 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.10), residues: 7009 helix: 2.40 (0.14), residues: 1443 sheet: 0.28 (0.12), residues: 1803 loop : -0.76 (0.10), residues: 3763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 436 HIS 0.003 0.001 HIS M 66 PHE 0.021 0.001 PHE M 817 TYR 0.018 0.001 TYR K1067 ARG 0.005 0.000 ARG M 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8185.75 seconds wall clock time: 148 minutes 24.50 seconds (8904.50 seconds total)