Starting phenix.real_space_refine on Thu Feb 15 07:48:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns6_12561/02_2024/7ns6_12561.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns6_12561/02_2024/7ns6_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_12561/02_2024/7ns6_12561.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns6_12561/02_2024/7ns6_12561.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns6_12561/02_2024/7ns6_12561.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ns6_12561/02_2024/7ns6_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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 9 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: 9 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: 22.23, per 1000 atoms: 0.40 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: 18.28 Conformation dependent library (CDL) restraints added in 7.4 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: 6.00 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: 30.86 Time building geometry restraints manager: 19.91 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 - 20.99: 32110 20.99 - 41.97: 2036 41.97 - 62.96: 298 62.96 - 83.95: 52 83.95 - 104.93: 17 Dihedral angle restraints: 34513 sinusoidal: 13900 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 34510 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: 11.550 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: 0.070 Extract box with map and model: 42.890 Check model and map are aligned: 0.630 Set scattering table: 0.390 Process input model: 127.370 Find NCS groups from input model: 4.230 Set up NCS constraints: 0.260 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: 0.020 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.990 ------------------------------------------------------------------------------- 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 : 13.444 104.935 21055 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 : 4.792 Fit side-chains revert: symmetry clash REVERT: G 70 ILE cc_start: 0.8643 (tt) cc_final: 0.8418 (tp) REVERT: G 119 ASP cc_start: 0.9199 (m-30) cc_final: 0.8706 (p0) REVERT: H 30 ASP cc_start: 0.9184 (p0) cc_final: 0.8776 (t0) REVERT: T 83 MET cc_start: 0.8581 (mpp) cc_final: 0.8133 (mpp) REVERT: O 119 ASP cc_start: 0.8716 (t0) cc_final: 0.8477 (t0) REVERT: M 177 MET cc_start: 0.1446 (mpp) cc_final: 0.1134 (mpp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.5367 time to fit residues: 126.7045 Evaluate side-chains 98 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 4.839 ------------------------------------------------------------------------------- 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: 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 ** 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: 0.8226 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 57195 Z= 0.305 Angle : 0.629 13.546 77851 Z= 0.324 Chirality : 0.047 0.445 8898 Planarity : 0.004 0.061 10040 Dihedral : 6.577 74.748 8726 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.12 % Rotamer: Outliers : 0.40 % Allowed : 8.41 % Favored : 91.20 % 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: 0.45 (0.10), residues: 7009 helix: 2.74 (0.13), residues: 1416 sheet: 0.54 (0.12), residues: 1810 loop : -0.80 (0.09), residues: 3783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 121 HIS 0.008 0.001 HIS N1101 PHE 0.036 0.002 PHE M 817 TYR 0.025 0.002 TYR K1067 ARG 0.023 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 128 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 4.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 ASP cc_start: 0.9115 (p0) cc_final: 0.8775 (t0) REVERT: U 83 MET cc_start: 0.8746 (mpp) cc_final: 0.8219 (mpp) REVERT: J 177 MET cc_start: 0.0992 (ptp) cc_final: 0.0645 (ptp) REVERT: N 177 MET cc_start: 0.1868 (OUTLIER) cc_final: 0.0676 (mpp) outliers start: 24 outliers final: 11 residues processed: 121 average time/residue: 0.5098 time to fit residues: 112.9721 Evaluate side-chains 107 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 4.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 119 ASP Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 709 ASN Chi-restraints excluded: chain M residue 1050 MET Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 801 ASN Chi-restraints excluded: chain J residue 869 MET Chi-restraints excluded: chain J residue 1074 ASN Chi-restraints excluded: chain L residue 900 MET Chi-restraints excluded: chain N residue 177 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 356 optimal weight: 2.9990 chunk 198 optimal weight: 20.0000 chunk 533 optimal weight: 5.9990 chunk 436 optimal weight: 2.9990 chunk 176 optimal weight: 0.3980 chunk 642 optimal weight: 9.9990 chunk 693 optimal weight: 3.9990 chunk 572 optimal weight: 10.0000 chunk 636 optimal weight: 0.6980 chunk 218 optimal weight: 9.9990 chunk 515 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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** ** 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 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 57195 Z= 0.289 Angle : 0.593 19.318 77851 Z= 0.305 Chirality : 0.046 0.594 8898 Planarity : 0.004 0.039 10040 Dihedral : 6.128 66.563 8726 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.17 % Allowed : 11.39 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.10), residues: 7009 helix: 2.59 (0.14), residues: 1417 sheet: 0.51 (0.12), residues: 1768 loop : -0.80 (0.09), residues: 3824 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 0.028 0.001 PHE L 927 TYR 0.023 0.001 TYR K1067 ARG 0.031 0.001 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 168 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 97 time to evaluate : 4.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 2 VAL cc_start: 0.7323 (OUTLIER) cc_final: 0.6911 (m) REVERT: H 30 ASP cc_start: 0.9112 (p0) cc_final: 0.8830 (t0) REVERT: I 740 MET cc_start: 0.8458 (tmm) cc_final: 0.8150 (tmm) REVERT: K 153 MET cc_start: 0.8209 (pmm) cc_final: 0.7912 (pmm) REVERT: M 756 TYR cc_start: 0.8318 (t80) cc_final: 0.8021 (t80) REVERT: J 981 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8462 (pp) REVERT: N 166 CYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6172 (m) REVERT: N 177 MET cc_start: 0.2322 (mpp) cc_final: 0.1275 (mpp) outliers start: 71 outliers final: 21 residues processed: 157 average time/residue: 0.4920 time to fit residues: 142.4269 Evaluate side-chains 111 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 4.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 119 ASP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain T residue 2 VAL Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain I residue 214 ARG Chi-restraints excluded: chain I residue 312 ILE Chi-restraints excluded: chain K residue 177 MET Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 976 VAL Chi-restraints excluded: chain M residue 599 THR Chi-restraints excluded: chain J residue 599 THR Chi-restraints excluded: chain J residue 801 ASN Chi-restraints excluded: chain J residue 869 MET Chi-restraints excluded: chain J residue 981 LEU Chi-restraints excluded: chain L residue 996 LEU Chi-restraints excluded: chain L residue 1050 MET Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 641 ASN 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: 5.9990 chunk 333 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 chunk 431 optimal weight: 10.0000 chunk 644 optimal weight: 7.9990 chunk 682 optimal weight: 4.9990 chunk 336 optimal weight: 7.9990 chunk 610 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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** H 126 GLN ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 ASN ** I 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 710 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1106 GLN K 146 HIS ** K 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1106 GLN M 207 HIS M 360 ASN ** J1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1005 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** ** L1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1011 GLN L1135 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: 0.8417 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 57195 Z= 0.517 Angle : 0.729 13.356 77851 Z= 0.374 Chirality : 0.048 0.498 8898 Planarity : 0.004 0.058 10040 Dihedral : 6.642 59.248 8726 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.57 % Favored : 95.42 % Rotamer: Outliers : 2.67 % Allowed : 12.31 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.10), residues: 7009 helix: 2.10 (0.14), residues: 1428 sheet: 0.14 (0.11), residues: 1850 loop : -1.00 (0.09), residues: 3731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP M 64 HIS 0.007 0.002 HIS J1064 PHE 0.035 0.002 PHE I 906 TYR 0.028 0.002 TYR T 118 ARG 0.007 0.001 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 254 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 92 time to evaluate : 4.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 96 CYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6581 (p) REVERT: S 2 VAL cc_start: 0.7783 (OUTLIER) cc_final: 0.7497 (m) REVERT: S 83 MET cc_start: 0.8744 (mpp) cc_final: 0.8411 (mpp) REVERT: K 24 LEU cc_start: 0.2728 (OUTLIER) cc_final: 0.2342 (mp) REVERT: K 153 MET cc_start: 0.8535 (pmm) cc_final: 0.8231 (pmm) REVERT: K 166 CYS cc_start: 0.5776 (OUTLIER) cc_final: 0.5288 (m) REVERT: K 179 LEU cc_start: 0.4517 (OUTLIER) cc_final: 0.4180 (mm) REVERT: K 563 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8771 (mt0) REVERT: L 878 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9100 (tt) outliers start: 162 outliers final: 70 residues processed: 238 average time/residue: 0.4828 time to fit residues: 212.3748 Evaluate side-chains 166 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 89 time to evaluate : 5.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 58 THR Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 119 ASP Chi-restraints excluded: chain T residue 2 VAL Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 125 THR Chi-restraints excluded: chain I residue 214 ARG Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 307 THR Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 398 ASP Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 572 THR Chi-restraints excluded: chain I residue 599 THR Chi-restraints excluded: chain I residue 817 PHE Chi-restraints excluded: chain I residue 878 LEU Chi-restraints excluded: chain I residue 976 VAL Chi-restraints excluded: chain I residue 996 LEU Chi-restraints excluded: chain K residue 15 CYS Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 166 CYS Chi-restraints excluded: chain K residue 177 MET Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 415 THR Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 599 THR Chi-restraints excluded: chain K residue 709 ASN Chi-restraints excluded: chain K residue 856 ASN Chi-restraints excluded: chain K residue 976 VAL Chi-restraints excluded: chain K residue 996 LEU Chi-restraints excluded: chain M residue 312 ILE Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 503 VAL Chi-restraints excluded: chain M residue 599 THR Chi-restraints excluded: chain M residue 1136 THR Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain J residue 563 GLN Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 599 THR Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 801 ASN Chi-restraints excluded: chain J residue 869 MET Chi-restraints excluded: chain J residue 996 LEU Chi-restraints excluded: chain J residue 1074 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 445 VAL Chi-restraints excluded: chain L residue 590 CYS Chi-restraints excluded: chain L residue 599 THR Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 869 MET Chi-restraints excluded: chain L residue 878 LEU Chi-restraints excluded: chain L residue 1050 MET Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 551 VAL Chi-restraints excluded: chain N residue 569 ILE Chi-restraints excluded: chain N residue 599 THR Chi-restraints excluded: chain N residue 697 MET Chi-restraints excluded: chain N residue 869 MET Chi-restraints excluded: chain N residue 996 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 568 optimal weight: 2.9990 chunk 387 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 508 optimal weight: 5.9990 chunk 281 optimal weight: 6.9990 chunk 582 optimal weight: 0.9990 chunk 471 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 348 optimal weight: 0.9980 chunk 612 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 239 GLN I 901 GLN ** I1002 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 755 GLN ** J1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 801 ASN L 955 ASN ** L1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 146 HIS ** N1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 57195 Z= 0.178 Angle : 0.553 16.231 77851 Z= 0.281 Chirality : 0.045 0.574 8898 Planarity : 0.003 0.040 10040 Dihedral : 6.129 59.724 8726 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 13.42 % Favored : 84.72 % 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: 0.18 (0.10), residues: 7009 helix: 2.36 (0.14), residues: 1428 sheet: 0.28 (0.12), residues: 1800 loop : -0.85 (0.10), residues: 3781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 121 HIS 0.006 0.001 HIS I 66 PHE 0.013 0.001 PHE K 429 TYR 0.019 0.001 TYR K1067 ARG 0.005 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 204 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 91 time to evaluate : 4.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 2 VAL cc_start: 0.7840 (OUTLIER) cc_final: 0.7580 (m) REVERT: H 30 ASP cc_start: 0.9233 (p0) cc_final: 0.8810 (t0) REVERT: K 24 LEU cc_start: 0.2768 (OUTLIER) cc_final: 0.2444 (mp) REVERT: K 153 MET cc_start: 0.8408 (pmm) cc_final: 0.8045 (pmm) REVERT: K 166 CYS cc_start: 0.5762 (OUTLIER) cc_final: 0.5360 (m) REVERT: K 563 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8653 (mt0) REVERT: J 712 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8783 (mm) REVERT: J 981 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8690 (pp) REVERT: J 1077 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8841 (p) REVERT: L 177 MET cc_start: 0.1908 (pmm) cc_final: 0.1144 (pmm) REVERT: L 671 CYS cc_start: 0.6393 (OUTLIER) cc_final: 0.5861 (p) REVERT: N 166 CYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6363 (m) REVERT: N 215 ASP cc_start: 0.7445 (OUTLIER) cc_final: 0.6488 (p0) outliers start: 113 outliers final: 47 residues processed: 191 average time/residue: 0.4749 time to fit residues: 166.1018 Evaluate side-chains 144 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 87 time to evaluate : 4.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 119 ASP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain T residue 2 VAL Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 96 CYS Chi-restraints excluded: chain I residue 312 ILE Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 599 THR Chi-restraints excluded: chain I residue 976 VAL Chi-restraints excluded: chain I residue 996 LEU Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 166 CYS Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 238 PHE Chi-restraints excluded: chain K residue 415 THR Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 569 ILE Chi-restraints excluded: chain K residue 709 ASN Chi-restraints excluded: chain K residue 740 MET Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 456 PHE Chi-restraints excluded: chain M residue 740 MET Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 563 GLN Chi-restraints excluded: chain J residue 712 ILE Chi-restraints excluded: chain J residue 801 ASN Chi-restraints excluded: chain J residue 869 MET Chi-restraints excluded: chain J residue 981 LEU Chi-restraints excluded: chain J residue 996 LEU Chi-restraints excluded: chain J residue 1077 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 599 THR Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 996 LEU Chi-restraints excluded: chain L residue 1050 MET Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 215 ASP Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 869 MET Chi-restraints excluded: chain N residue 976 VAL Chi-restraints excluded: chain N residue 996 LEU Chi-restraints excluded: chain N residue 1125 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 229 optimal weight: 10.0000 chunk 614 optimal weight: 8.9990 chunk 134 optimal weight: 5.9990 chunk 400 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 683 optimal weight: 7.9990 chunk 567 optimal weight: 4.9990 chunk 316 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 chunk 358 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 949 GLN ** I1002 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 955 ASN ** J1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1005 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1106 GLN ** N1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 57195 Z= 0.406 Angle : 0.633 12.882 77851 Z= 0.321 Chirality : 0.045 0.571 8898 Planarity : 0.004 0.042 10040 Dihedral : 6.295 59.669 8726 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.70 % Allowed : 13.53 % Favored : 83.76 % 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: 0.07 (0.10), residues: 7009 helix: 2.27 (0.14), residues: 1426 sheet: 0.15 (0.11), residues: 1854 loop : -0.91 (0.10), residues: 3729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 116 HIS 0.005 0.001 HIS J1064 PHE 0.021 0.002 PHE I 906 TYR 0.023 0.002 TYR K1067 ARG 0.013 0.001 ARG M 214 *********************** 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 253 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 89 time to evaluate : 4.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 2 VAL cc_start: 0.7969 (OUTLIER) cc_final: 0.7738 (m) REVERT: H 30 ASP cc_start: 0.9250 (p0) cc_final: 0.8816 (t0) REVERT: H 43 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7803 (mppt) REVERT: I 468 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8295 (mm) REVERT: K 24 LEU cc_start: 0.3180 (OUTLIER) cc_final: 0.2821 (mp) REVERT: K 153 MET cc_start: 0.8552 (pmm) cc_final: 0.8189 (pmm) REVERT: K 166 CYS cc_start: 0.6116 (OUTLIER) cc_final: 0.5832 (m) REVERT: K 563 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8751 (mt0) REVERT: J 981 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8798 (pp) REVERT: L 856 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8616 (p0) REVERT: N 166 CYS cc_start: 0.6919 (OUTLIER) cc_final: 0.6234 (m) REVERT: N 215 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.6954 (p0) REVERT: N 752 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8761 (pp) REVERT: N 985 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8192 (p0) outliers start: 164 outliers final: 95 residues processed: 237 average time/residue: 0.4874 time to fit residues: 208.5549 Evaluate side-chains 193 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 86 time to evaluate : 4.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 119 ASP Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain T residue 2 VAL Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain O residue 125 THR Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 96 CYS Chi-restraints excluded: chain I residue 307 THR Chi-restraints excluded: chain I residue 312 ILE Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 398 ASP Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 468 ILE Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 572 THR Chi-restraints excluded: chain I residue 599 THR Chi-restraints excluded: chain I residue 976 VAL Chi-restraints excluded: chain I residue 996 LEU Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain K residue 15 CYS Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 166 CYS Chi-restraints excluded: chain K residue 177 MET Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 238 PHE Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 569 ILE Chi-restraints excluded: chain K residue 599 THR Chi-restraints excluded: chain K residue 658 ASN Chi-restraints excluded: chain K residue 740 MET Chi-restraints excluded: chain K residue 856 ASN Chi-restraints excluded: chain K residue 976 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 996 LEU Chi-restraints excluded: chain M residue 15 CYS Chi-restraints excluded: chain M residue 176 LEU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 312 ILE Chi-restraints excluded: chain M residue 456 PHE Chi-restraints excluded: chain M residue 478 THR Chi-restraints excluded: chain M residue 723 THR Chi-restraints excluded: chain M residue 740 MET Chi-restraints excluded: chain M residue 859 THR Chi-restraints excluded: chain M residue 916 LEU Chi-restraints excluded: chain M residue 1136 THR Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 307 THR Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 333 THR Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 534 VAL Chi-restraints excluded: chain J residue 563 GLN Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 732 THR Chi-restraints excluded: chain J residue 801 ASN Chi-restraints excluded: chain J residue 869 MET Chi-restraints excluded: chain J residue 981 LEU Chi-restraints excluded: chain J residue 996 LEU Chi-restraints excluded: chain J residue 1104 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 312 ILE Chi-restraints excluded: chain L residue 440 ASN Chi-restraints excluded: chain L residue 445 VAL Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 590 CYS Chi-restraints excluded: chain L residue 599 THR Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 794 ILE Chi-restraints excluded: chain L residue 856 ASN Chi-restraints excluded: chain L residue 869 MET Chi-restraints excluded: chain L residue 896 ILE Chi-restraints excluded: chain L residue 1050 MET Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 215 ASP Chi-restraints excluded: chain N residue 238 PHE Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 358 ILE Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 569 ILE Chi-restraints excluded: chain N residue 599 THR Chi-restraints excluded: chain N residue 752 LEU Chi-restraints excluded: chain N residue 867 ASP Chi-restraints excluded: chain N residue 869 MET Chi-restraints excluded: chain N residue 976 VAL Chi-restraints excluded: chain N residue 985 ASP Chi-restraints excluded: chain N residue 996 LEU Chi-restraints excluded: chain N residue 1077 THR Chi-restraints excluded: chain N residue 1125 ASN 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: 4.9990 chunk 389 optimal weight: 0.1980 chunk 498 optimal weight: 7.9990 chunk 386 optimal weight: 0.6980 chunk 575 optimal weight: 4.9990 chunk 381 optimal weight: 2.9990 chunk 680 optimal weight: 2.9990 chunk 425 optimal weight: 9.9990 chunk 414 optimal weight: 50.0000 chunk 314 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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** ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 ASN ** I1002 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** J 955 ASN ** 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** L1106 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: 0.8385 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 57195 Z= 0.217 Angle : 0.547 11.828 77851 Z= 0.277 Chirality : 0.044 0.525 8898 Planarity : 0.003 0.042 10040 Dihedral : 6.056 58.403 8726 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.01 % Allowed : 14.55 % Favored : 83.43 % 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: 0.17 (0.10), residues: 7009 helix: 2.39 (0.14), residues: 1429 sheet: 0.19 (0.12), residues: 1813 loop : -0.84 (0.10), residues: 3767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 121 HIS 0.003 0.001 HIS M 519 PHE 0.017 0.001 PHE K 140 TYR 0.020 0.001 TYR K1067 ARG 0.008 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 213 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 91 time to evaluate : 4.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 2 VAL cc_start: 0.7892 (OUTLIER) cc_final: 0.7628 (m) REVERT: H 30 ASP cc_start: 0.9216 (p0) cc_final: 0.8801 (t0) REVERT: I 468 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8357 (mm) REVERT: K 24 LEU cc_start: 0.3308 (OUTLIER) cc_final: 0.2933 (mp) REVERT: K 153 MET cc_start: 0.8473 (pmm) cc_final: 0.8134 (pmm) REVERT: K 166 CYS cc_start: 0.5713 (OUTLIER) cc_final: 0.5408 (m) REVERT: K 563 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8718 (mt0) REVERT: M 177 MET cc_start: 0.2180 (mpp) cc_final: 0.1857 (mpp) REVERT: M 856 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8679 (p0) REVERT: J 981 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8756 (pp) REVERT: L 856 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8584 (p0) REVERT: N 118 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8747 (mt) REVERT: N 166 CYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6221 (m) REVERT: N 215 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7253 (p0) REVERT: N 985 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8350 (p0) outliers start: 122 outliers final: 83 residues processed: 202 average time/residue: 0.4871 time to fit residues: 182.5756 Evaluate side-chains 181 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 86 time to evaluate : 4.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 119 ASP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain T residue 2 VAL Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 96 CYS Chi-restraints excluded: chain I residue 312 ILE Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 468 ILE Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 480 CYS Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 572 THR Chi-restraints excluded: chain I residue 599 THR Chi-restraints excluded: chain I residue 976 VAL Chi-restraints excluded: chain I residue 996 LEU Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain K residue 15 CYS Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 166 CYS Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 238 PHE Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 569 ILE Chi-restraints excluded: chain K residue 658 ASN Chi-restraints excluded: chain K residue 740 MET Chi-restraints excluded: chain K residue 856 ASN Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 996 LEU Chi-restraints excluded: chain M residue 15 CYS Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 312 ILE Chi-restraints excluded: chain M residue 599 THR Chi-restraints excluded: chain M residue 723 THR Chi-restraints excluded: chain M residue 856 ASN Chi-restraints excluded: chain M residue 916 LEU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 534 VAL Chi-restraints excluded: chain J residue 563 GLN Chi-restraints excluded: chain J residue 599 THR Chi-restraints excluded: chain J residue 740 MET Chi-restraints excluded: chain J residue 801 ASN Chi-restraints excluded: chain J residue 869 MET Chi-restraints excluded: chain J residue 976 VAL Chi-restraints excluded: chain J residue 981 LEU Chi-restraints excluded: chain J residue 996 LEU Chi-restraints excluded: chain J residue 1104 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 445 VAL Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 590 CYS Chi-restraints excluded: chain L residue 599 THR Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 794 ILE Chi-restraints excluded: chain L residue 856 ASN Chi-restraints excluded: chain L residue 869 MET Chi-restraints excluded: chain L residue 996 LEU Chi-restraints excluded: chain L residue 1050 MET Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 166 CYS Chi-restraints excluded: chain N residue 215 ASP Chi-restraints excluded: chain N residue 238 PHE Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 358 ILE Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 569 ILE Chi-restraints excluded: chain N residue 599 THR Chi-restraints excluded: chain N residue 869 MET Chi-restraints excluded: chain N residue 976 VAL Chi-restraints excluded: chain N residue 985 ASP Chi-restraints excluded: chain N residue 996 LEU Chi-restraints excluded: chain N residue 1077 THR Chi-restraints excluded: chain N residue 1101 HIS Chi-restraints excluded: chain N residue 1125 ASN Chi-restraints excluded: chain N residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 420 optimal weight: 6.9990 chunk 271 optimal weight: 0.6980 chunk 406 optimal weight: 0.8980 chunk 204 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 432 optimal weight: 9.9990 chunk 463 optimal weight: 0.9990 chunk 336 optimal weight: 8.9990 chunk 63 optimal weight: 0.2980 chunk 534 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1101 HIS ** K 544 ASN ** 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 519 HIS ** L 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 644 GLN ** L 801 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: 0.8360 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 57195 Z= 0.153 Angle : 0.525 10.705 77851 Z= 0.264 Chirality : 0.044 0.499 8898 Planarity : 0.003 0.041 10040 Dihedral : 5.846 58.358 8726 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.93 % Allowed : 14.85 % Favored : 83.22 % 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: 0.24 (0.10), residues: 7009 helix: 2.43 (0.14), residues: 1434 sheet: 0.25 (0.12), residues: 1801 loop : -0.80 (0.10), residues: 3774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 121 HIS 0.003 0.001 HIS M 66 PHE 0.017 0.001 PHE M 817 TYR 0.019 0.001 TYR S 104 ARG 0.007 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 206 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 89 time to evaluate : 4.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 2 VAL cc_start: 0.7933 (OUTLIER) cc_final: 0.7691 (m) REVERT: H 30 ASP cc_start: 0.9150 (p0) cc_final: 0.8796 (t0) REVERT: I 468 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8349 (mm) REVERT: K 24 LEU cc_start: 0.3209 (OUTLIER) cc_final: 0.2881 (mp) REVERT: K 153 MET cc_start: 0.8456 (pmm) cc_final: 0.8127 (pmm) REVERT: K 166 CYS cc_start: 0.5464 (OUTLIER) cc_final: 0.5191 (m) REVERT: K 563 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8680 (mt0) REVERT: M 177 MET cc_start: 0.2172 (mpp) cc_final: 0.0894 (mpp) REVERT: M 856 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8487 (p0) REVERT: J 981 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8732 (pp) REVERT: L 856 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8536 (p0) REVERT: N 215 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7407 (p0) outliers start: 117 outliers final: 90 residues processed: 198 average time/residue: 0.4807 time to fit residues: 174.2020 Evaluate side-chains 185 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 86 time to evaluate : 4.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 119 ASP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain T residue 2 VAL Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 96 CYS Chi-restraints excluded: chain I residue 312 ILE Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 468 ILE Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 480 CYS Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 572 THR Chi-restraints excluded: chain I residue 599 THR Chi-restraints excluded: chain I residue 976 VAL Chi-restraints excluded: chain I residue 996 LEU Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain K residue 15 CYS Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 166 CYS Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 238 PHE Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 534 VAL Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 569 ILE Chi-restraints excluded: chain K residue 599 THR Chi-restraints excluded: chain K residue 740 MET Chi-restraints excluded: chain K residue 856 ASN Chi-restraints excluded: chain K residue 976 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 996 LEU Chi-restraints excluded: chain M residue 15 CYS Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 312 ILE Chi-restraints excluded: chain M residue 327 VAL Chi-restraints excluded: chain M residue 599 THR Chi-restraints excluded: chain M residue 856 ASN Chi-restraints excluded: chain M residue 859 THR Chi-restraints excluded: chain M residue 916 LEU Chi-restraints excluded: chain M residue 1136 THR Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 534 VAL Chi-restraints excluded: chain J residue 563 GLN Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 740 MET Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 801 ASN Chi-restraints excluded: chain J residue 869 MET Chi-restraints excluded: chain J residue 976 VAL Chi-restraints excluded: chain J residue 981 LEU Chi-restraints excluded: chain J residue 996 LEU Chi-restraints excluded: chain J residue 1104 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 238 PHE Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 445 VAL Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 590 CYS Chi-restraints excluded: chain L residue 599 THR Chi-restraints excluded: chain L residue 671 CYS Chi-restraints excluded: chain L residue 794 ILE Chi-restraints excluded: chain L residue 856 ASN Chi-restraints excluded: chain L residue 996 LEU Chi-restraints excluded: chain L residue 1050 MET Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 215 ASP Chi-restraints excluded: chain N residue 238 PHE Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 358 ILE Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 599 THR Chi-restraints excluded: chain N residue 705 VAL Chi-restraints excluded: chain N residue 869 MET Chi-restraints excluded: chain N residue 976 VAL Chi-restraints excluded: chain N residue 996 LEU Chi-restraints excluded: chain N residue 1077 THR Chi-restraints excluded: chain N residue 1101 HIS Chi-restraints excluded: chain N residue 1125 ASN Chi-restraints excluded: chain N residue 1136 THR 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: 8.9990 chunk 594 optimal weight: 9.9990 chunk 634 optimal weight: 9.9990 chunk 381 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 497 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 573 optimal weight: 4.9990 chunk 599 optimal weight: 4.9990 chunk 631 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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** ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 207 HIS ** I 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 955 ASN ** I1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 955 ASN ** K1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 314 GLN ** M 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 949 GLN M 955 ASN J 955 ASN ** L 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1106 GLN L1113 GLN N 360 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 57195 Z= 0.534 Angle : 0.697 12.839 77851 Z= 0.354 Chirality : 0.047 0.571 8898 Planarity : 0.004 0.063 10040 Dihedral : 6.350 59.900 8726 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.11 % Allowed : 14.93 % Favored : 82.96 % 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: -0.03 (0.10), residues: 7009 helix: 2.12 (0.14), residues: 1429 sheet: 0.15 (0.12), residues: 1787 loop : -0.97 (0.10), residues: 3793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 64 HIS 0.009 0.001 HIS I1101 PHE 0.036 0.002 PHE K 456 TYR 0.025 0.002 TYR M1138 ARG 0.011 0.001 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 209 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 81 time to evaluate : 4.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 2 VAL cc_start: 0.8130 (OUTLIER) cc_final: 0.7891 (m) REVERT: T 83 MET cc_start: 0.8613 (mpp) cc_final: 0.8336 (mpp) REVERT: I 468 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8407 (mm) REVERT: K 153 MET cc_start: 0.8665 (pmm) cc_final: 0.8274 (pmm) REVERT: K 166 CYS cc_start: 0.6073 (OUTLIER) cc_final: 0.5745 (m) REVERT: K 563 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8756 (mt0) REVERT: M 177 MET cc_start: 0.2550 (mpp) cc_final: 0.2188 (mpp) REVERT: M 856 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8656 (p0) REVERT: J 981 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8846 (pp) outliers start: 128 outliers final: 107 residues processed: 198 average time/residue: 0.4758 time to fit residues: 175.0880 Evaluate side-chains 193 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 80 time to evaluate : 4.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 119 ASP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain T residue 2 VAL Chi-restraints excluded: chain T residue 125 THR Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 96 CYS Chi-restraints excluded: chain I residue 240 THR Chi-restraints excluded: chain I residue 307 THR Chi-restraints excluded: chain I residue 312 ILE Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 398 ASP Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 468 ILE Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 572 THR Chi-restraints excluded: chain I residue 599 THR Chi-restraints excluded: chain I residue 976 VAL Chi-restraints excluded: chain I residue 996 LEU Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain K residue 15 CYS Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 166 CYS Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 238 PHE Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 534 VAL Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 569 ILE Chi-restraints excluded: chain K residue 599 THR Chi-restraints excluded: chain K residue 658 ASN Chi-restraints excluded: chain K residue 740 MET Chi-restraints excluded: chain K residue 856 ASN Chi-restraints excluded: chain K residue 976 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 996 LEU Chi-restraints excluded: chain M residue 15 CYS Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 312 ILE Chi-restraints excluded: chain M residue 599 THR Chi-restraints excluded: chain M residue 723 THR Chi-restraints excluded: chain M residue 856 ASN Chi-restraints excluded: chain M residue 916 LEU Chi-restraints excluded: chain M residue 1050 MET Chi-restraints excluded: chain M residue 1136 THR Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 534 VAL Chi-restraints excluded: chain J residue 563 GLN Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 599 THR Chi-restraints excluded: chain J residue 732 THR Chi-restraints excluded: chain J residue 740 MET Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 801 ASN Chi-restraints excluded: chain J residue 869 MET Chi-restraints excluded: chain J residue 976 VAL Chi-restraints excluded: chain J residue 981 LEU Chi-restraints excluded: chain J residue 996 LEU Chi-restraints excluded: chain J residue 1104 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 238 PHE Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 440 ASN Chi-restraints excluded: chain L residue 445 VAL Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 590 CYS Chi-restraints excluded: chain L residue 599 THR Chi-restraints excluded: chain L residue 794 ILE Chi-restraints excluded: chain L residue 869 MET Chi-restraints excluded: chain L residue 996 LEU Chi-restraints excluded: chain L residue 1050 MET Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 212 LEU Chi-restraints excluded: chain N residue 238 PHE Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 358 ILE Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 569 ILE Chi-restraints excluded: chain N residue 599 THR Chi-restraints excluded: chain N residue 705 VAL Chi-restraints excluded: chain N residue 791 THR Chi-restraints excluded: chain N residue 867 ASP Chi-restraints excluded: chain N residue 869 MET Chi-restraints excluded: chain N residue 976 VAL Chi-restraints excluded: chain N residue 996 LEU Chi-restraints excluded: chain N residue 1077 THR Chi-restraints excluded: chain N residue 1101 HIS Chi-restraints excluded: chain N residue 1125 ASN Chi-restraints excluded: chain N residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 416 optimal weight: 6.9990 chunk 670 optimal weight: 0.9990 chunk 409 optimal weight: 5.9990 chunk 318 optimal weight: 8.9990 chunk 466 optimal weight: 0.6980 chunk 703 optimal weight: 6.9990 chunk 647 optimal weight: 10.0000 chunk 560 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 432 optimal weight: 10.0000 chunk 343 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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** ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 282 ASN I 955 ASN ** I1002 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 ** J 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 196 ASN ** L 448 ASN ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 57195 Z= 0.335 Angle : 0.589 11.784 77851 Z= 0.300 Chirality : 0.044 0.530 8898 Planarity : 0.004 0.047 10040 Dihedral : 6.156 58.541 8726 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.99 % Allowed : 15.05 % Favored : 82.96 % 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: 0.00 (0.10), residues: 7009 helix: 2.25 (0.14), residues: 1430 sheet: 0.10 (0.12), residues: 1806 loop : -0.95 (0.10), residues: 3773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I1102 HIS 0.004 0.001 HIS I1064 PHE 0.017 0.001 PHE M 817 TYR 0.022 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 204 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 83 time to evaluate : 4.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 30 ASP cc_start: 0.9253 (p0) cc_final: 0.8837 (t0) REVERT: T 83 MET cc_start: 0.8588 (mpp) cc_final: 0.8334 (mpp) REVERT: I 468 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8399 (mm) REVERT: K 24 LEU cc_start: 0.3819 (OUTLIER) cc_final: 0.3341 (mp) REVERT: K 153 MET cc_start: 0.8598 (pmm) cc_final: 0.8273 (pmm) REVERT: K 166 CYS cc_start: 0.6067 (OUTLIER) cc_final: 0.5635 (m) REVERT: K 563 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8728 (mt0) REVERT: M 177 MET cc_start: 0.2526 (mpp) cc_final: 0.1121 (mpp) REVERT: M 856 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8515 (p0) REVERT: J 981 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8876 (pp) REVERT: L 740 MET cc_start: 0.8920 (ppp) cc_final: 0.8702 (ppp) REVERT: N 118 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8994 (mt) outliers start: 121 outliers final: 104 residues processed: 194 average time/residue: 0.4955 time to fit residues: 178.7704 Evaluate side-chains 193 residues out of total 6186 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 82 time to evaluate : 4.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 30 ASP Chi-restraints excluded: chain G residue 119 ASP Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 96 CYS Chi-restraints excluded: chain S residue 119 ASP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain T residue 2 VAL Chi-restraints excluded: chain T residue 125 THR Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 96 CYS Chi-restraints excluded: chain U residue 2 VAL Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 96 CYS Chi-restraints excluded: chain I residue 51 THR Chi-restraints excluded: chain I residue 307 THR Chi-restraints excluded: chain I residue 312 ILE Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 468 ILE Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 551 VAL Chi-restraints excluded: chain I residue 572 THR Chi-restraints excluded: chain I residue 599 THR Chi-restraints excluded: chain I residue 976 VAL Chi-restraints excluded: chain I residue 996 LEU Chi-restraints excluded: chain I residue 1136 THR Chi-restraints excluded: chain K residue 15 CYS Chi-restraints excluded: chain K residue 24 LEU Chi-restraints excluded: chain K residue 166 CYS Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 238 PHE Chi-restraints excluded: chain K residue 240 THR Chi-restraints excluded: chain K residue 312 ILE Chi-restraints excluded: chain K residue 364 ASP Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 525 CYS Chi-restraints excluded: chain K residue 534 VAL Chi-restraints excluded: chain K residue 563 GLN Chi-restraints excluded: chain K residue 569 ILE Chi-restraints excluded: chain K residue 599 THR Chi-restraints excluded: chain K residue 658 ASN Chi-restraints excluded: chain K residue 740 MET Chi-restraints excluded: chain K residue 856 ASN Chi-restraints excluded: chain K residue 976 VAL Chi-restraints excluded: chain K residue 988 GLU Chi-restraints excluded: chain K residue 996 LEU Chi-restraints excluded: chain M residue 15 CYS Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 240 THR Chi-restraints excluded: chain M residue 312 ILE Chi-restraints excluded: chain M residue 599 THR Chi-restraints excluded: chain M residue 723 THR Chi-restraints excluded: chain M residue 856 ASN Chi-restraints excluded: chain M residue 859 THR Chi-restraints excluded: chain M residue 916 LEU Chi-restraints excluded: chain M residue 1050 MET Chi-restraints excluded: chain M residue 1136 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 534 VAL Chi-restraints excluded: chain J residue 563 GLN Chi-restraints excluded: chain J residue 572 THR Chi-restraints excluded: chain J residue 599 THR Chi-restraints excluded: chain J residue 732 THR Chi-restraints excluded: chain J residue 791 THR Chi-restraints excluded: chain J residue 801 ASN Chi-restraints excluded: chain J residue 869 MET Chi-restraints excluded: chain J residue 976 VAL Chi-restraints excluded: chain J residue 981 LEU Chi-restraints excluded: chain J residue 996 LEU Chi-restraints excluded: chain J residue 1104 VAL Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 238 PHE Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 445 VAL Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 590 CYS Chi-restraints excluded: chain L residue 599 THR Chi-restraints excluded: chain L residue 794 ILE Chi-restraints excluded: chain L residue 869 MET Chi-restraints excluded: chain L residue 996 LEU Chi-restraints excluded: chain L residue 1050 MET Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 118 LEU Chi-restraints excluded: chain N residue 238 PHE Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 358 ILE Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 569 ILE Chi-restraints excluded: chain N residue 599 THR Chi-restraints excluded: chain N residue 705 VAL Chi-restraints excluded: chain N residue 791 THR Chi-restraints excluded: chain N residue 867 ASP Chi-restraints excluded: chain N residue 869 MET Chi-restraints excluded: chain N residue 976 VAL Chi-restraints excluded: chain N residue 996 LEU Chi-restraints excluded: chain N residue 1077 THR Chi-restraints excluded: chain N residue 1101 HIS Chi-restraints excluded: chain N residue 1125 ASN Chi-restraints excluded: chain N residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 444 optimal weight: 10.0000 chunk 596 optimal weight: 9.9990 chunk 171 optimal weight: 0.7980 chunk 516 optimal weight: 8.9990 chunk 82 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 560 optimal weight: 0.7980 chunk 234 optimal weight: 0.9990 chunk 576 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** T 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 544 ASN ** 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** J 641 ASN J 955 ASN ** L 448 ASN ** 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 360 ASN ** N1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.046782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.032824 restraints weight = 445006.761| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 4.42 r_work: 0.2927 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 57195 Z= 0.152 Angle : 0.531 9.980 77851 Z= 0.268 Chirality : 0.044 0.485 8898 Planarity : 0.003 0.045 10040 Dihedral : 5.837 58.938 8726 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.83 % Allowed : 15.21 % Favored : 82.96 % 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: 0.13 (0.10), residues: 7009 helix: 2.34 (0.14), residues: 1438 sheet: 0.20 (0.12), residues: 1765 loop : -0.88 (0.10), residues: 3806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 121 HIS 0.003 0.001 HIS K 66 PHE 0.022 0.001 PHE M 817 TYR 0.021 0.001 TYR S 60 ARG 0.011 0.000 ARG K 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8436.01 seconds wall clock time: 152 minutes 46.71 seconds (9166.71 seconds total)