Starting phenix.real_space_refine on Sat Feb 17 10:50:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t7v_8369/02_2024/5t7v_8369.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t7v_8369/02_2024/5t7v_8369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t7v_8369/02_2024/5t7v_8369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t7v_8369/02_2024/5t7v_8369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t7v_8369/02_2024/5t7v_8369.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5t7v_8369/02_2024/5t7v_8369.pdb" } resolution = 3.6 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= 0.003 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4364 5.49 5 Mg 17 5.21 5 S 78 5.16 5 C 62036 2.51 5 N 23294 2.21 5 O 36212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "S1 ARG 53": "NH1" <-> "NH2" Residue "S2 ARG 111": "NH1" <-> "NH2" Residue "S3 TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S3 ARG 107": "NH1" <-> "NH2" Residue "S8 ARG 4": "NH1" <-> "NH2" Residue "S9 ARG 36": "NH1" <-> "NH2" Residue "SA ARG 10": "NH1" <-> "NH2" Residue "SA ARG 20": "NH1" <-> "NH2" Residue "SD ARG 30": "NH1" <-> "NH2" Residue "SD ARG 76": "NH1" <-> "NH2" Residue "SD ARG 157": "NH1" <-> "NH2" Residue "SE ARG 11": "NH1" <-> "NH2" Residue "SF ARG 61": "NH1" <-> "NH2" Residue "SF ARG 72": "NH1" <-> "NH2" Residue "L1 ARG 23": "NH1" <-> "NH2" Residue "L1 ARG 29": "NH1" <-> "NH2" Residue "L1 ARG 41": "NH1" <-> "NH2" Residue "L1 ARG 52": "NH1" <-> "NH2" Residue "L1 ARG 53": "NH1" <-> "NH2" Residue "L1 ARG 64": "NH1" <-> "NH2" Residue "L1 ARG 91": "NH1" <-> "NH2" Residue "L1 ARG 103": "NH1" <-> "NH2" Residue "L1 ARG 111": "NH1" <-> "NH2" Residue "L3 ARG 3": "NH1" <-> "NH2" Residue "L3 ARG 13": "NH1" <-> "NH2" Residue "L3 ARG 48": "NH1" <-> "NH2" Residue "L3 ARG 70": "NH1" <-> "NH2" Residue "L4 ARG 67": "NH1" <-> "NH2" Residue "L4 ARG 78": "NH1" <-> "NH2" Residue "L4 ARG 84": "NH1" <-> "NH2" Residue "L5 ARG 84": "NH1" <-> "NH2" Residue "L5 ARG 88": "NH1" <-> "NH2" Residue "L6 ARG 32": "NH1" <-> "NH2" Residue "L6 ARG 76": "NH1" <-> "NH2" Residue "L9 ARG 22": "NH1" <-> "NH2" Residue "L9 ARG 28": "NH1" <-> "NH2" Residue "L9 ARG 49": "NH1" <-> "NH2" Residue "L9 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 ARG 79": "NH1" <-> "NH2" Residue "LA ARG 18": "NH1" <-> "NH2" Residue "LA ARG 37": "NH1" <-> "NH2" Residue "LB ARG 29": "NH1" <-> "NH2" Residue "LB ARG 47": "NH1" <-> "NH2" Residue "LB ARG 52": "NH1" <-> "NH2" Residue "LB ARG 60": "NH1" <-> "NH2" Residue "LC ARG 86": "NH1" <-> "NH2" Residue "LC ARG 92": "NH1" <-> "NH2" Residue "LC ARG 138": "NH1" <-> "NH2" Residue "LD ARG 10": "NH1" <-> "NH2" Residue "LD ARG 44": "NH1" <-> "NH2" Residue "LD GLU 58": "OE1" <-> "OE2" Residue "LE ARG 6": "NH1" <-> "NH2" Residue "LE ARG 7": "NH1" <-> "NH2" Residue "LE ARG 16": "NH1" <-> "NH2" Residue "LG ARG 4": "NH1" <-> "NH2" Residue "LG ARG 20": "NH1" <-> "NH2" Residue "LG ARG 22": "NH1" <-> "NH2" Residue "LG ARG 34": "NH1" <-> "NH2" Residue "LH ARG 13": "NH1" <-> "NH2" Residue "LH ARG 42": "NH1" <-> "NH2" Residue "LH ARG 57": "NH1" <-> "NH2" Residue "LJ ARG 54": "NH1" <-> "NH2" Residue "LJ ARG 107": "NH1" <-> "NH2" Residue "LJ ARG 168": "NH1" <-> "NH2" Residue "LL ARG 3": "NH1" <-> "NH2" Residue "LL ARG 163": "NH1" <-> "NH2" Residue "LL ARG 170": "NH1" <-> "NH2" Residue "LM ARG 2": "NH1" <-> "NH2" Residue "LM ARG 14": "NH1" <-> "NH2" Residue "LM ARG 38": "NH1" <-> "NH2" Residue "LP ARG 10": "NH1" <-> "NH2" Residue "LP ARG 45": "NH1" <-> "NH2" Residue "LP ARG 51": "NH1" <-> "NH2" Residue "LP ARG 56": "NH1" <-> "NH2" Residue "LP ARG 60": "NH1" <-> "NH2" Residue "LP ARG 115": "NH1" <-> "NH2" Residue "LP GLU 136": "OE1" <-> "OE2" Residue "LQ ARG 67": "NH1" <-> "NH2" Residue "LR ARG 113": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 126001 Number of models: 1 Model: "" Number of chains: 44 Chain: "A" Number of atoms: 30390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1419, 30390 Inner-chain residues flagged as termini: ['pdbres=" C A 132 "', 'pdbres=" C A 193 "', 'pdbres=" U A1063 "'] Classifications: {'RNA': 1419} Modifications used: {'5*END': 4, 'rna2p_pur': 111, 'rna2p_pyr': 66, 'rna3p_pur': 691, 'rna3p_pyr': 551} Link IDs: {'rna2p': 177, 'rna3p': 1241} Chain breaks: 4 Chain: "S1" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 6, 'TRANS': 75} Chain: "S2" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 850 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 7, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S3" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1011 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 8, 'TRANS': 127} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "S6" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 725 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S7" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 594 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S8" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 674 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S9" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "SA" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 475 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'TRANS': 75} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 47 Chain: "SC" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1604 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "SD" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1132 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 146} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "SE" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 763 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "SF" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1012 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 59339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2768, 59339 Inner-chain residues flagged as termini: ['pdbres=" G B 317 "', 'pdbres=" A B1459 "', 'pdbres=" A B1539 "', 'pdbres=" G B1555 "'] Classifications: {'RNA': 2768} Modifications used: {'5*END': 5, 'rna2p_pur': 284, 'rna2p_pyr': 147, 'rna3p_pur': 1303, 'rna3p_pyr': 1034} Link IDs: {'rna2p': 431, 'rna3p': 2336} Chain breaks: 4 Chain: "C" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2424 Classifications: {'RNA': 114} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 100} Chain: "L1" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 914 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L2" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2086 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 257} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L3" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L4" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L5" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 852 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L6" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 684 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 84} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "L7" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 758 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 95} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "L8" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L9" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 590 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "LA" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 462 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "LB" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 502 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "LC" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1617 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "LD" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 440 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "LE" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 421 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "LF" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 386 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "LG" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 371 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "LH" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 520 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "LI" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 295 Classifications: {'peptide': 37} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "LJ" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1538 Classifications: {'peptide': 204} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "LL" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1357 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 166} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "LM" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1137 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "LN" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 910 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "LO" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1081 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "LP" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1088 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "LQ" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 954 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "LR" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 896 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 114} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1577 Classifications: {'RNA': 74} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 63} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' MG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Time building chain proxies: 46.63, per 1000 atoms: 0.37 Number of scatterers: 126001 At special positions: 0 Unit cell: (268.4, 229.9, 247.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 4364 15.00 Mg 17 11.99 O 36212 8.00 N 23294 7.00 C 62036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYSLI 14 " - pdb=" SG CYSLI 27 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 45.60 Conformation dependent library (CDL) restraints added in 5.6 seconds 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7600 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 56 sheets defined 21.6% alpha, 14.8% beta 479 base pairs and 2049 stacking pairs defined. Time for finding SS restraints: 34.00 Creating SS restraints... Processing helix chain 'S1' and resid 14 through 22 removed outlier: 4.188A pdb=" N ILES1 18 " --> pdb=" O ASPS1 14 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASPS1 19 " --> pdb=" O HISS1 15 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLNS1 20 " --> pdb=" O ARGS1 16 " (cutoff:3.500A) Processing helix chain 'S1' and resid 23 through 33 removed outlier: 3.736A pdb=" N SERS1 32 " --> pdb=" O THRS1 28 " (cutoff:3.500A) Processing helix chain 'S1' and resid 80 through 85 removed outlier: 3.837A pdb=" N ASPS1 85 " --> pdb=" O PROS1 81 " (cutoff:3.500A) Processing helix chain 'S2' and resid 47 through 51 removed outlier: 3.780A pdb=" N GLYS2 51 " --> pdb=" O ALAS2 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'S2' and resid 47 through 51' Processing helix chain 'S2' and resid 59 through 67 removed outlier: 4.082A pdb=" N ALAS2 63 " --> pdb=" O THRS2 59 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLNS2 64 " --> pdb=" O PROS2 60 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N METS2 65 " --> pdb=" O PHES2 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SERS2 67 " --> pdb=" O ALAS2 63 " (cutoff:3.500A) Processing helix chain 'S2' and resid 68 through 76 removed outlier: 3.956A pdb=" N LYSS2 72 " --> pdb=" O GLUS2 68 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SERS2 73 " --> pdb=" O THRS2 69 " (cutoff:3.500A) Processing helix chain 'S3' and resid 3 through 10 removed outlier: 3.516A pdb=" N VALS3 8 " --> pdb=" O ILES3 4 " (cutoff:3.500A) Processing helix chain 'S6' and resid 7 through 14 removed outlier: 3.901A pdb=" N ILES6 11 " --> pdb=" O ARGS6 7 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILES6 12 " --> pdb=" O LYSS6 8 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYSS6 13 " --> pdb=" O ASNS6 9 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLUS6 14 " --> pdb=" O GLUS6 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'S6' and resid 7 through 14' Processing helix chain 'S6' and resid 26 through 43 removed outlier: 3.525A pdb=" N ALAS6 34 " --> pdb=" O ALAS6 30 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALAS6 38 " --> pdb=" O ALAS6 34 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLUS6 41 " --> pdb=" O ASNS6 37 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HISS6 42 " --> pdb=" O ALAS6 38 " (cutoff:3.500A) Processing helix chain 'S6' and resid 51 through 72 removed outlier: 3.648A pdb=" N LEUS6 57 " --> pdb=" O ARGS6 53 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VALS6 60 " --> pdb=" O LEUS6 56 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLYS6 61 " --> pdb=" O LEUS6 57 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HISS6 65 " --> pdb=" O GLYS6 61 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SERS6 72 " --> pdb=" O ASNS6 68 " (cutoff:3.500A) Processing helix chain 'S6' and resid 74 through 86 removed outlier: 3.679A pdb=" N TYRS6 78 " --> pdb=" O ASPS6 74 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARGS6 79 " --> pdb=" O ILES6 75 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEUS6 85 " --> pdb=" O LEUS6 81 " (cutoff:3.500A) Processing helix chain 'S7' and resid 71 through 77 removed outlier: 4.017A pdb=" N LEUS7 75 " --> pdb=" O VALS7 71 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYSS7 77 " --> pdb=" O ASNS7 73 " (cutoff:3.500A) Processing helix chain 'S9' and resid 46 through 51 Processing helix chain 'S9' and resid 54 through 59 removed outlier: 3.841A pdb=" N ARGS9 58 " --> pdb=" O ALAS9 54 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N METS9 59 " --> pdb=" O LYSS9 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'S9' and resid 54 through 59' Processing helix chain 'S9' and resid 61 through 70 removed outlier: 3.566A pdb=" N HISS9 69 " --> pdb=" O LYSS9 65 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N METS9 70 " --> pdb=" O ARGS9 66 " (cutoff:3.500A) Processing helix chain 'SA' and resid 7 through 34 removed outlier: 3.567A pdb=" N THRSA 13 " --> pdb=" O LYSSA 9 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYSSA 16 " --> pdb=" O LYSSA 12 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLUSA 18 " --> pdb=" O THRSA 14 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALASA 19 " --> pdb=" O GLUSA 15 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARGSA 20 " --> pdb=" O LYSSA 16 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASNSA 21 " --> pdb=" O ALASA 17 " (cutoff:3.500A) Processing helix chain 'SA' and resid 34 through 39 Processing helix chain 'SA' and resid 50 through 55 Processing helix chain 'SA' and resid 69 through 74 removed outlier: 4.454A pdb=" N ARGSA 73 " --> pdb=" O LYSSA 70 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILESA 74 " --> pdb=" O ALASA 71 " (cutoff:3.500A) Processing helix chain 'SC' and resid 9 through 14 Processing helix chain 'SC' and resid 47 through 52 Processing helix chain 'SC' and resid 54 through 59 removed outlier: 3.717A pdb=" N ARGSC 58 " --> pdb=" O LYSSC 54 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYRSC 59 " --> pdb=" O GLNSC 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 54 through 59' Processing helix chain 'SC' and resid 64 through 73 removed outlier: 4.002A pdb=" N PHESC 68 " --> pdb=" O THRSC 64 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARGSC 69 " --> pdb=" O GLUSC 65 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASPSC 73 " --> pdb=" O ARGSC 69 " (cutoff:3.500A) Processing helix chain 'SC' and resid 74 through 78 Processing helix chain 'SC' and resid 85 through 91 Processing helix chain 'SC' and resid 93 through 101 Processing helix chain 'SC' and resid 108 through 116 removed outlier: 4.246A pdb=" N VALSC 114 " --> pdb=" O ALASC 110 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASNSC 115 " --> pdb=" O ARGSC 111 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HISSC 116 " --> pdb=" O GLNSC 112 " (cutoff:3.500A) Processing helix chain 'SC' and resid 148 through 157 Processing helix chain 'SC' and resid 194 through 199 removed outlier: 3.796A pdb=" N SERSC 199 " --> pdb=" O GLUSC 196 " (cutoff:3.500A) Processing helix chain 'SD' and resid 57 through 68 removed outlier: 4.097A pdb=" N LYSSD 61 " --> pdb=" O PROSD 57 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYSSD 62 " --> pdb=" O GLUSD 58 " (cutoff:3.500A) Processing helix chain 'SD' and resid 109 through 116 removed outlier: 3.756A pdb=" N VALSD 114 " --> pdb=" O PROSD 110 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUSD 115 " --> pdb=" O VALSD 111 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLUSD 116 " --> pdb=" O ARGSD 112 " (cutoff:3.500A) Processing helix chain 'SD' and resid 134 through 145 Processing helix chain 'SD' and resid 150 through 156 removed outlier: 3.678A pdb=" N LEUSD 156 " --> pdb=" O ASPSD 152 " (cutoff:3.500A) Processing helix chain 'SE' and resid 22 through 27 Processing helix chain 'SE' and resid 75 through 80 Processing helix chain 'SF' and resid 6 through 20 removed outlier: 3.739A pdb=" N ARGSF 15 " --> pdb=" O LEUSF 11 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VALSF 20 " --> pdb=" O ASNSF 16 " (cutoff:3.500A) Processing helix chain 'SF' and resid 33 through 41 removed outlier: 4.281A pdb=" N GLUSF 38 " --> pdb=" O LYSSF 34 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILESF 39 " --> pdb=" O GLUSF 35 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEUSF 40 " --> pdb=" O ILESF 36 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYSSF 41 " --> pdb=" O ALASF 37 " (cutoff:3.500A) Processing helix chain 'SF' and resid 116 through 121 removed outlier: 3.757A pdb=" N LYSSF 120 " --> pdb=" O GLUSF 117 " (cutoff:3.500A) Processing helix chain 'L1' and resid 6 through 11 Processing helix chain 'L1' and resid 100 through 104 removed outlier: 3.841A pdb=" N SERL1 104 " --> pdb=" O TYRL1 101 " (cutoff:3.500A) Processing helix chain 'L2' and resid 131 through 135 removed outlier: 3.744A pdb=" N ILEL2 135 " --> pdb=" O LEUL2 132 " (cutoff:3.500A) Processing helix chain 'L2' and resid 199 through 203 removed outlier: 3.880A pdb=" N LEUL2 202 " --> pdb=" O GLNL2 199 " (cutoff:3.500A) Processing helix chain 'L2' and resid 221 through 225 removed outlier: 3.967A pdb=" N VALL2 224 " --> pdb=" O ARGL2 221 " (cutoff:3.500A) Processing helix chain 'L3' and resid 8 through 13 removed outlier: 3.783A pdb=" N ALAL3 12 " --> pdb=" O THRL3 8 " (cutoff:3.500A) Processing helix chain 'L3' and resid 18 through 22 removed outlier: 4.095A pdb=" N LYSL3 22 " --> pdb=" O LYSL3 19 " (cutoff:3.500A) Processing helix chain 'L3' and resid 31 through 40 removed outlier: 3.528A pdb=" N ALAL3 35 " --> pdb=" O LEUL3 31 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLNL3 37 " --> pdb=" O LYSL3 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLNL3 38 " --> pdb=" O VALL3 34 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VALL3 39 " --> pdb=" O ALAL3 35 " (cutoff:3.500A) Processing helix chain 'L3' and resid 46 through 51 removed outlier: 4.015A pdb=" N ARGL3 51 " --> pdb=" O PHEL3 47 " (cutoff:3.500A) Processing helix chain 'L3' and resid 52 through 57 Processing helix chain 'L3' and resid 57 through 70 removed outlier: 3.628A pdb=" N TRPL3 61 " --> pdb=" O PHEL3 57 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THRL3 63 " --> pdb=" O LYSL3 59 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARGL3 70 " --> pdb=" O ASNL3 66 " (cutoff:3.500A) Processing helix chain 'L3' and resid 78 through 86 removed outlier: 3.769A pdb=" N GLYL3 82 " --> pdb=" O ARGL3 78 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYSL3 84 " --> pdb=" O METL3 80 " (cutoff:3.500A) Processing helix chain 'L3' and resid 96 through 102 removed outlier: 3.610A pdb=" N ILEL3 100 " --> pdb=" O SERL3 96 " (cutoff:3.500A) Processing helix chain 'L3' and resid 102 through 116 removed outlier: 4.037A pdb=" N GLNL3 108 " --> pdb=" O LYSL3 104 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEUL3 109 " --> pdb=" O ALAL3 105 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VALL3 110 " --> pdb=" O PHEL3 106 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALAL3 116 " --> pdb=" O LYSL3 112 " (cutoff:3.500A) Processing helix chain 'L5' and resid 28 through 34 removed outlier: 3.621A pdb=" N ILEL5 33 " --> pdb=" O ALAL5 29 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALAL5 34 " --> pdb=" O ALAL5 30 " (cutoff:3.500A) Processing helix chain 'L5' and resid 43 through 55 removed outlier: 3.535A pdb=" N VALL5 50 " --> pdb=" O VALL5 46 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SERL5 53 " --> pdb=" O LYSL5 49 " (cutoff:3.500A) Processing helix chain 'L6' and resid 35 through 40 removed outlier: 3.776A pdb=" N LYSL6 39 " --> pdb=" O LYSL6 35 " (cutoff:3.500A) Processing helix chain 'L6' and resid 42 through 47 removed outlier: 3.968A pdb=" N PHEL6 46 " --> pdb=" O VALL6 42 " (cutoff:3.500A) Processing helix chain 'L7' and resid 66 through 68 No H-bonds generated for 'chain 'L7' and resid 66 through 68' Processing helix chain 'L8' and resid 14 through 20 Processing helix chain 'L8' and resid 45 through 56 removed outlier: 3.701A pdb=" N LYSL8 50 " --> pdb=" O VALL8 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VALL8 51 " --> pdb=" O GLUL8 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILEL8 52 " --> pdb=" O PHEL8 48 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLUL8 54 " --> pdb=" O LYSL8 50 " (cutoff:3.500A) Processing helix chain 'L9' and resid 62 through 66 removed outlier: 4.039A pdb=" N THRL9 66 " --> pdb=" O GLYL9 63 " (cutoff:3.500A) Processing helix chain 'LB' and resid 13 through 22 removed outlier: 4.146A pdb=" N LYSLB 19 " --> pdb=" O GLULB 15 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYSLB 22 " --> pdb=" O ILELB 18 " (cutoff:3.500A) Processing helix chain 'LB' and resid 26 through 31 Processing helix chain 'LB' and resid 41 through 46 removed outlier: 4.107A pdb=" N THRLB 45 " --> pdb=" O ALALB 41 " (cutoff:3.500A) Processing helix chain 'LB' and resid 55 through 60 removed outlier: 3.747A pdb=" N GLULB 59 " --> pdb=" O THRLB 55 " (cutoff:3.500A) Processing helix chain 'LC' and resid 71 through 80 removed outlier: 3.736A pdb=" N GLYLC 75 " --> pdb=" O LYSLC 71 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N HISLC 76 " --> pdb=" O PROLC 72 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALALC 77 " --> pdb=" O ALALC 73 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYSLC 79 " --> pdb=" O GLYLC 75 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALALC 80 " --> pdb=" O HISLC 76 " (cutoff:3.500A) Processing helix chain 'LC' and resid 106 through 110 removed outlier: 3.854A pdb=" N THRLC 109 " --> pdb=" O SERLC 106 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHELC 110 " --> pdb=" O VALLC 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 106 through 110' Processing helix chain 'LC' and resid 129 through 135 removed outlier: 3.694A pdb=" N HISLC 134 " --> pdb=" O ALALC 130 " (cutoff:3.500A) Processing helix chain 'LD' and resid 17 through 27 removed outlier: 3.574A pdb=" N LYSLD 21 " --> pdb=" O GLULD 17 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VALLD 23 " --> pdb=" O GLNLD 19 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLYLD 27 " --> pdb=" O VALLD 23 " (cutoff:3.500A) Processing helix chain 'LD' and resid 42 through 48 removed outlier: 4.290A pdb=" N ASNLD 48 " --> pdb=" O ARGLD 44 " (cutoff:3.500A) Processing helix chain 'LE' and resid 9 through 17 removed outlier: 3.601A pdb=" N ASNLE 14 " --> pdb=" O LYSLE 10 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARGLE 16 " --> pdb=" O ARGLE 12 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARGLE 17 " --> pdb=" O LYSLE 13 " (cutoff:3.500A) Processing helix chain 'LG' and resid 11 through 18 Processing helix chain 'LG' and resid 18 through 23 Processing helix chain 'LG' and resid 27 through 36 removed outlier: 3.738A pdb=" N ARGLG 36 " --> pdb=" O LEULG 32 " (cutoff:3.500A) Processing helix chain 'LH' and resid 7 through 12 removed outlier: 3.719A pdb=" N LYSLH 12 " --> pdb=" O ARGLH 8 " (cutoff:3.500A) Processing helix chain 'LH' and resid 37 through 42 removed outlier: 3.727A pdb=" N ARGLH 42 " --> pdb=" O THRLH 38 " (cutoff:3.500A) Processing helix chain 'LH' and resid 51 through 56 removed outlier: 3.888A pdb=" N LYSLH 56 " --> pdb=" O LYSLH 52 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 29 through 34 removed outlier: 3.928A pdb=" N LEULJ 33 " --> pdb=" O ASNLJ 29 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 37 through 42 Processing helix chain 'LJ' and resid 102 through 111 removed outlier: 3.583A pdb=" N ARGLJ 107 " --> pdb=" O LYSLJ 103 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEULJ 108 " --> pdb=" O LYSLJ 104 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALALJ 109 " --> pdb=" O METLJ 105 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEULJ 110 " --> pdb=" O ARGLJ 106 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARGLJ 111 " --> pdb=" O ARGLJ 107 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 114 through 119 removed outlier: 3.659A pdb=" N ALALJ 118 " --> pdb=" O LEULJ 114 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLNLJ 119 " --> pdb=" O SERLJ 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 114 through 119' Processing helix chain 'LJ' and resid 135 through 146 removed outlier: 3.667A pdb=" N ASNLJ 141 " --> pdb=" O LYSLJ 137 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VALLJ 142 " --> pdb=" O GLULJ 138 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THRLJ 145 " --> pdb=" O ASNLJ 141 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 179 through 181 No H-bonds generated for 'chain 'LJ' and resid 179 through 181' Processing helix chain 'LJ' and resid 196 through 200 removed outlier: 3.566A pdb=" N LYSLJ 200 " --> pdb=" O GLULJ 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 196 through 200' Processing helix chain 'LJ' and resid 201 through 207 removed outlier: 3.732A pdb=" N LEULJ 206 " --> pdb=" O VALLJ 202 " (cutoff:3.500A) Processing helix chain 'LL' and resid 59 through 68 removed outlier: 3.748A pdb=" N ASNLL 64 " --> pdb=" O GLULL 60 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N HISLL 65 " --> pdb=" O ASPLL 61 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLYLL 66 " --> pdb=" O ARGLL 62 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THRLL 67 " --> pdb=" O THRLL 63 " (cutoff:3.500A) Processing helix chain 'LL' and resid 72 through 77 Processing helix chain 'LL' and resid 137 through 144 Processing helix chain 'LL' and resid 148 through 152 Processing helix chain 'LM' and resid 25 through 30 removed outlier: 3.523A pdb=" N LEULM 29 " --> pdb=" O THRLM 25 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SERLM 30 " --> pdb=" O LEULM 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'LM' and resid 25 through 30' Processing helix chain 'LM' and resid 30 through 35 removed outlier: 3.600A pdb=" N ALALM 34 " --> pdb=" O SERLM 30 " (cutoff:3.500A) Processing helix chain 'LM' and resid 59 through 63 removed outlier: 4.070A pdb=" N LYSLM 62 " --> pdb=" O ASNLM 59 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILELM 63 " --> pdb=" O ALALM 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'LM' and resid 59 through 63' Processing helix chain 'LM' and resid 68 through 73 Processing helix chain 'LM' and resid 91 through 97 removed outlier: 4.047A pdb=" N ARGLM 95 " --> pdb=" O GLYLM 91 " (cutoff:3.500A) Processing helix chain 'LM' and resid 97 through 107 removed outlier: 3.880A pdb=" N LEULM 101 " --> pdb=" O ASNLM 97 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILELM 102 " --> pdb=" O PROLM 98 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLULM 103 " --> pdb=" O GLULM 99 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYSLM 107 " --> pdb=" O GLULM 103 " (cutoff:3.500A) Processing helix chain 'LM' and resid 115 through 121 removed outlier: 3.731A pdb=" N GLYLM 120 " --> pdb=" O GLYLM 116 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYSLM 121 " --> pdb=" O GLULM 117 " (cutoff:3.500A) Processing helix chain 'LM' and resid 133 through 137 removed outlier: 3.567A pdb=" N GLNLM 136 " --> pdb=" O HISLM 133 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLNLM 137 " --> pdb=" O ALALM 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'LM' and resid 133 through 137' Processing helix chain 'LO' and resid 79 through 83 removed outlier: 3.907A pdb=" N ASNLO 83 " --> pdb=" O ASPLO 80 " (cutoff:3.500A) Processing helix chain 'LO' and resid 131 through 140 removed outlier: 3.891A pdb=" N ALALO 135 " --> pdb=" O SERLO 131 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILELO 136 " --> pdb=" O ALALO 132 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASPLO 137 " --> pdb=" O ALALO 133 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYSLO 139 " --> pdb=" O ALALO 135 " (cutoff:3.500A) Processing helix chain 'LP' and resid 47 through 59 removed outlier: 3.720A pdb=" N ILELP 52 " --> pdb=" O GLULP 48 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALALP 53 " --> pdb=" O SERLP 49 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N METLP 54 " --> pdb=" O ALALP 50 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYRLP 57 " --> pdb=" O ALALP 53 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N METLP 58 " --> pdb=" O METLP 54 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYSLP 59 " --> pdb=" O THRLP 55 " (cutoff:3.500A) Processing helix chain 'LP' and resid 110 through 115 Processing helix chain 'LP' and resid 118 through 123 removed outlier: 3.738A pdb=" N HISLP 123 " --> pdb=" O ARGLP 119 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 16 through 22 removed outlier: 4.047A pdb=" N THRLQ 22 " --> pdb=" O ARGLQ 18 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 23 through 28 removed outlier: 3.750A pdb=" N SERLQ 27 " --> pdb=" O SERLQ 23 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 39 through 43 Processing helix chain 'LQ' and resid 48 through 54 removed outlier: 3.686A pdb=" N LYSLQ 53 " --> pdb=" O THRLQ 49 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLYLQ 54 " --> pdb=" O LEULQ 50 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 56 through 62 Processing helix chain 'LQ' and resid 63 through 66 removed outlier: 3.943A pdb=" N LEULQ 66 " --> pdb=" O ALALQ 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 63 through 66' Processing helix chain 'LQ' and resid 81 through 85 removed outlier: 3.800A pdb=" N LEULQ 85 " --> pdb=" O ALALQ 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 81 through 85' Processing helix chain 'LQ' and resid 88 through 93 removed outlier: 3.776A pdb=" N ARGLQ 92 " --> pdb=" O GLULQ 88 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYRLQ 93 " --> pdb=" O ILELQ 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 88 through 93' Processing helix chain 'LR' and resid 10 through 19 removed outlier: 3.830A pdb=" N ARGLR 17 " --> pdb=" O LYSLR 13 " (cutoff:3.500A) Processing helix chain 'LR' and resid 70 through 76 Processing helix chain 'LR' and resid 76 through 88 removed outlier: 3.735A pdb=" N ILELR 80 " --> pdb=" O VALLR 76 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYSLR 83 " --> pdb=" O ALALR 79 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALALR 85 " --> pdb=" O ALALR 81 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASPLR 86 " --> pdb=" O LYSLR 82 " (cutoff:3.500A) Processing helix chain 'LR' and resid 103 through 115 removed outlier: 3.506A pdb=" N GLULR 110 " --> pdb=" O LYSLR 106 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARGLR 113 " --> pdb=" O ALALR 109 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLULR 114 " --> pdb=" O GLULR 110 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SERLR 115 " --> pdb=" O ALALR 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'S1' and resid 41 through 52 removed outlier: 3.915A pdb=" N GLUS1 45 " --> pdb=" O THRS1 69 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THRS1 69 " --> pdb=" O GLUS1 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S2' and resid 41 through 46 removed outlier: 3.565A pdb=" N VALS2 32 " --> pdb=" O SERS2 45 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THRS2 85 " --> pdb=" O ALAS2 21 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VALS2 82 " --> pdb=" O ALAS2 109 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ARGS2 111 " --> pdb=" O VALS2 82 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VALS2 84 " --> pdb=" O ARGS2 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S3' and resid 45 through 47 removed outlier: 3.696A pdb=" N VALS3 46 " --> pdb=" O ARGS3 69 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILES3 76 " --> pdb=" O VALS3 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S7' and resid 4 through 7 removed outlier: 3.533A pdb=" N TYRS7 18 " --> pdb=" O TYRS7 40 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLYS7 38 " --> pdb=" O ILES7 20 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VALS7 22 " --> pdb=" O GLNS7 36 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLNS7 36 " --> pdb=" O VALS7 22 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'S8' and resid 13 through 14 removed outlier: 3.980A pdb=" N TYRS8 46 " --> pdb=" O VALS8 25 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N PHES8 75 " --> pdb=" O LYSS8 45 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LYSS8 47 " --> pdb=" O PHES8 75 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEUS8 77 " --> pdb=" O LYSS8 47 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N HISS8 49 " --> pdb=" O LEUS8 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S8' and resid 30 through 31 Processing sheet with id=AA7, first strand: chain 'SC' and resid 138 through 139 removed outlier: 3.533A pdb=" N ILESC 139 " --> pdb=" O GLYSC 174 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLYSC 174 " --> pdb=" O ILESC 139 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N THRSC 175 " --> pdb=" O ASNSC 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'SD' and resid 12 through 21 removed outlier: 3.654A pdb=" N VALSD 38 " --> pdb=" O ARGSD 14 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEUSD 36 " --> pdb=" O VALSD 16 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILESD 18 " --> pdb=" O THRSD 34 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THRSD 34 " --> pdb=" O ILESD 18 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARGSD 20 " --> pdb=" O ARGSD 32 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ARGSD 32 " --> pdb=" O ARGSD 20 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VALSD 46 " --> pdb=" O VALSD 72 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'SD' and resid 85 through 89 removed outlier: 3.964A pdb=" N PHESD 95 " --> pdb=" O SERSD 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'SE' and resid 39 through 47 removed outlier: 3.786A pdb=" N GLUSE 39 " --> pdb=" O ARGSE 64 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYRSE 60 " --> pdb=" O TRPSE 43 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYSSE 45 " --> pdb=" O GLYSE 58 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLYSE 58 " --> pdb=" O LYSSE 45 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASNSE 61 " --> pdb=" O TYRSE 8 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARGSE 88 " --> pdb=" O ILESE 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'SF' and resid 24 through 28 removed outlier: 3.864A pdb=" N LEUSF 27 " --> pdb=" O LEUSF 60 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARGSF 61 " --> pdb=" O VALSF 49 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VALSF 49 " --> pdb=" O ARGSF 61 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHESF 63 " --> pdb=" O LYSSF 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'SF' and resid 78 through 79 removed outlier: 3.665A pdb=" N LYSSF 78 " --> pdb=" O TYRSF 130 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLUSF 126 " --> pdb=" O SERSF 107 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEUSF 105 " --> pdb=" O ILESF 128 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L1' and resid 83 through 91 removed outlier: 6.954A pdb=" N HISL1 31 " --> pdb=" O GLUL1 84 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILEL1 86 " --> pdb=" O ARGL1 29 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARGL1 29 " --> pdb=" O ILEL1 86 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N VALL1 88 " --> pdb=" O THRL1 27 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N THRL1 27 " --> pdb=" O VALL1 88 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASPL1 26 " --> pdb=" O VALL1 49 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLYL1 47 " --> pdb=" O LEUL1 28 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N GLUL1 46 " --> pdb=" O ILEL1 66 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILEL1 66 " --> pdb=" O GLUL1 46 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THRL1 75 " --> pdb=" O TYRLN 76 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L2' and resid 34 through 35 Processing sheet with id=AB6, first strand: chain 'L2' and resid 101 through 104 removed outlier: 6.779A pdb=" N LEUL2 93 " --> pdb=" O ASPL2 79 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILEL2 74 " --> pdb=" O VALL2 116 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VALL2 116 " --> pdb=" O ILEL2 74 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L2' and resid 141 through 142 Processing sheet with id=AB8, first strand: chain 'L2' and resid 144 through 145 removed outlier: 5.802A pdb=" N ILEL2 144 " --> pdb=" O GLNL2 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L2' and resid 163 through 167 removed outlier: 6.768A pdb=" N LEUL2 173 " --> pdb=" O LEUL2 165 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LYSL2 167 " --> pdb=" O TYRL2 171 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYRL2 171 " --> pdb=" O LYSL2 167 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L4' and resid 3 through 6 Processing sheet with id=AC2, first strand: chain 'L4' and resid 19 through 23 removed outlier: 3.967A pdb=" N ILEL4 20 " --> pdb=" O LEUL4 95 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEUL4 95 " --> pdb=" O ILEL4 20 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L4' and resid 32 through 35 removed outlier: 3.604A pdb=" N PHEL4 33 " --> pdb=" O ALAL4 60 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L4' and resid 73 through 76 Processing sheet with id=AC5, first strand: chain 'L5' and resid 3 through 10 removed outlier: 3.609A pdb=" N ALAL5 3 " --> pdb=" O VALL5 107 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILEL5 105 " --> pdb=" O ALAL5 5 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N SERL5 101 " --> pdb=" O THRL5 9 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYSL5 98 " --> pdb=" O LEUL5 82 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THRL5 100 " --> pdb=" O PROL5 80 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N HISL5 102 " --> pdb=" O GLUL5 78 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLUL5 78 " --> pdb=" O HISL5 102 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THRL5 104 " --> pdb=" O ALAL5 76 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALAL5 76 " --> pdb=" O THRL5 104 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VALL5 106 " --> pdb=" O ALAL5 74 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALAL5 74 " --> pdb=" O VALL5 106 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N SERL5 108 " --> pdb=" O LYSL5 72 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYSL5 72 " --> pdb=" O SERL5 108 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L6' and resid 7 through 10 removed outlier: 3.536A pdb=" N ARGL6 9 " --> pdb=" O ASPL6 28 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARGL6 76 " --> pdb=" O VALL6 29 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ARGL6 75 " --> pdb=" O ASNL6 57 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASNL6 57 " --> pdb=" O ARGL6 75 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LYSL6 77 " --> pdb=" O ILEL6 55 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ILEL6 55 " --> pdb=" O LYSL6 77 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILEL6 79 " --> pdb=" O VALL6 53 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VALL6 53 " --> pdb=" O ILEL6 79 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N THRL6 81 " --> pdb=" O ALAL6 51 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYSL6 49 " --> pdb=" O LYSL6 83 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L6' and resid 62 through 65 removed outlier: 4.053A pdb=" N METL6 65 " --> pdb=" O TYRL6 68 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYRL6 68 " --> pdb=" O METL6 65 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L7' and resid 32 through 33 Processing sheet with id=AC9, first strand: chain 'L7' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'L7' and resid 81 through 84 Processing sheet with id=AD2, first strand: chain 'L8' and resid 7 through 8 removed outlier: 4.190A pdb=" N ILEL8 7 " --> pdb=" O LYSL8 42 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYSL8 42 " --> pdb=" O ILEL8 7 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N ILEL8 89 " --> pdb=" O LYSL8 26 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N PHEL8 91 " --> pdb=" O PROL8 28 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VALL8 30 " --> pdb=" O PHEL8 91 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALAL8 93 " --> pdb=" O VALL8 30 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N TYRL8 32 " --> pdb=" O ALAL8 93 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASPL8 90 " --> pdb=" O ALAL8 75 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L8' and resid 79 through 80 removed outlier: 4.134A pdb=" N ASPL8 80 " --> pdb=" O GLNL8 85 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLNL8 85 " --> pdb=" O ASPL8 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'L9' and resid 54 through 55 Processing sheet with id=AD5, first strand: chain 'L9' and resid 59 through 60 Processing sheet with id=AD6, first strand: chain 'LA' and resid 13 through 17 removed outlier: 3.551A pdb=" N TRPLA 29 " --> pdb=" O SERLA 13 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLYLA 15 " --> pdb=" O ARGLA 27 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THRLA 25 " --> pdb=" O ARGLA 17 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'LA' and resid 33 through 38 removed outlier: 3.563A pdb=" N VALLA 36 " --> pdb=" O VALLA 47 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILELA 38 " --> pdb=" O LYSLA 45 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYSLA 45 " --> pdb=" O ILELA 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'LC' and resid 178 through 182 removed outlier: 6.106A pdb=" N GLNLC 180 " --> pdb=" O VALLC 118 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VALLC 118 " --> pdb=" O GLNLC 180 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLULC 209 " --> pdb=" O THRLC 119 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LYSLC 9 " --> pdb=" O GLULC 29 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLULC 29 " --> pdb=" O LYSLC 9 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLYLC 11 " --> pdb=" O VALLC 27 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'LC' and resid 35 through 39 removed outlier: 6.898A pdb=" N GLNLC 50 " --> pdb=" O LEULC 36 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYSLC 38 " --> pdb=" O ALALC 48 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALALC 48 " --> pdb=" O LYSLC 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'LD' and resid 34 through 36 removed outlier: 3.519A pdb=" N VALLD 35 " --> pdb=" O ILELD 6 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'LE' and resid 27 through 30 removed outlier: 3.626A pdb=" N GLULE 35 " --> pdb=" O CYSLE 30 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'LF' and resid 2 through 8 removed outlier: 3.661A pdb=" N LYSLF 21 " --> pdb=" O VALLF 3 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N TYRLF 17 " --> pdb=" O LEULF 7 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'LH' and resid 15 through 16 Processing sheet with id=AE5, first strand: chain 'LI' and resid 2 through 3 removed outlier: 7.073A pdb=" N LYSLI 2 " --> pdb=" O ARGLI 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'LI' and resid 15 through 19 Processing sheet with id=AE7, first strand: chain 'LJ' and resid 123 through 126 removed outlier: 6.246A pdb=" N THRLJ 124 " --> pdb=" O ILELJ 194 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLNLJ 174 " --> pdb=" O VALLJ 152 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'LL' and resid 16 through 18 removed outlier: 3.520A pdb=" N LYSLL 27 " --> pdb=" O THRLL 16 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THRLL 18 " --> pdb=" O THRLL 25 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'LL' and resid 42 through 44 removed outlier: 4.166A pdb=" N THRLL 42 " --> pdb=" O VALLL 53 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'LL' and resid 121 through 125 Processing sheet with id=AF2, first strand: chain 'LL' and resid 95 through 99 removed outlier: 3.532A pdb=" N GLNLL 99 " --> pdb=" O ASPLL 102 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'LM' and resid 16 through 20 removed outlier: 3.558A pdb=" N ILELM 58 " --> pdb=" O ILELM 19 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'LN' and resid 9 through 10 removed outlier: 6.650A pdb=" N LYSLN 9 " --> pdb=" O CYSLN 84 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALALN 83 " --> pdb=" O VALLN 63 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VALLN 38 " --> pdb=" O VALLN 24 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VALLN 24 " --> pdb=" O VALLN 38 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VALLN 40 " --> pdb=" O ILELN 22 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THRLN 42 " --> pdb=" O LEULN 20 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'LO' and resid 75 through 77 removed outlier: 5.936A pdb=" N ALALO 75 " --> pdb=" O LYSLO 110 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYSLO 127 " --> pdb=" O ILELO 109 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'LO' and resid 90 through 91 Processing sheet with id=AF7, first strand: chain 'LP' and resid 63 through 66 removed outlier: 3.545A pdb=" N ALALP 107 " --> pdb=" O LYSLP 63 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEULP 34 " --> pdb=" O LEULP 103 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLULP 105 " --> pdb=" O PHELP 32 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHELP 32 " --> pdb=" O GLULP 105 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'LP' and resid 40 through 42 removed outlier: 3.854A pdb=" N SERLP 40 " --> pdb=" O VALLP 97 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THRLP 72 " --> pdb=" O ILELP 94 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'LQ' and resid 29 through 33 removed outlier: 6.795A pdb=" N SERLQ 116 " --> pdb=" O GLNLQ 106 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'LQ' and resid 70 through 71 Processing sheet with id=AG2, first strand: chain 'LR' and resid 30 through 35 removed outlier: 3.592A pdb=" N GLNLR 43 " --> pdb=" O ASNLR 32 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALALR 42 " --> pdb=" O ALALR 56 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALALR 54 " --> pdb=" O ILELR 44 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ASPLR 46 " --> pdb=" O THRLR 52 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N THRLR 52 " --> pdb=" O ASPLR 46 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1079 hydrogen bonds 1766 hydrogen bond angles 0 basepair planarities 479 basepair parallelities 2049 stacking parallelities Total time for adding SS restraints: 147.31 Time building geometry restraints manager: 50.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 14139 1.32 - 1.44: 61200 1.44 - 1.57: 53423 1.57 - 1.69: 8720 1.69 - 1.81: 140 Bond restraints: 137622 Sorted by residual: bond pdb=" CA SERLC 157 " pdb=" C SERLC 157 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.34e-02 5.57e+03 1.86e+01 bond pdb=" C SERS3 40 " pdb=" N PROS3 41 " ideal model delta sigma weight residual 1.334 1.397 -0.064 2.34e-02 1.83e+03 7.37e+00 bond pdb=" CA ASPL6 5 " pdb=" CB ASPL6 5 " ideal model delta sigma weight residual 1.526 1.488 0.039 1.53e-02 4.27e+03 6.39e+00 bond pdb=" CA LEUL2 255 " pdb=" CB LEUL2 255 " ideal model delta sigma weight residual 1.528 1.464 0.064 2.61e-02 1.47e+03 6.07e+00 bond pdb=" CB GLNLJ 82 " pdb=" CG GLNLJ 82 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.77e+00 ... (remaining 137617 not shown) Histogram of bond angle deviations from ideal: 97.39 - 105.16: 20804 105.16 - 112.93: 81593 112.93 - 120.71: 61710 120.71 - 128.48: 37599 128.48 - 136.25: 5756 Bond angle restraints: 207462 Sorted by residual: angle pdb=" CA LEUS3 38 " pdb=" CB LEUS3 38 " pdb=" CG LEUS3 38 " ideal model delta sigma weight residual 116.30 136.05 -19.75 3.50e+00 8.16e-02 3.18e+01 angle pdb=" O4' U B2533 " pdb=" C1' U B2533 " pdb=" C2' U B2533 " ideal model delta sigma weight residual 107.60 102.00 5.60 1.00e+00 1.00e+00 3.14e+01 angle pdb=" C3' C A 336 " pdb=" O3' C A 336 " pdb=" P A A 337 " ideal model delta sigma weight residual 120.20 128.30 -8.10 1.50e+00 4.44e-01 2.91e+01 angle pdb=" C3' U B1503 " pdb=" O3' U B1503 " pdb=" P U B1504 " ideal model delta sigma weight residual 120.20 128.20 -8.00 1.50e+00 4.44e-01 2.84e+01 angle pdb=" C ALALC 80 " pdb=" N ASPLC 81 " pdb=" CA ASPLC 81 " ideal model delta sigma weight residual 122.46 129.82 -7.36 1.41e+00 5.03e-01 2.73e+01 ... (remaining 207457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 77289 35.94 - 71.87: 9529 71.87 - 107.81: 1155 107.81 - 143.75: 26 143.75 - 179.69: 63 Dihedral angle restraints: 88062 sinusoidal: 76245 harmonic: 11817 Sorted by residual: dihedral pdb=" O4' U A 6 " pdb=" C1' U A 6 " pdb=" N1 U A 6 " pdb=" C2 U A 6 " ideal model delta sinusoidal sigma weight residual 200.00 20.78 179.22 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U B 403 " pdb=" C1' U B 403 " pdb=" N1 U B 403 " pdb=" C2 U B 403 " ideal model delta sinusoidal sigma weight residual -160.00 15.15 -175.15 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U D 39 " pdb=" C1' U D 39 " pdb=" N1 U D 39 " pdb=" C2 U D 39 " ideal model delta sinusoidal sigma weight residual 200.00 28.69 171.31 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 88059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 24134 0.079 - 0.158: 2458 0.158 - 0.237: 192 0.237 - 0.316: 22 0.316 - 0.396: 5 Chirality restraints: 26811 Sorted by residual: chirality pdb=" C3' U B1510 " pdb=" C4' U B1510 " pdb=" O3' U B1510 " pdb=" C2' U B1510 " both_signs ideal model delta sigma weight residual False -2.48 -2.08 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" C3' C A1354 " pdb=" C4' C A1354 " pdb=" O3' C A1354 " pdb=" C2' C A1354 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C3' A C 55 " pdb=" C4' A C 55 " pdb=" O3' A C 55 " pdb=" C2' A C 55 " both_signs ideal model delta sigma weight residual False -2.48 -2.14 -0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 26808 not shown) Planarity restraints: 10019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRPL2 213 " -0.027 2.00e-02 2.50e+03 2.15e-02 1.15e+01 pdb=" CG TRPL2 213 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRPL2 213 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRPL2 213 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRPL2 213 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRPL2 213 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRPL2 213 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRPL2 213 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRPL2 213 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRPL2 213 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 683 " -0.043 2.00e-02 2.50e+03 1.88e-02 1.05e+01 pdb=" N9 G B 683 " 0.040 2.00e-02 2.50e+03 pdb=" C8 G B 683 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B 683 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 683 " 0.006 2.00e-02 2.50e+03 pdb=" C6 G B 683 " -0.019 2.00e-02 2.50e+03 pdb=" O6 G B 683 " -0.002 2.00e-02 2.50e+03 pdb=" N1 G B 683 " -0.012 2.00e-02 2.50e+03 pdb=" C2 G B 683 " 0.004 2.00e-02 2.50e+03 pdb=" N2 G B 683 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G B 683 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G B 683 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THRL2 50 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C THRL2 50 " -0.056 2.00e-02 2.50e+03 pdb=" O THRL2 50 " 0.021 2.00e-02 2.50e+03 pdb=" N VALL2 51 " 0.019 2.00e-02 2.50e+03 ... (remaining 10016 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 8235 2.67 - 3.23: 96640 3.23 - 3.79: 222577 3.79 - 4.34: 301052 4.34 - 4.90: 432807 Nonbonded interactions: 1061311 Sorted by model distance: nonbonded pdb=" OP1 A B 784 " pdb="MG MG B3012 " model vdw 2.118 2.170 nonbonded pdb=" OP2 U B1680 " pdb="MG MG B3009 " model vdw 2.121 2.170 nonbonded pdb=" O2' G B2007 " pdb=" OP2 U B2009 " model vdw 2.228 2.440 nonbonded pdb=" O2' G B1492 " pdb=" O2' A B1575 " model vdw 2.229 2.440 nonbonded pdb=" OP1 G B2298 " pdb=" OG SERL9 26 " model vdw 2.236 2.440 ... (remaining 1061306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 11.310 Check model and map are aligned: 1.340 Set scattering table: 0.840 Process input model: 356.550 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.270 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:1.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 376.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 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 : 0.008 0.084 137622 Z= 0.467 Angle : 0.985 19.746 207462 Z= 0.484 Chirality : 0.049 0.396 26811 Planarity : 0.006 0.068 10019 Dihedral : 23.636 179.686 80459 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.80 % Favored : 88.08 % Rotamer: Outliers : 0.38 % Allowed : 2.40 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -5.19 (0.10), residues: 4076 helix: -4.76 (0.07), residues: 833 sheet: -2.66 (0.17), residues: 706 loop : -3.38 (0.09), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.005 TRPL2 213 HIS 0.026 0.003 HISL5 102 PHE 0.043 0.004 PHELB 30 TYR 0.041 0.004 TYRSE 60 ARG 0.018 0.002 ARGLE 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 946 time to evaluate : 4.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILEL1 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILEL4 100 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSL5 111 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHEL6 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSL7 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILEL8 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULF 47 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ARGLM 144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLO 145 " (corrupted residue). Skipping it. REVERT: S3 14 SER cc_start: 0.8820 (p) cc_final: 0.8535 (t) REVERT: S3 74 ILE cc_start: 0.5660 (OUTLIER) cc_final: 0.4801 (tp) REVERT: S6 69 TYR cc_start: 0.5550 (t80) cc_final: 0.5201 (t80) REVERT: S8 73 LYS cc_start: 0.6302 (ttmt) cc_final: 0.5905 (mmtt) REVERT: S9 70 MET cc_start: 0.7051 (mmm) cc_final: 0.6066 (mmt) REVERT: SD 18 ILE cc_start: 0.7899 (pt) cc_final: 0.7665 (pt) REVERT: SF 65 LYS cc_start: 0.7153 (tttm) cc_final: 0.6668 (ttpt) REVERT: L1 23 ARG cc_start: 0.6809 (mmt90) cc_final: 0.5798 (mpt180) REVERT: L2 60 ARG cc_start: 0.8785 (mtt180) cc_final: 0.8583 (mtt180) REVERT: L2 139 THR cc_start: 0.8576 (m) cc_final: 0.8042 (p) REVERT: L2 255 LEU cc_start: 0.7843 (tp) cc_final: 0.7290 (tp) REVERT: L2 266 SER cc_start: 0.7782 (m) cc_final: 0.7438 (t) REVERT: L4 28 ASN cc_start: 0.8243 (m-40) cc_final: 0.7993 (m110) REVERT: L5 98 LYS cc_start: 0.7237 (tttp) cc_final: 0.6552 (mtpp) REVERT: L6 75 ARG cc_start: 0.7651 (ptt90) cc_final: 0.7311 (ptt180) REVERT: L9 19 LYS cc_start: 0.8813 (mtpt) cc_final: 0.8441 (mtmm) REVERT: LA 3 LYS cc_start: 0.8843 (mtmm) cc_final: 0.8505 (mtmm) REVERT: LB 5 GLU cc_start: 0.7422 (mp0) cc_final: 0.7157 (mp0) REVERT: LE 21 LYS cc_start: 0.9159 (ptpt) cc_final: 0.8895 (ptpp) REVERT: LG 42 VAL cc_start: 0.8480 (t) cc_final: 0.8241 (m) outliers start: 13 outliers final: 6 residues processed: 955 average time/residue: 1.1597 time to fit residues: 1831.2018 Evaluate side-chains 678 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 671 time to evaluate : 4.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S3 residue 74 ILE Chi-restraints excluded: chain SD residue 106 ILE Chi-restraints excluded: chain L2 residue 219 THR Chi-restraints excluded: chain L6 residue 6 ILE Chi-restraints excluded: chain LM residue 85 ILE Chi-restraints excluded: chain LO residue 145 VAL Chi-restraints excluded: chain LP residue 68 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 704 optimal weight: 2.9990 chunk 632 optimal weight: 1.9990 chunk 350 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 426 optimal weight: 5.9990 chunk 337 optimal weight: 4.9990 chunk 653 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 397 optimal weight: 8.9990 chunk 486 optimal weight: 10.0000 chunk 757 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S2 18 ASN S2 77 HIS S3 25 ASN S3 72 ASN S6 37 ASN S6 42 HIS S7 41 ASN S7 62 ASN SC 8 ASN SC 85 ASN SF 48 ASN SF 99 ASN L2 11 ASN L2 86 ASN L2 232 HIS L3 44 GLN L5 77 ASN L7 2 HIS L9 37 GLN ** LB 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 66 ASN LC 145 HIS ** LE 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 25 ASN LF 40 ASN LJ 46 GLN LJ 148 GLN LL 48 ASN LL 73 ASN LL 74 ASN LL 77 GLN LM 11 ASN LM 24 GLN LM 59 ASN LO 104 ASN LP 35 GLN LR 37 ASN LR 48 ASN ** LR 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 137622 Z= 0.225 Angle : 0.665 11.569 207462 Z= 0.340 Chirality : 0.038 0.303 26811 Planarity : 0.005 0.066 10019 Dihedral : 24.321 179.133 72304 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.54 % Favored : 90.38 % Rotamer: Outliers : 2.57 % Allowed : 9.30 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -4.53 (0.11), residues: 4076 helix: -3.94 (0.11), residues: 882 sheet: -2.28 (0.18), residues: 773 loop : -2.99 (0.10), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPL2 213 HIS 0.008 0.001 HISL5 102 PHE 0.018 0.002 PHELB 30 TYR 0.020 0.002 TYRSE 8 ARG 0.020 0.001 ARGLL 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 700 time to evaluate : 4.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILEL1 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILEL4 100 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSL5 111 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHEL6 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSL7 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILEL8 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLULF 47 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ARGLM 144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULP 136 " (corrupted residue). Skipping it. REVERT: S3 14 SER cc_start: 0.8820 (p) cc_final: 0.8522 (t) REVERT: S8 73 LYS cc_start: 0.6047 (ttmt) cc_final: 0.5712 (mmtt) REVERT: S9 70 MET cc_start: 0.7088 (mmm) cc_final: 0.6130 (mmt) REVERT: SC 108 ARG cc_start: 0.5127 (mmm-85) cc_final: 0.3861 (ptp90) REVERT: SF 65 LYS cc_start: 0.7186 (tttm) cc_final: 0.6869 (ttpt) REVERT: L1 23 ARG cc_start: 0.6650 (mmt90) cc_final: 0.6319 (ptp90) REVERT: L2 255 LEU cc_start: 0.7650 (tp) cc_final: 0.7172 (tp) REVERT: L2 266 SER cc_start: 0.7913 (m) cc_final: 0.7616 (t) REVERT: L4 23 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: L6 75 ARG cc_start: 0.7740 (ptt90) cc_final: 0.7491 (ptt90) REVERT: L9 19 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8374 (mtmm) REVERT: L9 84 LYS cc_start: 0.8481 (mmtt) cc_final: 0.8241 (mmtm) REVERT: LA 17 ARG cc_start: 0.8133 (ttm-80) cc_final: 0.7862 (ttm-80) REVERT: LA 36 VAL cc_start: 0.8873 (p) cc_final: 0.8584 (m) REVERT: LE 21 LYS cc_start: 0.9107 (ptpt) cc_final: 0.8833 (ptpp) REVERT: LG 42 VAL cc_start: 0.8495 (t) cc_final: 0.8278 (m) REVERT: LL 104 ILE cc_start: 0.6633 (OUTLIER) cc_final: 0.6047 (tt) REVERT: LO 64 ARG cc_start: 0.8418 (ttt90) cc_final: 0.8187 (ttt90) outliers start: 88 outliers final: 57 residues processed: 743 average time/residue: 1.2303 time to fit residues: 1548.6911 Evaluate side-chains 698 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 639 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S3 residue 36 THR Chi-restraints excluded: chain S3 residue 74 ILE Chi-restraints excluded: chain S3 residue 106 VAL Chi-restraints excluded: chain S3 residue 117 THR Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S7 residue 3 VAL Chi-restraints excluded: chain S7 residue 41 ASN Chi-restraints excluded: chain S7 residue 70 THR Chi-restraints excluded: chain SC residue 71 THR Chi-restraints excluded: chain SC residue 182 ARG Chi-restraints excluded: chain SD residue 84 THR Chi-restraints excluded: chain SD residue 106 ILE Chi-restraints excluded: chain SF residue 46 ILE Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain L1 residue 62 THR Chi-restraints excluded: chain L1 residue 83 ILE Chi-restraints excluded: chain L2 residue 17 THR Chi-restraints excluded: chain L2 residue 24 ILE Chi-restraints excluded: chain L2 residue 27 THR Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 112 VAL Chi-restraints excluded: chain L2 residue 115 ILE Chi-restraints excluded: chain L2 residue 219 THR Chi-restraints excluded: chain L4 residue 19 GLU Chi-restraints excluded: chain L4 residue 20 ILE Chi-restraints excluded: chain L4 residue 23 GLU Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L6 residue 6 ILE Chi-restraints excluded: chain L6 residue 17 SER Chi-restraints excluded: chain L6 residue 28 ASP Chi-restraints excluded: chain L7 residue 26 THR Chi-restraints excluded: chain L7 residue 40 ILE Chi-restraints excluded: chain L8 residue 60 VAL Chi-restraints excluded: chain L8 residue 92 LEU Chi-restraints excluded: chain LC residue 65 SER Chi-restraints excluded: chain LC residue 115 VAL Chi-restraints excluded: chain LD residue 7 THR Chi-restraints excluded: chain LF residue 32 MET Chi-restraints excluded: chain LG residue 41 LYS Chi-restraints excluded: chain LH residue 55 MET Chi-restraints excluded: chain LI residue 16 VAL Chi-restraints excluded: chain LJ residue 7 LEU Chi-restraints excluded: chain LJ residue 96 SER Chi-restraints excluded: chain LJ residue 163 VAL Chi-restraints excluded: chain LJ residue 165 LEU Chi-restraints excluded: chain LJ residue 182 ASN Chi-restraints excluded: chain LL residue 17 VAL Chi-restraints excluded: chain LL residue 104 ILE Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LN residue 116 SER Chi-restraints excluded: chain LO residue 23 VAL Chi-restraints excluded: chain LO residue 42 SER Chi-restraints excluded: chain LO residue 46 VAL Chi-restraints excluded: chain LO residue 102 VAL Chi-restraints excluded: chain LO residue 131 SER Chi-restraints excluded: chain LP residue 68 ILE Chi-restraints excluded: chain LQ residue 42 SER Chi-restraints excluded: chain LQ residue 103 ILE Chi-restraints excluded: chain LR residue 89 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 420 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 630 optimal weight: 6.9990 chunk 515 optimal weight: 10.0000 chunk 208 optimal weight: 0.6980 chunk 758 optimal weight: 1.9990 chunk 819 optimal weight: 9.9990 chunk 675 optimal weight: 6.9990 chunk 752 optimal weight: 2.9990 chunk 258 optimal weight: 20.0000 chunk 608 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S2 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S6 65 HIS S7 41 ASN ** S8 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S8 53 ASN SC 118 HIS SF 99 ASN L5 60 HIS LA 34 GLN ** LB 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 14 GLN ** LE 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 148 GLN LL 77 GLN LM 11 ASN LM 24 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 137622 Z= 0.248 Angle : 0.643 11.985 207462 Z= 0.330 Chirality : 0.037 0.294 26811 Planarity : 0.005 0.063 10019 Dihedral : 24.216 178.614 72301 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.43 % Favored : 89.52 % Rotamer: Outliers : 3.68 % Allowed : 10.58 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -4.05 (0.11), residues: 4076 helix: -3.26 (0.13), residues: 883 sheet: -2.02 (0.18), residues: 752 loop : -2.78 (0.11), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPL2 213 HIS 0.010 0.002 HISL5 102 PHE 0.017 0.002 PHELO 66 TYR 0.017 0.002 TYRSE 8 ARG 0.007 0.001 ARGL1 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 659 time to evaluate : 4.834 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILEL1 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSL5 111 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHEL6 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSL7 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILEL8 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLULF 47 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARGLM 144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULP 136 " (corrupted residue). Skipping it. REVERT: S3 14 SER cc_start: 0.8847 (p) cc_final: 0.8519 (t) REVERT: S8 73 LYS cc_start: 0.6062 (ttmt) cc_final: 0.5674 (mmtt) REVERT: SC 108 ARG cc_start: 0.5293 (mmm-85) cc_final: 0.4281 (ptp-170) REVERT: L1 23 ARG cc_start: 0.6754 (mmt90) cc_final: 0.6266 (ptp90) REVERT: L1 42 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7893 (mp) REVERT: L2 139 THR cc_start: 0.8582 (m) cc_final: 0.8125 (p) REVERT: L2 255 LEU cc_start: 0.7646 (tp) cc_final: 0.7204 (tp) REVERT: L2 266 SER cc_start: 0.7952 (m) cc_final: 0.7669 (t) REVERT: L4 23 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: L6 75 ARG cc_start: 0.7693 (ptt90) cc_final: 0.7360 (ptt90) REVERT: L9 84 LYS cc_start: 0.8484 (mmtt) cc_final: 0.8276 (mmtm) REVERT: LA 36 VAL cc_start: 0.8878 (p) cc_final: 0.8611 (m) REVERT: LB 30 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: LC 190 GLU cc_start: 0.5884 (OUTLIER) cc_final: 0.5670 (pt0) REVERT: LE 21 LYS cc_start: 0.9013 (ptpt) cc_final: 0.8804 (ptpp) REVERT: LE 27 MET cc_start: 0.7362 (ptp) cc_final: 0.7010 (ptp) REVERT: LG 41 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7720 (ttpp) REVERT: LG 42 VAL cc_start: 0.8526 (t) cc_final: 0.8246 (m) REVERT: LJ 35 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6868 (mp0) REVERT: LL 50 ILE cc_start: 0.7119 (mp) cc_final: 0.6880 (pt) REVERT: LM 12 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6805 (pp) outliers start: 126 outliers final: 95 residues processed: 729 average time/residue: 1.1000 time to fit residues: 1367.3961 Evaluate side-chains 718 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 617 time to evaluate : 4.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 67 SER Chi-restraints excluded: chain S3 residue 74 ILE Chi-restraints excluded: chain S3 residue 106 VAL Chi-restraints excluded: chain S3 residue 117 THR Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S7 residue 3 VAL Chi-restraints excluded: chain S7 residue 68 THR Chi-restraints excluded: chain S7 residue 70 THR Chi-restraints excluded: chain S8 residue 40 VAL Chi-restraints excluded: chain S8 residue 72 THR Chi-restraints excluded: chain SC residue 71 THR Chi-restraints excluded: chain SC residue 182 ARG Chi-restraints excluded: chain SD residue 84 THR Chi-restraints excluded: chain SD residue 106 ILE Chi-restraints excluded: chain SD residue 134 ILE Chi-restraints excluded: chain SE residue 62 ILE Chi-restraints excluded: chain SF residue 10 MET Chi-restraints excluded: chain SF residue 38 GLU Chi-restraints excluded: chain SF residue 46 ILE Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain L1 residue 32 VAL Chi-restraints excluded: chain L1 residue 42 ILE Chi-restraints excluded: chain L1 residue 62 THR Chi-restraints excluded: chain L1 residue 63 VAL Chi-restraints excluded: chain L1 residue 78 LEU Chi-restraints excluded: chain L1 residue 83 ILE Chi-restraints excluded: chain L2 residue 17 THR Chi-restraints excluded: chain L2 residue 24 ILE Chi-restraints excluded: chain L2 residue 27 THR Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 112 VAL Chi-restraints excluded: chain L2 residue 115 ILE Chi-restraints excluded: chain L2 residue 192 ILE Chi-restraints excluded: chain L2 residue 195 VAL Chi-restraints excluded: chain L2 residue 219 THR Chi-restraints excluded: chain L3 residue 77 SER Chi-restraints excluded: chain L4 residue 6 GLU Chi-restraints excluded: chain L4 residue 19 GLU Chi-restraints excluded: chain L4 residue 20 ILE Chi-restraints excluded: chain L4 residue 23 GLU Chi-restraints excluded: chain L4 residue 41 VAL Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L6 residue 6 ILE Chi-restraints excluded: chain L6 residue 28 ASP Chi-restraints excluded: chain L6 residue 42 VAL Chi-restraints excluded: chain L7 residue 26 THR Chi-restraints excluded: chain L7 residue 40 ILE Chi-restraints excluded: chain L7 residue 63 ILE Chi-restraints excluded: chain L8 residue 60 VAL Chi-restraints excluded: chain L8 residue 70 ILE Chi-restraints excluded: chain L8 residue 92 LEU Chi-restraints excluded: chain L9 residue 72 ASP Chi-restraints excluded: chain LB residue 30 PHE Chi-restraints excluded: chain LC residue 65 SER Chi-restraints excluded: chain LC residue 115 VAL Chi-restraints excluded: chain LC residue 152 SER Chi-restraints excluded: chain LC residue 190 GLU Chi-restraints excluded: chain LD residue 7 THR Chi-restraints excluded: chain LD residue 54 VAL Chi-restraints excluded: chain LD residue 57 GLU Chi-restraints excluded: chain LE residue 3 VAL Chi-restraints excluded: chain LF residue 16 ASN Chi-restraints excluded: chain LF residue 32 MET Chi-restraints excluded: chain LG residue 41 LYS Chi-restraints excluded: chain LH residue 14 VAL Chi-restraints excluded: chain LH residue 49 LEU Chi-restraints excluded: chain LH residue 55 MET Chi-restraints excluded: chain LI residue 16 VAL Chi-restraints excluded: chain LJ residue 7 LEU Chi-restraints excluded: chain LJ residue 96 SER Chi-restraints excluded: chain LJ residue 123 LEU Chi-restraints excluded: chain LJ residue 163 VAL Chi-restraints excluded: chain LJ residue 165 LEU Chi-restraints excluded: chain LJ residue 182 ASN Chi-restraints excluded: chain LJ residue 190 ASP Chi-restraints excluded: chain LJ residue 202 VAL Chi-restraints excluded: chain LL residue 4 VAL Chi-restraints excluded: chain LL residue 37 LEU Chi-restraints excluded: chain LL residue 52 VAL Chi-restraints excluded: chain LL residue 68 THR Chi-restraints excluded: chain LL residue 86 VAL Chi-restraints excluded: chain LM residue 12 ILE Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 85 ILE Chi-restraints excluded: chain LN residue 6 THR Chi-restraints excluded: chain LN residue 63 VAL Chi-restraints excluded: chain LN residue 116 SER Chi-restraints excluded: chain LN residue 117 LEU Chi-restraints excluded: chain LO residue 23 VAL Chi-restraints excluded: chain LO residue 42 SER Chi-restraints excluded: chain LO residue 46 VAL Chi-restraints excluded: chain LO residue 102 VAL Chi-restraints excluded: chain LP residue 37 THR Chi-restraints excluded: chain LP residue 68 ILE Chi-restraints excluded: chain LP residue 120 LEU Chi-restraints excluded: chain LQ residue 42 SER Chi-restraints excluded: chain LQ residue 44 VAL Chi-restraints excluded: chain LQ residue 103 ILE Chi-restraints excluded: chain LR residue 89 ILE Chi-restraints excluded: chain LR residue 113 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 749 optimal weight: 7.9990 chunk 570 optimal weight: 0.8980 chunk 393 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 362 optimal weight: 10.0000 chunk 509 optimal weight: 10.0000 chunk 761 optimal weight: 3.9990 chunk 806 optimal weight: 5.9990 chunk 397 optimal weight: 10.0000 chunk 721 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S2 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S6 65 HIS S7 41 ASN ** S8 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SC 67 GLN SC 118 HIS SF 99 ASN L4 28 ASN L6 69 GLN L8 20 GLN LA 34 GLN ** LB 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 14 GLN LC 166 GLN ** LE 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 46 GLN LJ 174 GLN LM 11 ASN ** LR 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 137622 Z= 0.247 Angle : 0.629 13.002 207462 Z= 0.322 Chirality : 0.037 0.300 26811 Planarity : 0.005 0.057 10019 Dihedral : 24.133 178.453 72301 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.16 % Favored : 89.82 % Rotamer: Outliers : 3.95 % Allowed : 12.31 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.12), residues: 4076 helix: -2.97 (0.14), residues: 893 sheet: -1.86 (0.18), residues: 764 loop : -2.71 (0.11), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPL2 213 HIS 0.008 0.001 HISL5 102 PHE 0.016 0.002 PHELO 66 TYR 0.019 0.002 TYRS6 78 ARG 0.008 0.001 ARGS6 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 648 time to evaluate : 4.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILEL1 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSL5 111 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHEL6 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSL7 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILEL8 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLULF 47 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARGLM 144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULP 136 " (corrupted residue). Skipping it. REVERT: S3 14 SER cc_start: 0.8907 (p) cc_final: 0.8526 (t) REVERT: S6 83 LYS cc_start: 0.6382 (pttt) cc_final: 0.6028 (ptmm) REVERT: S7 41 ASN cc_start: 0.5651 (OUTLIER) cc_final: 0.4799 (m110) REVERT: S8 73 LYS cc_start: 0.5948 (ttmt) cc_final: 0.5664 (mmtt) REVERT: SC 108 ARG cc_start: 0.5345 (mmm-85) cc_final: 0.4268 (ptp-170) REVERT: L1 23 ARG cc_start: 0.6679 (mmt90) cc_final: 0.6192 (ptp90) REVERT: L1 42 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7923 (mp) REVERT: L4 23 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: L8 79 PHE cc_start: 0.7322 (t80) cc_final: 0.7082 (t80) REVERT: L9 84 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8294 (mmtm) REVERT: LA 36 VAL cc_start: 0.8847 (p) cc_final: 0.8576 (m) REVERT: LB 30 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: LD 44 ARG cc_start: 0.7965 (tpp80) cc_final: 0.7685 (tpp80) REVERT: LE 27 MET cc_start: 0.7392 (ptp) cc_final: 0.7071 (ptp) REVERT: LG 42 VAL cc_start: 0.8557 (t) cc_final: 0.8301 (m) REVERT: LJ 35 GLU cc_start: 0.7539 (mt-10) cc_final: 0.6891 (mp0) REVERT: LM 12 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6717 (pp) REVERT: LN 112 MET cc_start: 0.6717 (mmm) cc_final: 0.6376 (ttt) outliers start: 135 outliers final: 103 residues processed: 719 average time/residue: 1.2107 time to fit residues: 1487.6300 Evaluate side-chains 722 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 614 time to evaluate : 4.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S3 residue 74 ILE Chi-restraints excluded: chain S3 residue 106 VAL Chi-restraints excluded: chain S3 residue 117 THR Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S7 residue 41 ASN Chi-restraints excluded: chain S7 residue 68 THR Chi-restraints excluded: chain S7 residue 70 THR Chi-restraints excluded: chain S8 residue 65 GLU Chi-restraints excluded: chain S8 residue 72 THR Chi-restraints excluded: chain S8 residue 83 GLU Chi-restraints excluded: chain SC residue 71 THR Chi-restraints excluded: chain SC residue 182 ARG Chi-restraints excluded: chain SD residue 84 THR Chi-restraints excluded: chain SD residue 106 ILE Chi-restraints excluded: chain SD residue 134 ILE Chi-restraints excluded: chain SE residue 91 VAL Chi-restraints excluded: chain SF residue 46 ILE Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain L1 residue 42 ILE Chi-restraints excluded: chain L1 residue 62 THR Chi-restraints excluded: chain L1 residue 63 VAL Chi-restraints excluded: chain L1 residue 78 LEU Chi-restraints excluded: chain L1 residue 83 ILE Chi-restraints excluded: chain L2 residue 17 THR Chi-restraints excluded: chain L2 residue 24 ILE Chi-restraints excluded: chain L2 residue 27 THR Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 112 VAL Chi-restraints excluded: chain L2 residue 115 ILE Chi-restraints excluded: chain L2 residue 192 ILE Chi-restraints excluded: chain L2 residue 195 VAL Chi-restraints excluded: chain L2 residue 219 THR Chi-restraints excluded: chain L2 residue 226 ASN Chi-restraints excluded: chain L3 residue 77 SER Chi-restraints excluded: chain L4 residue 6 GLU Chi-restraints excluded: chain L4 residue 19 GLU Chi-restraints excluded: chain L4 residue 20 ILE Chi-restraints excluded: chain L4 residue 23 GLU Chi-restraints excluded: chain L4 residue 41 VAL Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L5 residue 97 ASN Chi-restraints excluded: chain L6 residue 6 ILE Chi-restraints excluded: chain L6 residue 28 ASP Chi-restraints excluded: chain L6 residue 42 VAL Chi-restraints excluded: chain L7 residue 26 THR Chi-restraints excluded: chain L7 residue 63 ILE Chi-restraints excluded: chain L8 residue 60 VAL Chi-restraints excluded: chain L8 residue 70 ILE Chi-restraints excluded: chain L8 residue 92 LEU Chi-restraints excluded: chain L9 residue 72 ASP Chi-restraints excluded: chain LA residue 38 ILE Chi-restraints excluded: chain LB residue 30 PHE Chi-restraints excluded: chain LB residue 45 THR Chi-restraints excluded: chain LC residue 115 VAL Chi-restraints excluded: chain LC residue 152 SER Chi-restraints excluded: chain LD residue 7 THR Chi-restraints excluded: chain LD residue 36 VAL Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 54 VAL Chi-restraints excluded: chain LD residue 57 GLU Chi-restraints excluded: chain LE residue 3 VAL Chi-restraints excluded: chain LF residue 16 ASN Chi-restraints excluded: chain LF residue 32 MET Chi-restraints excluded: chain LG residue 41 LYS Chi-restraints excluded: chain LH residue 14 VAL Chi-restraints excluded: chain LH residue 49 LEU Chi-restraints excluded: chain LH residue 55 MET Chi-restraints excluded: chain LI residue 16 VAL Chi-restraints excluded: chain LJ residue 7 LEU Chi-restraints excluded: chain LJ residue 123 LEU Chi-restraints excluded: chain LJ residue 129 PHE Chi-restraints excluded: chain LJ residue 163 VAL Chi-restraints excluded: chain LJ residue 165 LEU Chi-restraints excluded: chain LJ residue 182 ASN Chi-restraints excluded: chain LJ residue 190 ASP Chi-restraints excluded: chain LJ residue 202 VAL Chi-restraints excluded: chain LL residue 4 VAL Chi-restraints excluded: chain LL residue 17 VAL Chi-restraints excluded: chain LL residue 37 LEU Chi-restraints excluded: chain LL residue 50 ILE Chi-restraints excluded: chain LL residue 52 VAL Chi-restraints excluded: chain LL residue 68 THR Chi-restraints excluded: chain LL residue 86 VAL Chi-restraints excluded: chain LL residue 121 ILE Chi-restraints excluded: chain LM residue 12 ILE Chi-restraints excluded: chain LM residue 30 SER Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 85 ILE Chi-restraints excluded: chain LM residue 99 GLU Chi-restraints excluded: chain LN residue 6 THR Chi-restraints excluded: chain LN residue 63 VAL Chi-restraints excluded: chain LN residue 116 SER Chi-restraints excluded: chain LN residue 117 LEU Chi-restraints excluded: chain LO residue 12 SER Chi-restraints excluded: chain LO residue 23 VAL Chi-restraints excluded: chain LO residue 42 SER Chi-restraints excluded: chain LO residue 46 VAL Chi-restraints excluded: chain LP residue 7 VAL Chi-restraints excluded: chain LP residue 37 THR Chi-restraints excluded: chain LP residue 68 ILE Chi-restraints excluded: chain LP residue 120 LEU Chi-restraints excluded: chain LQ residue 42 SER Chi-restraints excluded: chain LQ residue 103 ILE Chi-restraints excluded: chain LR residue 45 ILE Chi-restraints excluded: chain LR residue 57 SER Chi-restraints excluded: chain LR residue 89 ILE Chi-restraints excluded: chain LR residue 113 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 671 optimal weight: 6.9990 chunk 457 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 600 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 687 optimal weight: 9.9990 chunk 557 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 411 optimal weight: 9.9990 chunk 723 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S2 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S8 49 HIS SC 50 GLN SC 118 HIS SC 159 ASN SE 77 GLN SF 99 ASN L3 38 GLN L4 63 ASN ** L5 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 69 GLN L8 20 GLN LA 34 GLN ** LB 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 166 GLN LD 40 ASN ** LE 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 174 GLN ** LL 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LM 11 ASN ** LR 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 137622 Z= 0.363 Angle : 0.749 12.074 207462 Z= 0.376 Chirality : 0.041 0.323 26811 Planarity : 0.006 0.058 10019 Dihedral : 24.259 178.746 72301 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.71 % Favored : 87.24 % Rotamer: Outliers : 4.68 % Allowed : 13.39 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.12), residues: 4076 helix: -2.92 (0.14), residues: 894 sheet: -1.88 (0.18), residues: 776 loop : -2.77 (0.11), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPL2 213 HIS 0.010 0.002 HISL5 102 PHE 0.021 0.002 PHELO 66 TYR 0.027 0.002 TYRLP 9 ARG 0.010 0.001 ARGS7 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 630 time to evaluate : 4.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILEL1 115 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSL5 111 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHEL6 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSL7 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILEL8 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLULF 47 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARGLM 144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLO 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULP 136 " (corrupted residue). Skipping it. REVERT: S2 18 ASN cc_start: 0.5502 (m-40) cc_final: 0.4973 (m-40) REVERT: S3 14 SER cc_start: 0.8935 (p) cc_final: 0.8535 (t) REVERT: S6 83 LYS cc_start: 0.6627 (pttt) cc_final: 0.6009 (ptmm) REVERT: S8 73 LYS cc_start: 0.6110 (ttmt) cc_final: 0.5564 (mmtt) REVERT: SD 57 PRO cc_start: 0.7133 (Cg_exo) cc_final: 0.6930 (Cg_exo) REVERT: L1 23 ARG cc_start: 0.6790 (mmt90) cc_final: 0.6253 (ptp90) REVERT: L1 42 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7994 (mp) REVERT: L1 87 GLU cc_start: 0.7693 (pt0) cc_final: 0.7429 (pt0) REVERT: L4 23 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: L5 83 LYS cc_start: 0.8415 (mttt) cc_final: 0.7801 (mtmm) REVERT: LA 36 VAL cc_start: 0.8855 (p) cc_final: 0.8584 (m) REVERT: LB 30 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: LC 128 GLN cc_start: 0.6725 (OUTLIER) cc_final: 0.6391 (mp10) REVERT: LD 44 ARG cc_start: 0.8008 (tpp80) cc_final: 0.7745 (tpp80) REVERT: LE 27 MET cc_start: 0.7443 (ptp) cc_final: 0.7165 (ptp) REVERT: LG 42 VAL cc_start: 0.8573 (t) cc_final: 0.8282 (m) REVERT: LJ 132 GLU cc_start: 0.6573 (mp0) cc_final: 0.6248 (mt-10) REVERT: LM 12 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6874 (pp) REVERT: LN 66 LYS cc_start: 0.8878 (ttmm) cc_final: 0.8619 (ttmt) REVERT: LN 110 ASN cc_start: 0.6971 (OUTLIER) cc_final: 0.6377 (p0) REVERT: LN 112 MET cc_start: 0.6530 (mmm) cc_final: 0.6282 (ttt) outliers start: 160 outliers final: 130 residues processed: 726 average time/residue: 1.0918 time to fit residues: 1350.4094 Evaluate side-chains 747 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 611 time to evaluate : 4.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S3 residue 7 LEU Chi-restraints excluded: chain S3 residue 74 ILE Chi-restraints excluded: chain S3 residue 106 VAL Chi-restraints excluded: chain S3 residue 117 THR Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S7 residue 3 VAL Chi-restraints excluded: chain S7 residue 68 THR Chi-restraints excluded: chain S7 residue 70 THR Chi-restraints excluded: chain S8 residue 40 VAL Chi-restraints excluded: chain S8 residue 72 THR Chi-restraints excluded: chain S8 residue 83 GLU Chi-restraints excluded: chain SC residue 46 GLU Chi-restraints excluded: chain SC residue 71 THR Chi-restraints excluded: chain SC residue 182 ARG Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 80 THR Chi-restraints excluded: chain SD residue 84 THR Chi-restraints excluded: chain SD residue 85 ILE Chi-restraints excluded: chain SD residue 106 ILE Chi-restraints excluded: chain SD residue 134 ILE Chi-restraints excluded: chain SE residue 62 ILE Chi-restraints excluded: chain SE residue 91 VAL Chi-restraints excluded: chain SF residue 38 GLU Chi-restraints excluded: chain SF residue 46 ILE Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain L1 residue 32 VAL Chi-restraints excluded: chain L1 residue 42 ILE Chi-restraints excluded: chain L1 residue 62 THR Chi-restraints excluded: chain L1 residue 63 VAL Chi-restraints excluded: chain L1 residue 78 LEU Chi-restraints excluded: chain L1 residue 83 ILE Chi-restraints excluded: chain L1 residue 99 LEU Chi-restraints excluded: chain L2 residue 10 THR Chi-restraints excluded: chain L2 residue 17 THR Chi-restraints excluded: chain L2 residue 24 ILE Chi-restraints excluded: chain L2 residue 27 THR Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 112 VAL Chi-restraints excluded: chain L2 residue 115 ILE Chi-restraints excluded: chain L2 residue 139 THR Chi-restraints excluded: chain L2 residue 192 ILE Chi-restraints excluded: chain L2 residue 195 VAL Chi-restraints excluded: chain L2 residue 219 THR Chi-restraints excluded: chain L2 residue 226 ASN Chi-restraints excluded: chain L3 residue 77 SER Chi-restraints excluded: chain L3 residue 88 ILE Chi-restraints excluded: chain L4 residue 6 GLU Chi-restraints excluded: chain L4 residue 19 GLU Chi-restraints excluded: chain L4 residue 20 ILE Chi-restraints excluded: chain L4 residue 23 GLU Chi-restraints excluded: chain L4 residue 41 VAL Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L5 residue 97 ASN Chi-restraints excluded: chain L6 residue 6 ILE Chi-restraints excluded: chain L6 residue 17 SER Chi-restraints excluded: chain L6 residue 28 ASP Chi-restraints excluded: chain L6 residue 34 ASN Chi-restraints excluded: chain L6 residue 42 VAL Chi-restraints excluded: chain L7 residue 26 THR Chi-restraints excluded: chain L7 residue 63 ILE Chi-restraints excluded: chain L7 residue 65 VAL Chi-restraints excluded: chain L8 residue 60 VAL Chi-restraints excluded: chain L8 residue 70 ILE Chi-restraints excluded: chain L8 residue 92 LEU Chi-restraints excluded: chain L9 residue 66 THR Chi-restraints excluded: chain L9 residue 72 ASP Chi-restraints excluded: chain LA residue 38 ILE Chi-restraints excluded: chain LB residue 30 PHE Chi-restraints excluded: chain LB residue 45 THR Chi-restraints excluded: chain LC residue 115 VAL Chi-restraints excluded: chain LC residue 121 VAL Chi-restraints excluded: chain LC residue 128 GLN Chi-restraints excluded: chain LC residue 152 SER Chi-restraints excluded: chain LC residue 177 VAL Chi-restraints excluded: chain LD residue 7 THR Chi-restraints excluded: chain LD residue 33 SER Chi-restraints excluded: chain LD residue 36 VAL Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 54 VAL Chi-restraints excluded: chain LD residue 57 GLU Chi-restraints excluded: chain LE residue 3 VAL Chi-restraints excluded: chain LF residue 16 ASN Chi-restraints excluded: chain LF residue 32 MET Chi-restraints excluded: chain LH residue 49 LEU Chi-restraints excluded: chain LH residue 55 MET Chi-restraints excluded: chain LI residue 16 VAL Chi-restraints excluded: chain LJ residue 7 LEU Chi-restraints excluded: chain LJ residue 96 SER Chi-restraints excluded: chain LJ residue 123 LEU Chi-restraints excluded: chain LJ residue 129 PHE Chi-restraints excluded: chain LJ residue 135 LYS Chi-restraints excluded: chain LJ residue 163 VAL Chi-restraints excluded: chain LJ residue 165 LEU Chi-restraints excluded: chain LJ residue 182 ASN Chi-restraints excluded: chain LJ residue 190 ASP Chi-restraints excluded: chain LJ residue 202 VAL Chi-restraints excluded: chain LL residue 4 VAL Chi-restraints excluded: chain LL residue 17 VAL Chi-restraints excluded: chain LL residue 37 LEU Chi-restraints excluded: chain LL residue 50 ILE Chi-restraints excluded: chain LL residue 68 THR Chi-restraints excluded: chain LL residue 75 MET Chi-restraints excluded: chain LL residue 86 VAL Chi-restraints excluded: chain LL residue 121 ILE Chi-restraints excluded: chain LL residue 124 SER Chi-restraints excluded: chain LM residue 12 ILE Chi-restraints excluded: chain LM residue 30 SER Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 85 ILE Chi-restraints excluded: chain LM residue 99 GLU Chi-restraints excluded: chain LN residue 6 THR Chi-restraints excluded: chain LN residue 42 THR Chi-restraints excluded: chain LN residue 63 VAL Chi-restraints excluded: chain LN residue 110 ASN Chi-restraints excluded: chain LN residue 116 SER Chi-restraints excluded: chain LN residue 117 LEU Chi-restraints excluded: chain LO residue 12 SER Chi-restraints excluded: chain LO residue 23 VAL Chi-restraints excluded: chain LO residue 42 SER Chi-restraints excluded: chain LO residue 46 VAL Chi-restraints excluded: chain LO residue 145 VAL Chi-restraints excluded: chain LP residue 7 VAL Chi-restraints excluded: chain LP residue 37 THR Chi-restraints excluded: chain LP residue 68 ILE Chi-restraints excluded: chain LP residue 120 LEU Chi-restraints excluded: chain LQ residue 11 ASP Chi-restraints excluded: chain LQ residue 42 SER Chi-restraints excluded: chain LQ residue 44 VAL Chi-restraints excluded: chain LQ residue 103 ILE Chi-restraints excluded: chain LR residue 45 ILE Chi-restraints excluded: chain LR residue 57 SER Chi-restraints excluded: chain LR residue 63 ILE Chi-restraints excluded: chain LR residue 89 ILE Chi-restraints excluded: chain LR residue 113 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 271 optimal weight: 10.0000 chunk 725 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 473 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 806 optimal weight: 7.9990 chunk 669 optimal weight: 1.9990 chunk 373 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 266 optimal weight: 10.0000 chunk 423 optimal weight: 10.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S2 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S6 65 HIS S7 41 ASN L4 63 ASN ** L5 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 20 GLN ** LB 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LM 11 ASN LO 70 ASN LR 39 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 137622 Z= 0.431 Angle : 0.810 12.195 207462 Z= 0.403 Chirality : 0.044 0.347 26811 Planarity : 0.006 0.066 10019 Dihedral : 24.325 179.272 72301 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.56 % Favored : 87.39 % Rotamer: Outliers : 5.29 % Allowed : 14.97 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.11), residues: 4076 helix: -2.98 (0.14), residues: 902 sheet: -1.98 (0.19), residues: 756 loop : -2.85 (0.11), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPL2 213 HIS 0.011 0.002 HISL5 102 PHE 0.024 0.003 PHELO 66 TYR 0.023 0.003 TYRS8 36 ARG 0.012 0.001 ARGLQ 109 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 637 time to evaluate : 4.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSL5 111 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHEL6 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSL7 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILEL8 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULF 47 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARGLM 144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLO 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULP 136 " (corrupted residue). Skipping it. REVERT: S3 14 SER cc_start: 0.8954 (p) cc_final: 0.8531 (t) REVERT: S6 58 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8547 (mmmt) REVERT: S6 83 LYS cc_start: 0.6643 (pttt) cc_final: 0.6045 (ptmm) REVERT: S8 73 LYS cc_start: 0.5896 (ttmt) cc_final: 0.5376 (mmtt) REVERT: S8 75 PHE cc_start: 0.4880 (m-80) cc_final: 0.4583 (m-80) REVERT: SC 124 LYS cc_start: 0.6725 (tttm) cc_final: 0.6491 (tttp) REVERT: L1 23 ARG cc_start: 0.6885 (mmt90) cc_final: 0.6278 (ptp90) REVERT: L1 42 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7993 (mp) REVERT: L1 87 GLU cc_start: 0.7735 (pt0) cc_final: 0.7431 (pt0) REVERT: L4 23 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7772 (mt-10) REVERT: L5 2 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6211 (pt0) REVERT: L5 83 LYS cc_start: 0.8374 (mttt) cc_final: 0.7785 (mtmm) REVERT: L8 79 PHE cc_start: 0.7509 (t80) cc_final: 0.7306 (t80) REVERT: LB 30 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8338 (m-80) REVERT: LC 128 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6863 (mp10) REVERT: LD 44 ARG cc_start: 0.8034 (tpp80) cc_final: 0.7773 (tpp80) REVERT: LE 27 MET cc_start: 0.7441 (ptp) cc_final: 0.7232 (ptp) REVERT: LE 35 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5559 (mm-30) REVERT: LJ 132 GLU cc_start: 0.6821 (mp0) cc_final: 0.6444 (mt-10) REVERT: LM 12 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6807 (pp) REVERT: LN 66 LYS cc_start: 0.8941 (ttmm) cc_final: 0.8630 (ttmt) REVERT: LN 110 ASN cc_start: 0.7081 (OUTLIER) cc_final: 0.6468 (p0) REVERT: LN 112 MET cc_start: 0.6532 (mmm) cc_final: 0.6307 (ttt) outliers start: 181 outliers final: 149 residues processed: 747 average time/residue: 1.2436 time to fit residues: 1606.1912 Evaluate side-chains 768 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 611 time to evaluate : 4.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S3 residue 74 ILE Chi-restraints excluded: chain S3 residue 106 VAL Chi-restraints excluded: chain S3 residue 117 THR Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S7 residue 3 VAL Chi-restraints excluded: chain S7 residue 68 THR Chi-restraints excluded: chain S7 residue 70 THR Chi-restraints excluded: chain S8 residue 35 LEU Chi-restraints excluded: chain S8 residue 40 VAL Chi-restraints excluded: chain S8 residue 65 GLU Chi-restraints excluded: chain S8 residue 72 THR Chi-restraints excluded: chain S8 residue 83 GLU Chi-restraints excluded: chain SC residue 46 GLU Chi-restraints excluded: chain SC residue 71 THR Chi-restraints excluded: chain SC residue 182 ARG Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 80 THR Chi-restraints excluded: chain SD residue 84 THR Chi-restraints excluded: chain SD residue 85 ILE Chi-restraints excluded: chain SD residue 106 ILE Chi-restraints excluded: chain SD residue 134 ILE Chi-restraints excluded: chain SE residue 62 ILE Chi-restraints excluded: chain SE residue 91 VAL Chi-restraints excluded: chain SF residue 46 ILE Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain SF residue 106 VAL Chi-restraints excluded: chain SF residue 108 THR Chi-restraints excluded: chain L1 residue 32 VAL Chi-restraints excluded: chain L1 residue 42 ILE Chi-restraints excluded: chain L1 residue 50 ILE Chi-restraints excluded: chain L1 residue 62 THR Chi-restraints excluded: chain L1 residue 63 VAL Chi-restraints excluded: chain L1 residue 78 LEU Chi-restraints excluded: chain L1 residue 83 ILE Chi-restraints excluded: chain L1 residue 99 LEU Chi-restraints excluded: chain L2 residue 17 THR Chi-restraints excluded: chain L2 residue 24 ILE Chi-restraints excluded: chain L2 residue 27 THR Chi-restraints excluded: chain L2 residue 53 HIS Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 112 VAL Chi-restraints excluded: chain L2 residue 115 ILE Chi-restraints excluded: chain L2 residue 139 THR Chi-restraints excluded: chain L2 residue 192 ILE Chi-restraints excluded: chain L2 residue 195 VAL Chi-restraints excluded: chain L2 residue 219 THR Chi-restraints excluded: chain L2 residue 226 ASN Chi-restraints excluded: chain L3 residue 9 VAL Chi-restraints excluded: chain L3 residue 77 SER Chi-restraints excluded: chain L3 residue 88 ILE Chi-restraints excluded: chain L4 residue 6 GLU Chi-restraints excluded: chain L4 residue 19 GLU Chi-restraints excluded: chain L4 residue 20 ILE Chi-restraints excluded: chain L4 residue 23 GLU Chi-restraints excluded: chain L4 residue 34 THR Chi-restraints excluded: chain L4 residue 41 VAL Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L5 residue 2 GLU Chi-restraints excluded: chain L5 residue 11 ARG Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L5 residue 97 ASN Chi-restraints excluded: chain L6 residue 6 ILE Chi-restraints excluded: chain L6 residue 14 GLU Chi-restraints excluded: chain L6 residue 17 SER Chi-restraints excluded: chain L6 residue 28 ASP Chi-restraints excluded: chain L6 residue 29 VAL Chi-restraints excluded: chain L6 residue 34 ASN Chi-restraints excluded: chain L6 residue 42 VAL Chi-restraints excluded: chain L6 residue 80 VAL Chi-restraints excluded: chain L7 residue 8 ASN Chi-restraints excluded: chain L7 residue 26 THR Chi-restraints excluded: chain L7 residue 63 ILE Chi-restraints excluded: chain L7 residue 65 VAL Chi-restraints excluded: chain L8 residue 38 ASN Chi-restraints excluded: chain L8 residue 60 VAL Chi-restraints excluded: chain L8 residue 70 ILE Chi-restraints excluded: chain L8 residue 92 LEU Chi-restraints excluded: chain L9 residue 67 LEU Chi-restraints excluded: chain L9 residue 72 ASP Chi-restraints excluded: chain LA residue 38 ILE Chi-restraints excluded: chain LB residue 30 PHE Chi-restraints excluded: chain LB residue 32 LEU Chi-restraints excluded: chain LB residue 45 THR Chi-restraints excluded: chain LC residue 15 VAL Chi-restraints excluded: chain LC residue 115 VAL Chi-restraints excluded: chain LC residue 121 VAL Chi-restraints excluded: chain LC residue 128 GLN Chi-restraints excluded: chain LC residue 152 SER Chi-restraints excluded: chain LC residue 176 THR Chi-restraints excluded: chain LC residue 177 VAL Chi-restraints excluded: chain LD residue 7 THR Chi-restraints excluded: chain LD residue 33 SER Chi-restraints excluded: chain LD residue 36 VAL Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 54 VAL Chi-restraints excluded: chain LD residue 57 GLU Chi-restraints excluded: chain LE residue 3 VAL Chi-restraints excluded: chain LE residue 8 THR Chi-restraints excluded: chain LE residue 35 GLU Chi-restraints excluded: chain LF residue 16 ASN Chi-restraints excluded: chain LF residue 32 MET Chi-restraints excluded: chain LH residue 49 LEU Chi-restraints excluded: chain LI residue 16 VAL Chi-restraints excluded: chain LJ residue 7 LEU Chi-restraints excluded: chain LJ residue 53 ASN Chi-restraints excluded: chain LJ residue 70 THR Chi-restraints excluded: chain LJ residue 82 GLN Chi-restraints excluded: chain LJ residue 96 SER Chi-restraints excluded: chain LJ residue 123 LEU Chi-restraints excluded: chain LJ residue 129 PHE Chi-restraints excluded: chain LJ residue 135 LYS Chi-restraints excluded: chain LJ residue 152 VAL Chi-restraints excluded: chain LJ residue 163 VAL Chi-restraints excluded: chain LJ residue 165 LEU Chi-restraints excluded: chain LJ residue 182 ASN Chi-restraints excluded: chain LJ residue 190 ASP Chi-restraints excluded: chain LJ residue 202 VAL Chi-restraints excluded: chain LL residue 4 VAL Chi-restraints excluded: chain LL residue 17 VAL Chi-restraints excluded: chain LL residue 37 LEU Chi-restraints excluded: chain LL residue 52 VAL Chi-restraints excluded: chain LL residue 68 THR Chi-restraints excluded: chain LL residue 75 MET Chi-restraints excluded: chain LL residue 86 VAL Chi-restraints excluded: chain LL residue 121 ILE Chi-restraints excluded: chain LL residue 124 SER Chi-restraints excluded: chain LM residue 12 ILE Chi-restraints excluded: chain LM residue 30 SER Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 85 ILE Chi-restraints excluded: chain LM residue 88 ILE Chi-restraints excluded: chain LM residue 99 GLU Chi-restraints excluded: chain LN residue 6 THR Chi-restraints excluded: chain LN residue 42 THR Chi-restraints excluded: chain LN residue 63 VAL Chi-restraints excluded: chain LN residue 89 ASP Chi-restraints excluded: chain LN residue 110 ASN Chi-restraints excluded: chain LN residue 116 SER Chi-restraints excluded: chain LN residue 117 LEU Chi-restraints excluded: chain LO residue 12 SER Chi-restraints excluded: chain LO residue 23 VAL Chi-restraints excluded: chain LO residue 42 SER Chi-restraints excluded: chain LO residue 46 VAL Chi-restraints excluded: chain LO residue 145 VAL Chi-restraints excluded: chain LP residue 7 VAL Chi-restraints excluded: chain LP residue 37 THR Chi-restraints excluded: chain LP residue 68 ILE Chi-restraints excluded: chain LP residue 120 LEU Chi-restraints excluded: chain LQ residue 11 ASP Chi-restraints excluded: chain LQ residue 42 SER Chi-restraints excluded: chain LQ residue 44 VAL Chi-restraints excluded: chain LQ residue 103 ILE Chi-restraints excluded: chain LR residue 45 ILE Chi-restraints excluded: chain LR residue 63 ILE Chi-restraints excluded: chain LR residue 89 ILE Chi-restraints excluded: chain LR residue 113 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 777 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 459 optimal weight: 6.9990 chunk 589 optimal weight: 0.8980 chunk 456 optimal weight: 6.9990 chunk 679 optimal weight: 3.9990 chunk 450 optimal weight: 20.0000 chunk 803 optimal weight: 1.9990 chunk 503 optimal weight: 8.9990 chunk 490 optimal weight: 8.9990 chunk 371 optimal weight: 30.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S2 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S2 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S6 50 HIS S7 41 ASN SC 50 GLN L4 63 ASN L8 20 GLN ** LB 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 11 ASN LR 37 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 137622 Z= 0.255 Angle : 0.651 11.436 207462 Z= 0.333 Chirality : 0.038 0.308 26811 Planarity : 0.005 0.057 10019 Dihedral : 24.150 179.290 72301 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.87 % Favored : 89.11 % Rotamer: Outliers : 5.06 % Allowed : 16.14 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.12), residues: 4076 helix: -2.67 (0.15), residues: 892 sheet: -1.76 (0.19), residues: 766 loop : -2.71 (0.11), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPL2 213 HIS 0.007 0.001 HISL5 102 PHE 0.015 0.002 PHES3 28 TYR 0.022 0.002 TYRLP 9 ARG 0.008 0.001 ARGSC 14 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 624 time to evaluate : 4.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSL5 111 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHEL6 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSL7 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILEL8 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULF 47 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARGLM 144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLO 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULP 136 " (corrupted residue). Skipping it. REVERT: S1 88 MET cc_start: 0.1694 (mtm) cc_final: 0.1456 (mtm) REVERT: S3 14 SER cc_start: 0.8878 (p) cc_final: 0.8522 (t) REVERT: S8 73 LYS cc_start: 0.5999 (ttmt) cc_final: 0.5406 (mmtt) REVERT: S8 75 PHE cc_start: 0.4823 (m-80) cc_final: 0.4562 (m-80) REVERT: SC 68 PHE cc_start: 0.4879 (OUTLIER) cc_final: 0.4415 (t80) REVERT: SF 24 LYS cc_start: 0.5881 (tttm) cc_final: 0.5618 (tttm) REVERT: L1 23 ARG cc_start: 0.6749 (mmt90) cc_final: 0.6173 (ptp90) REVERT: L1 42 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7989 (mp) REVERT: L2 10 THR cc_start: 0.7550 (OUTLIER) cc_final: 0.7346 (p) REVERT: L3 88 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6567 (mt) REVERT: L4 23 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: L5 2 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6098 (pt0) REVERT: L5 83 LYS cc_start: 0.8337 (mttt) cc_final: 0.7696 (mtmm) REVERT: LA 36 VAL cc_start: 0.8808 (p) cc_final: 0.8526 (m) REVERT: LB 30 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8210 (m-80) REVERT: LD 44 ARG cc_start: 0.7997 (tpp80) cc_final: 0.7765 (tpp80) REVERT: LE 27 MET cc_start: 0.7386 (ptp) cc_final: 0.7182 (ptp) REVERT: LG 41 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7823 (ttpp) REVERT: LJ 82 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8325 (mp10) REVERT: LJ 148 GLN cc_start: 0.7769 (mm110) cc_final: 0.7235 (mm-40) REVERT: LM 12 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6818 (pp) REVERT: LN 112 MET cc_start: 0.6440 (mmm) cc_final: 0.6131 (ttt) outliers start: 173 outliers final: 141 residues processed: 731 average time/residue: 1.0942 time to fit residues: 1365.9276 Evaluate side-chains 762 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 611 time to evaluate : 4.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S3 residue 7 LEU Chi-restraints excluded: chain S3 residue 20 ASP Chi-restraints excluded: chain S3 residue 74 ILE Chi-restraints excluded: chain S3 residue 106 VAL Chi-restraints excluded: chain S3 residue 117 THR Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S7 residue 68 THR Chi-restraints excluded: chain S7 residue 70 THR Chi-restraints excluded: chain S8 residue 35 LEU Chi-restraints excluded: chain S8 residue 40 VAL Chi-restraints excluded: chain S8 residue 72 THR Chi-restraints excluded: chain S8 residue 83 GLU Chi-restraints excluded: chain SC residue 46 GLU Chi-restraints excluded: chain SC residue 68 PHE Chi-restraints excluded: chain SC residue 71 THR Chi-restraints excluded: chain SC residue 182 ARG Chi-restraints excluded: chain SD residue 84 THR Chi-restraints excluded: chain SD residue 86 THR Chi-restraints excluded: chain SD residue 106 ILE Chi-restraints excluded: chain SD residue 134 ILE Chi-restraints excluded: chain SE residue 62 ILE Chi-restraints excluded: chain SE residue 87 ILE Chi-restraints excluded: chain SE residue 91 VAL Chi-restraints excluded: chain SF residue 46 ILE Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain SF residue 106 VAL Chi-restraints excluded: chain L1 residue 32 VAL Chi-restraints excluded: chain L1 residue 42 ILE Chi-restraints excluded: chain L1 residue 44 VAL Chi-restraints excluded: chain L1 residue 50 ILE Chi-restraints excluded: chain L1 residue 62 THR Chi-restraints excluded: chain L1 residue 63 VAL Chi-restraints excluded: chain L1 residue 78 LEU Chi-restraints excluded: chain L2 residue 10 THR Chi-restraints excluded: chain L2 residue 17 THR Chi-restraints excluded: chain L2 residue 24 ILE Chi-restraints excluded: chain L2 residue 27 THR Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 112 VAL Chi-restraints excluded: chain L2 residue 115 ILE Chi-restraints excluded: chain L2 residue 139 THR Chi-restraints excluded: chain L2 residue 192 ILE Chi-restraints excluded: chain L2 residue 195 VAL Chi-restraints excluded: chain L2 residue 219 THR Chi-restraints excluded: chain L2 residue 226 ASN Chi-restraints excluded: chain L3 residue 9 VAL Chi-restraints excluded: chain L3 residue 77 SER Chi-restraints excluded: chain L3 residue 88 ILE Chi-restraints excluded: chain L4 residue 6 GLU Chi-restraints excluded: chain L4 residue 19 GLU Chi-restraints excluded: chain L4 residue 20 ILE Chi-restraints excluded: chain L4 residue 23 GLU Chi-restraints excluded: chain L4 residue 34 THR Chi-restraints excluded: chain L4 residue 41 VAL Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L5 residue 2 GLU Chi-restraints excluded: chain L5 residue 11 ARG Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L5 residue 97 ASN Chi-restraints excluded: chain L6 residue 6 ILE Chi-restraints excluded: chain L6 residue 17 SER Chi-restraints excluded: chain L6 residue 28 ASP Chi-restraints excluded: chain L6 residue 29 VAL Chi-restraints excluded: chain L6 residue 34 ASN Chi-restraints excluded: chain L6 residue 42 VAL Chi-restraints excluded: chain L7 residue 8 ASN Chi-restraints excluded: chain L7 residue 26 THR Chi-restraints excluded: chain L7 residue 63 ILE Chi-restraints excluded: chain L7 residue 65 VAL Chi-restraints excluded: chain L7 residue 71 LEU Chi-restraints excluded: chain L8 residue 60 VAL Chi-restraints excluded: chain L8 residue 70 ILE Chi-restraints excluded: chain L8 residue 92 LEU Chi-restraints excluded: chain L9 residue 72 ASP Chi-restraints excluded: chain LA residue 8 THR Chi-restraints excluded: chain LA residue 38 ILE Chi-restraints excluded: chain LB residue 30 PHE Chi-restraints excluded: chain LB residue 32 LEU Chi-restraints excluded: chain LC residue 65 SER Chi-restraints excluded: chain LC residue 115 VAL Chi-restraints excluded: chain LC residue 121 VAL Chi-restraints excluded: chain LC residue 152 SER Chi-restraints excluded: chain LC residue 177 VAL Chi-restraints excluded: chain LD residue 7 THR Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 54 VAL Chi-restraints excluded: chain LD residue 57 GLU Chi-restraints excluded: chain LE residue 3 VAL Chi-restraints excluded: chain LE residue 8 THR Chi-restraints excluded: chain LF residue 16 ASN Chi-restraints excluded: chain LF residue 32 MET Chi-restraints excluded: chain LG residue 24 SER Chi-restraints excluded: chain LG residue 41 LYS Chi-restraints excluded: chain LH residue 49 LEU Chi-restraints excluded: chain LI residue 16 VAL Chi-restraints excluded: chain LJ residue 7 LEU Chi-restraints excluded: chain LJ residue 82 GLN Chi-restraints excluded: chain LJ residue 96 SER Chi-restraints excluded: chain LJ residue 119 GLN Chi-restraints excluded: chain LJ residue 123 LEU Chi-restraints excluded: chain LJ residue 129 PHE Chi-restraints excluded: chain LJ residue 135 LYS Chi-restraints excluded: chain LJ residue 146 LEU Chi-restraints excluded: chain LJ residue 152 VAL Chi-restraints excluded: chain LJ residue 163 VAL Chi-restraints excluded: chain LJ residue 165 LEU Chi-restraints excluded: chain LJ residue 182 ASN Chi-restraints excluded: chain LJ residue 190 ASP Chi-restraints excluded: chain LJ residue 202 VAL Chi-restraints excluded: chain LL residue 4 VAL Chi-restraints excluded: chain LL residue 17 VAL Chi-restraints excluded: chain LL residue 37 LEU Chi-restraints excluded: chain LL residue 52 VAL Chi-restraints excluded: chain LL residue 68 THR Chi-restraints excluded: chain LL residue 75 MET Chi-restraints excluded: chain LL residue 86 VAL Chi-restraints excluded: chain LL residue 121 ILE Chi-restraints excluded: chain LL residue 124 SER Chi-restraints excluded: chain LM residue 12 ILE Chi-restraints excluded: chain LM residue 30 SER Chi-restraints excluded: chain LM residue 46 THR Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 85 ILE Chi-restraints excluded: chain LM residue 99 GLU Chi-restraints excluded: chain LM residue 113 THR Chi-restraints excluded: chain LN residue 6 THR Chi-restraints excluded: chain LN residue 42 THR Chi-restraints excluded: chain LN residue 63 VAL Chi-restraints excluded: chain LN residue 85 VAL Chi-restraints excluded: chain LN residue 89 ASP Chi-restraints excluded: chain LN residue 116 SER Chi-restraints excluded: chain LN residue 117 LEU Chi-restraints excluded: chain LO residue 23 VAL Chi-restraints excluded: chain LO residue 42 SER Chi-restraints excluded: chain LO residue 46 VAL Chi-restraints excluded: chain LO residue 145 VAL Chi-restraints excluded: chain LP residue 7 VAL Chi-restraints excluded: chain LP residue 37 THR Chi-restraints excluded: chain LP residue 68 ILE Chi-restraints excluded: chain LP residue 120 LEU Chi-restraints excluded: chain LQ residue 11 ASP Chi-restraints excluded: chain LQ residue 42 SER Chi-restraints excluded: chain LQ residue 44 VAL Chi-restraints excluded: chain LQ residue 95 GLU Chi-restraints excluded: chain LQ residue 103 ILE Chi-restraints excluded: chain LR residue 10 VAL Chi-restraints excluded: chain LR residue 45 ILE Chi-restraints excluded: chain LR residue 63 ILE Chi-restraints excluded: chain LR residue 89 ILE Chi-restraints excluded: chain LR residue 113 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 497 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 chunk 480 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 511 optimal weight: 8.9990 chunk 547 optimal weight: 10.0000 chunk 397 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 631 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S2 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S3 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 41 ASN SC 70 ASN SC 192 GLN L3 29 HIS L4 63 ASN ** L5 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 20 GLN ** LB 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LM 11 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 137622 Z= 0.484 Angle : 0.868 13.482 207462 Z= 0.429 Chirality : 0.046 0.354 26811 Planarity : 0.006 0.065 10019 Dihedral : 24.381 179.807 72301 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.45 % Favored : 85.50 % Rotamer: Outliers : 5.55 % Allowed : 16.43 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.12), residues: 4076 helix: -2.89 (0.14), residues: 914 sheet: -1.95 (0.19), residues: 767 loop : -2.89 (0.11), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPL2 213 HIS 0.010 0.002 HISL5 102 PHE 0.024 0.003 PHELO 66 TYR 0.026 0.003 TYRLP 9 ARG 0.010 0.001 ARGLQ 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 635 time to evaluate : 4.752 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSL5 111 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHEL6 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSL7 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILEL8 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULF 47 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLH 65 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARGLM 144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLO 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULP 136 " (corrupted residue). Skipping it. REVERT: S2 64 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6466 (tt0) REVERT: S3 14 SER cc_start: 0.8875 (p) cc_final: 0.8481 (t) REVERT: S8 73 LYS cc_start: 0.5889 (ttmt) cc_final: 0.5392 (mmtt) REVERT: S8 75 PHE cc_start: 0.5026 (m-80) cc_final: 0.4729 (m-80) REVERT: SC 68 PHE cc_start: 0.5078 (OUTLIER) cc_final: 0.4506 (t80) REVERT: SF 24 LYS cc_start: 0.5676 (tttm) cc_final: 0.5359 (tttm) REVERT: L1 23 ARG cc_start: 0.6896 (mmt90) cc_final: 0.6245 (ptp90) REVERT: L1 42 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8054 (mp) REVERT: L2 188 CYS cc_start: 0.8598 (m) cc_final: 0.8334 (m) REVERT: L4 23 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: L5 2 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6234 (pt0) REVERT: L7 60 GLU cc_start: 0.7619 (mp0) cc_final: 0.7302 (mp0) REVERT: LB 30 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.8327 (m-80) REVERT: LC 128 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6948 (mp10) REVERT: LD 44 ARG cc_start: 0.8102 (tpp80) cc_final: 0.7875 (tpp80) REVERT: LE 10 LYS cc_start: 0.8241 (mtmt) cc_final: 0.8019 (mtmt) REVERT: LJ 132 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6449 (mt-10) REVERT: LM 12 ILE cc_start: 0.7152 (OUTLIER) cc_final: 0.6824 (pp) REVERT: LN 53 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8396 (mmtt) REVERT: LN 66 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8575 (ttmt) REVERT: LN 110 ASN cc_start: 0.6924 (OUTLIER) cc_final: 0.6512 (p0) REVERT: LN 112 MET cc_start: 0.6388 (mmm) cc_final: 0.6188 (ttt) REVERT: LO 29 LYS cc_start: 0.6358 (mttm) cc_final: 0.5859 (tmtt) outliers start: 190 outliers final: 158 residues processed: 753 average time/residue: 1.1615 time to fit residues: 1488.3611 Evaluate side-chains 785 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 617 time to evaluate : 4.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 64 GLN Chi-restraints excluded: chain S3 residue 20 ASP Chi-restraints excluded: chain S3 residue 74 ILE Chi-restraints excluded: chain S3 residue 106 VAL Chi-restraints excluded: chain S3 residue 117 THR Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S7 residue 68 THR Chi-restraints excluded: chain S7 residue 70 THR Chi-restraints excluded: chain S8 residue 35 LEU Chi-restraints excluded: chain S8 residue 40 VAL Chi-restraints excluded: chain S8 residue 50 ASP Chi-restraints excluded: chain S8 residue 72 THR Chi-restraints excluded: chain S8 residue 83 GLU Chi-restraints excluded: chain SC residue 46 GLU Chi-restraints excluded: chain SC residue 68 PHE Chi-restraints excluded: chain SC residue 71 THR Chi-restraints excluded: chain SC residue 182 ARG Chi-restraints excluded: chain SD residue 34 THR Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 84 THR Chi-restraints excluded: chain SD residue 86 THR Chi-restraints excluded: chain SD residue 105 VAL Chi-restraints excluded: chain SD residue 106 ILE Chi-restraints excluded: chain SD residue 134 ILE Chi-restraints excluded: chain SE residue 62 ILE Chi-restraints excluded: chain SE residue 87 ILE Chi-restraints excluded: chain SE residue 91 VAL Chi-restraints excluded: chain SF residue 46 ILE Chi-restraints excluded: chain SF residue 71 GLU Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain SF residue 106 VAL Chi-restraints excluded: chain L1 residue 32 VAL Chi-restraints excluded: chain L1 residue 42 ILE Chi-restraints excluded: chain L1 residue 50 ILE Chi-restraints excluded: chain L1 residue 62 THR Chi-restraints excluded: chain L1 residue 63 VAL Chi-restraints excluded: chain L1 residue 78 LEU Chi-restraints excluded: chain L1 residue 99 LEU Chi-restraints excluded: chain L2 residue 17 THR Chi-restraints excluded: chain L2 residue 24 ILE Chi-restraints excluded: chain L2 residue 27 THR Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 112 VAL Chi-restraints excluded: chain L2 residue 115 ILE Chi-restraints excluded: chain L2 residue 139 THR Chi-restraints excluded: chain L2 residue 192 ILE Chi-restraints excluded: chain L2 residue 195 VAL Chi-restraints excluded: chain L2 residue 219 THR Chi-restraints excluded: chain L2 residue 226 ASN Chi-restraints excluded: chain L3 residue 9 VAL Chi-restraints excluded: chain L3 residue 10 THR Chi-restraints excluded: chain L3 residue 77 SER Chi-restraints excluded: chain L3 residue 88 ILE Chi-restraints excluded: chain L4 residue 6 GLU Chi-restraints excluded: chain L4 residue 19 GLU Chi-restraints excluded: chain L4 residue 20 ILE Chi-restraints excluded: chain L4 residue 23 GLU Chi-restraints excluded: chain L4 residue 41 VAL Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L5 residue 2 GLU Chi-restraints excluded: chain L5 residue 11 ARG Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L5 residue 97 ASN Chi-restraints excluded: chain L6 residue 6 ILE Chi-restraints excluded: chain L6 residue 14 GLU Chi-restraints excluded: chain L6 residue 17 SER Chi-restraints excluded: chain L6 residue 28 ASP Chi-restraints excluded: chain L6 residue 29 VAL Chi-restraints excluded: chain L6 residue 34 ASN Chi-restraints excluded: chain L6 residue 42 VAL Chi-restraints excluded: chain L6 residue 50 VAL Chi-restraints excluded: chain L6 residue 80 VAL Chi-restraints excluded: chain L7 residue 8 ASN Chi-restraints excluded: chain L7 residue 26 THR Chi-restraints excluded: chain L7 residue 63 ILE Chi-restraints excluded: chain L7 residue 65 VAL Chi-restraints excluded: chain L7 residue 91 VAL Chi-restraints excluded: chain L8 residue 38 ASN Chi-restraints excluded: chain L8 residue 60 VAL Chi-restraints excluded: chain L8 residue 70 ILE Chi-restraints excluded: chain L8 residue 92 LEU Chi-restraints excluded: chain L9 residue 67 LEU Chi-restraints excluded: chain L9 residue 72 ASP Chi-restraints excluded: chain LA residue 38 ILE Chi-restraints excluded: chain LB residue 30 PHE Chi-restraints excluded: chain LB residue 32 LEU Chi-restraints excluded: chain LB residue 45 THR Chi-restraints excluded: chain LC residue 15 VAL Chi-restraints excluded: chain LC residue 115 VAL Chi-restraints excluded: chain LC residue 121 VAL Chi-restraints excluded: chain LC residue 128 GLN Chi-restraints excluded: chain LC residue 152 SER Chi-restraints excluded: chain LC residue 176 THR Chi-restraints excluded: chain LC residue 177 VAL Chi-restraints excluded: chain LD residue 7 THR Chi-restraints excluded: chain LD residue 33 SER Chi-restraints excluded: chain LD residue 36 VAL Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 54 VAL Chi-restraints excluded: chain LD residue 57 GLU Chi-restraints excluded: chain LE residue 3 VAL Chi-restraints excluded: chain LE residue 8 THR Chi-restraints excluded: chain LF residue 16 ASN Chi-restraints excluded: chain LF residue 32 MET Chi-restraints excluded: chain LG residue 24 SER Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LH residue 49 LEU Chi-restraints excluded: chain LH residue 55 MET Chi-restraints excluded: chain LH residue 65 LYS Chi-restraints excluded: chain LI residue 16 VAL Chi-restraints excluded: chain LJ residue 7 LEU Chi-restraints excluded: chain LJ residue 70 THR Chi-restraints excluded: chain LJ residue 82 GLN Chi-restraints excluded: chain LJ residue 96 SER Chi-restraints excluded: chain LJ residue 123 LEU Chi-restraints excluded: chain LJ residue 129 PHE Chi-restraints excluded: chain LJ residue 132 GLU Chi-restraints excluded: chain LJ residue 135 LYS Chi-restraints excluded: chain LJ residue 146 LEU Chi-restraints excluded: chain LJ residue 152 VAL Chi-restraints excluded: chain LJ residue 163 VAL Chi-restraints excluded: chain LJ residue 165 LEU Chi-restraints excluded: chain LJ residue 182 ASN Chi-restraints excluded: chain LJ residue 187 THR Chi-restraints excluded: chain LJ residue 190 ASP Chi-restraints excluded: chain LJ residue 202 VAL Chi-restraints excluded: chain LL residue 4 VAL Chi-restraints excluded: chain LL residue 17 VAL Chi-restraints excluded: chain LL residue 37 LEU Chi-restraints excluded: chain LL residue 50 ILE Chi-restraints excluded: chain LL residue 68 THR Chi-restraints excluded: chain LL residue 75 MET Chi-restraints excluded: chain LL residue 86 VAL Chi-restraints excluded: chain LL residue 121 ILE Chi-restraints excluded: chain LL residue 124 SER Chi-restraints excluded: chain LM residue 12 ILE Chi-restraints excluded: chain LM residue 30 SER Chi-restraints excluded: chain LM residue 46 THR Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 85 ILE Chi-restraints excluded: chain LM residue 99 GLU Chi-restraints excluded: chain LM residue 113 THR Chi-restraints excluded: chain LN residue 6 THR Chi-restraints excluded: chain LN residue 42 THR Chi-restraints excluded: chain LN residue 63 VAL Chi-restraints excluded: chain LN residue 85 VAL Chi-restraints excluded: chain LN residue 89 ASP Chi-restraints excluded: chain LN residue 110 ASN Chi-restraints excluded: chain LN residue 116 SER Chi-restraints excluded: chain LN residue 117 LEU Chi-restraints excluded: chain LO residue 23 VAL Chi-restraints excluded: chain LO residue 42 SER Chi-restraints excluded: chain LO residue 46 VAL Chi-restraints excluded: chain LO residue 145 VAL Chi-restraints excluded: chain LP residue 7 VAL Chi-restraints excluded: chain LP residue 37 THR Chi-restraints excluded: chain LP residue 68 ILE Chi-restraints excluded: chain LP residue 120 LEU Chi-restraints excluded: chain LQ residue 11 ASP Chi-restraints excluded: chain LQ residue 42 SER Chi-restraints excluded: chain LQ residue 44 VAL Chi-restraints excluded: chain LQ residue 95 GLU Chi-restraints excluded: chain LQ residue 103 ILE Chi-restraints excluded: chain LR residue 45 ILE Chi-restraints excluded: chain LR residue 63 ILE Chi-restraints excluded: chain LR residue 89 ILE Chi-restraints excluded: chain LR residue 113 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 731 optimal weight: 6.9990 chunk 770 optimal weight: 3.9990 chunk 702 optimal weight: 2.9990 chunk 749 optimal weight: 10.0000 chunk 769 optimal weight: 6.9990 chunk 450 optimal weight: 20.0000 chunk 326 optimal weight: 0.8980 chunk 588 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 676 optimal weight: 7.9990 chunk 708 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S7 41 ASN S8 53 ASN SC 39 ASN L4 63 ASN L8 20 GLN ** LB 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 147 ASN LM 11 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 137622 Z= 0.238 Angle : 0.641 12.556 207462 Z= 0.328 Chirality : 0.037 0.307 26811 Planarity : 0.005 0.062 10019 Dihedral : 24.130 179.231 72301 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.08 % Favored : 89.89 % Rotamer: Outliers : 4.91 % Allowed : 17.51 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.12), residues: 4076 helix: -2.57 (0.15), residues: 895 sheet: -1.75 (0.19), residues: 736 loop : -2.67 (0.11), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPL2 213 HIS 0.005 0.001 HISLH 31 PHE 0.017 0.002 PHELP 131 TYR 0.023 0.002 TYRS8 10 ARG 0.008 0.000 ARGL1 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 615 time to evaluate : 4.701 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSL5 111 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHEL6 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSL7 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILEL8 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULF 47 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLH 65 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARGLM 144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLO 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULP 136 " (corrupted residue). Skipping it. REVERT: S3 14 SER cc_start: 0.8858 (p) cc_final: 0.8525 (t) REVERT: S8 73 LYS cc_start: 0.5874 (ttmt) cc_final: 0.5338 (mmtt) REVERT: S8 75 PHE cc_start: 0.4827 (m-80) cc_final: 0.4621 (m-80) REVERT: SC 14 ARG cc_start: 0.6050 (mmm160) cc_final: 0.5797 (mmm160) REVERT: SC 68 PHE cc_start: 0.4790 (OUTLIER) cc_final: 0.4308 (t80) REVERT: SF 24 LYS cc_start: 0.5554 (tttm) cc_final: 0.5299 (tttm) REVERT: L1 23 ARG cc_start: 0.6731 (mmt90) cc_final: 0.6157 (ptp90) REVERT: L1 42 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.7960 (mp) REVERT: L2 189 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8017 (mtt-85) REVERT: L3 88 ILE cc_start: 0.7186 (OUTLIER) cc_final: 0.6564 (mt) REVERT: L4 23 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7610 (mt-10) REVERT: L5 2 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6082 (pt0) REVERT: L7 60 GLU cc_start: 0.7601 (mp0) cc_final: 0.7267 (mp0) REVERT: L7 74 LYS cc_start: 0.4995 (mmtp) cc_final: 0.3957 (ptmt) REVERT: LA 36 VAL cc_start: 0.8791 (p) cc_final: 0.8496 (m) REVERT: LB 30 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8275 (m-80) REVERT: LC 128 GLN cc_start: 0.6741 (OUTLIER) cc_final: 0.6310 (mp10) REVERT: LD 44 ARG cc_start: 0.7972 (tpp80) cc_final: 0.7761 (tpp80) REVERT: LJ 132 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6348 (mt-10) REVERT: LM 12 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6800 (pp) REVERT: LN 112 MET cc_start: 0.6446 (mmm) cc_final: 0.6071 (ttt) outliers start: 168 outliers final: 145 residues processed: 713 average time/residue: 1.0731 time to fit residues: 1311.5470 Evaluate side-chains 748 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 593 time to evaluate : 4.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S3 residue 7 LEU Chi-restraints excluded: chain S3 residue 36 THR Chi-restraints excluded: chain S3 residue 74 ILE Chi-restraints excluded: chain S3 residue 106 VAL Chi-restraints excluded: chain S3 residue 117 THR Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S7 residue 3 VAL Chi-restraints excluded: chain S7 residue 68 THR Chi-restraints excluded: chain S7 residue 70 THR Chi-restraints excluded: chain S8 residue 35 LEU Chi-restraints excluded: chain S8 residue 72 THR Chi-restraints excluded: chain S8 residue 83 GLU Chi-restraints excluded: chain SC residue 46 GLU Chi-restraints excluded: chain SC residue 68 PHE Chi-restraints excluded: chain SC residue 71 THR Chi-restraints excluded: chain SC residue 182 ARG Chi-restraints excluded: chain SD residue 34 THR Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 84 THR Chi-restraints excluded: chain SD residue 85 ILE Chi-restraints excluded: chain SD residue 86 THR Chi-restraints excluded: chain SD residue 106 ILE Chi-restraints excluded: chain SD residue 124 LEU Chi-restraints excluded: chain SD residue 134 ILE Chi-restraints excluded: chain SE residue 62 ILE Chi-restraints excluded: chain SF residue 46 ILE Chi-restraints excluded: chain SF residue 71 GLU Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain SF residue 106 VAL Chi-restraints excluded: chain L1 residue 32 VAL Chi-restraints excluded: chain L1 residue 42 ILE Chi-restraints excluded: chain L1 residue 50 ILE Chi-restraints excluded: chain L1 residue 62 THR Chi-restraints excluded: chain L1 residue 63 VAL Chi-restraints excluded: chain L1 residue 78 LEU Chi-restraints excluded: chain L1 residue 83 ILE Chi-restraints excluded: chain L2 residue 17 THR Chi-restraints excluded: chain L2 residue 24 ILE Chi-restraints excluded: chain L2 residue 27 THR Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 112 VAL Chi-restraints excluded: chain L2 residue 115 ILE Chi-restraints excluded: chain L2 residue 139 THR Chi-restraints excluded: chain L2 residue 189 ARG Chi-restraints excluded: chain L2 residue 192 ILE Chi-restraints excluded: chain L2 residue 195 VAL Chi-restraints excluded: chain L2 residue 219 THR Chi-restraints excluded: chain L2 residue 226 ASN Chi-restraints excluded: chain L3 residue 77 SER Chi-restraints excluded: chain L3 residue 88 ILE Chi-restraints excluded: chain L4 residue 19 GLU Chi-restraints excluded: chain L4 residue 20 ILE Chi-restraints excluded: chain L4 residue 23 GLU Chi-restraints excluded: chain L4 residue 41 VAL Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L5 residue 2 GLU Chi-restraints excluded: chain L5 residue 11 ARG Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L5 residue 97 ASN Chi-restraints excluded: chain L6 residue 6 ILE Chi-restraints excluded: chain L6 residue 17 SER Chi-restraints excluded: chain L6 residue 28 ASP Chi-restraints excluded: chain L6 residue 29 VAL Chi-restraints excluded: chain L6 residue 34 ASN Chi-restraints excluded: chain L6 residue 42 VAL Chi-restraints excluded: chain L6 residue 50 VAL Chi-restraints excluded: chain L7 residue 8 ASN Chi-restraints excluded: chain L7 residue 26 THR Chi-restraints excluded: chain L7 residue 63 ILE Chi-restraints excluded: chain L7 residue 65 VAL Chi-restraints excluded: chain L8 residue 38 ASN Chi-restraints excluded: chain L8 residue 46 VAL Chi-restraints excluded: chain L8 residue 60 VAL Chi-restraints excluded: chain L8 residue 70 ILE Chi-restraints excluded: chain L8 residue 92 LEU Chi-restraints excluded: chain L9 residue 67 LEU Chi-restraints excluded: chain L9 residue 72 ASP Chi-restraints excluded: chain LA residue 38 ILE Chi-restraints excluded: chain LB residue 30 PHE Chi-restraints excluded: chain LB residue 32 LEU Chi-restraints excluded: chain LB residue 55 THR Chi-restraints excluded: chain LC residue 15 VAL Chi-restraints excluded: chain LC residue 115 VAL Chi-restraints excluded: chain LC residue 121 VAL Chi-restraints excluded: chain LC residue 128 GLN Chi-restraints excluded: chain LC residue 152 SER Chi-restraints excluded: chain LC residue 176 THR Chi-restraints excluded: chain LC residue 177 VAL Chi-restraints excluded: chain LD residue 7 THR Chi-restraints excluded: chain LD residue 33 SER Chi-restraints excluded: chain LD residue 36 VAL Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 54 VAL Chi-restraints excluded: chain LE residue 3 VAL Chi-restraints excluded: chain LE residue 8 THR Chi-restraints excluded: chain LF residue 16 ASN Chi-restraints excluded: chain LF residue 32 MET Chi-restraints excluded: chain LG residue 24 SER Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LH residue 49 LEU Chi-restraints excluded: chain LH residue 65 LYS Chi-restraints excluded: chain LI residue 16 VAL Chi-restraints excluded: chain LJ residue 7 LEU Chi-restraints excluded: chain LJ residue 70 THR Chi-restraints excluded: chain LJ residue 123 LEU Chi-restraints excluded: chain LJ residue 129 PHE Chi-restraints excluded: chain LJ residue 132 GLU Chi-restraints excluded: chain LJ residue 135 LYS Chi-restraints excluded: chain LJ residue 146 LEU Chi-restraints excluded: chain LJ residue 152 VAL Chi-restraints excluded: chain LJ residue 163 VAL Chi-restraints excluded: chain LJ residue 165 LEU Chi-restraints excluded: chain LJ residue 182 ASN Chi-restraints excluded: chain LJ residue 187 THR Chi-restraints excluded: chain LJ residue 190 ASP Chi-restraints excluded: chain LJ residue 202 VAL Chi-restraints excluded: chain LL residue 4 VAL Chi-restraints excluded: chain LL residue 17 VAL Chi-restraints excluded: chain LL residue 37 LEU Chi-restraints excluded: chain LL residue 50 ILE Chi-restraints excluded: chain LL residue 75 MET Chi-restraints excluded: chain LL residue 86 VAL Chi-restraints excluded: chain LL residue 121 ILE Chi-restraints excluded: chain LL residue 124 SER Chi-restraints excluded: chain LM residue 12 ILE Chi-restraints excluded: chain LM residue 30 SER Chi-restraints excluded: chain LM residue 46 THR Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 85 ILE Chi-restraints excluded: chain LM residue 99 GLU Chi-restraints excluded: chain LM residue 113 THR Chi-restraints excluded: chain LN residue 6 THR Chi-restraints excluded: chain LN residue 63 VAL Chi-restraints excluded: chain LN residue 85 VAL Chi-restraints excluded: chain LN residue 89 ASP Chi-restraints excluded: chain LN residue 96 THR Chi-restraints excluded: chain LN residue 116 SER Chi-restraints excluded: chain LN residue 117 LEU Chi-restraints excluded: chain LO residue 23 VAL Chi-restraints excluded: chain LO residue 42 SER Chi-restraints excluded: chain LO residue 46 VAL Chi-restraints excluded: chain LO residue 145 VAL Chi-restraints excluded: chain LP residue 7 VAL Chi-restraints excluded: chain LP residue 37 THR Chi-restraints excluded: chain LP residue 68 ILE Chi-restraints excluded: chain LP residue 120 LEU Chi-restraints excluded: chain LQ residue 11 ASP Chi-restraints excluded: chain LQ residue 42 SER Chi-restraints excluded: chain LQ residue 44 VAL Chi-restraints excluded: chain LQ residue 95 GLU Chi-restraints excluded: chain LR residue 45 ILE Chi-restraints excluded: chain LR residue 63 ILE Chi-restraints excluded: chain LR residue 89 ILE Chi-restraints excluded: chain LR residue 113 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 746 optimal weight: 7.9990 chunk 491 optimal weight: 10.0000 chunk 792 optimal weight: 6.9990 chunk 483 optimal weight: 10.0000 chunk 375 optimal weight: 10.0000 chunk 550 optimal weight: 20.0000 chunk 830 optimal weight: 30.0000 chunk 764 optimal weight: 20.0000 chunk 661 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 511 optimal weight: 8.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S3 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 41 ASN L4 63 ASN ** L5 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L8 20 GLN ** LB 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LL 147 ASN LM 11 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 137622 Z= 0.435 Angle : 0.817 14.102 207462 Z= 0.406 Chirality : 0.044 0.338 26811 Planarity : 0.006 0.075 10019 Dihedral : 24.298 179.728 72301 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 14.06 % Favored : 85.89 % Rotamer: Outliers : 5.32 % Allowed : 17.42 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.12), residues: 4076 helix: -2.78 (0.15), residues: 905 sheet: -1.93 (0.19), residues: 761 loop : -2.81 (0.11), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPL2 213 HIS 0.010 0.002 HISL5 102 PHE 0.022 0.003 PHELO 66 TYR 0.022 0.003 TYRLJ 97 ARG 0.009 0.001 ARGLQ 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 614 time to evaluate : 4.766 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LEUL3 117 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYSL5 111 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "PHEL6 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSL7 102 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILEL8 94 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THRLA 60 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULD 58 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULF 47 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYSLH 65 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ARGLM 144 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VALLO 145 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLULP 136 " (corrupted residue). Skipping it. REVERT: S2 64 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.6430 (tt0) REVERT: S3 14 SER cc_start: 0.8903 (p) cc_final: 0.8502 (t) REVERT: S8 73 LYS cc_start: 0.5770 (ttmt) cc_final: 0.5308 (mmtt) REVERT: SC 14 ARG cc_start: 0.6105 (mmm160) cc_final: 0.5894 (mmm160) REVERT: SC 68 PHE cc_start: 0.5043 (OUTLIER) cc_final: 0.4561 (t80) REVERT: SF 24 LYS cc_start: 0.5630 (tttm) cc_final: 0.5370 (tttm) REVERT: L1 23 ARG cc_start: 0.6887 (mmt90) cc_final: 0.6228 (ptp90) REVERT: L1 42 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8045 (mp) REVERT: L2 188 CYS cc_start: 0.8575 (m) cc_final: 0.8319 (m) REVERT: L2 189 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8118 (mtt-85) REVERT: L4 23 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7708 (mt-10) REVERT: L5 2 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6227 (pt0) REVERT: L7 74 LYS cc_start: 0.5077 (mmtp) cc_final: 0.3955 (ptmt) REVERT: LB 30 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.8339 (m-80) REVERT: LC 128 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6867 (mp10) REVERT: LD 44 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7861 (tpp80) REVERT: LE 10 LYS cc_start: 0.8246 (mtmt) cc_final: 0.8016 (mtmt) REVERT: LJ 132 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6512 (mt-10) REVERT: LL 41 MET cc_start: 0.5835 (OUTLIER) cc_final: 0.5392 (mtm) REVERT: LM 12 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6897 (pp) REVERT: LN 112 MET cc_start: 0.6409 (mmm) cc_final: 0.6208 (ttt) REVERT: LO 29 LYS cc_start: 0.6344 (mttm) cc_final: 0.5846 (tmtt) outliers start: 182 outliers final: 159 residues processed: 728 average time/residue: 1.0817 time to fit residues: 1351.8449 Evaluate side-chains 789 residues out of total 3503 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 619 time to evaluate : 4.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S2 residue 64 GLN Chi-restraints excluded: chain S3 residue 20 ASP Chi-restraints excluded: chain S3 residue 36 THR Chi-restraints excluded: chain S3 residue 74 ILE Chi-restraints excluded: chain S3 residue 106 VAL Chi-restraints excluded: chain S3 residue 117 THR Chi-restraints excluded: chain S6 residue 45 THR Chi-restraints excluded: chain S7 residue 3 VAL Chi-restraints excluded: chain S7 residue 68 THR Chi-restraints excluded: chain S7 residue 70 THR Chi-restraints excluded: chain S8 residue 35 LEU Chi-restraints excluded: chain S8 residue 40 VAL Chi-restraints excluded: chain S8 residue 83 GLU Chi-restraints excluded: chain SC residue 46 GLU Chi-restraints excluded: chain SC residue 68 PHE Chi-restraints excluded: chain SC residue 71 THR Chi-restraints excluded: chain SC residue 182 ARG Chi-restraints excluded: chain SD residue 34 THR Chi-restraints excluded: chain SD residue 39 VAL Chi-restraints excluded: chain SD residue 61 LYS Chi-restraints excluded: chain SD residue 84 THR Chi-restraints excluded: chain SD residue 85 ILE Chi-restraints excluded: chain SD residue 86 THR Chi-restraints excluded: chain SD residue 106 ILE Chi-restraints excluded: chain SD residue 134 ILE Chi-restraints excluded: chain SE residue 62 ILE Chi-restraints excluded: chain SE residue 87 ILE Chi-restraints excluded: chain SE residue 91 VAL Chi-restraints excluded: chain SF residue 22 HIS Chi-restraints excluded: chain SF residue 46 ILE Chi-restraints excluded: chain SF residue 71 GLU Chi-restraints excluded: chain SF residue 81 SER Chi-restraints excluded: chain SF residue 106 VAL Chi-restraints excluded: chain L1 residue 32 VAL Chi-restraints excluded: chain L1 residue 42 ILE Chi-restraints excluded: chain L1 residue 50 ILE Chi-restraints excluded: chain L1 residue 62 THR Chi-restraints excluded: chain L1 residue 63 VAL Chi-restraints excluded: chain L1 residue 78 LEU Chi-restraints excluded: chain L1 residue 83 ILE Chi-restraints excluded: chain L2 residue 17 THR Chi-restraints excluded: chain L2 residue 24 ILE Chi-restraints excluded: chain L2 residue 27 THR Chi-restraints excluded: chain L2 residue 80 SER Chi-restraints excluded: chain L2 residue 112 VAL Chi-restraints excluded: chain L2 residue 115 ILE Chi-restraints excluded: chain L2 residue 139 THR Chi-restraints excluded: chain L2 residue 189 ARG Chi-restraints excluded: chain L2 residue 192 ILE Chi-restraints excluded: chain L2 residue 195 VAL Chi-restraints excluded: chain L2 residue 219 THR Chi-restraints excluded: chain L2 residue 226 ASN Chi-restraints excluded: chain L3 residue 9 VAL Chi-restraints excluded: chain L3 residue 77 SER Chi-restraints excluded: chain L3 residue 88 ILE Chi-restraints excluded: chain L4 residue 6 GLU Chi-restraints excluded: chain L4 residue 19 GLU Chi-restraints excluded: chain L4 residue 20 ILE Chi-restraints excluded: chain L4 residue 23 GLU Chi-restraints excluded: chain L4 residue 41 VAL Chi-restraints excluded: chain L4 residue 61 THR Chi-restraints excluded: chain L5 residue 2 GLU Chi-restraints excluded: chain L5 residue 11 ARG Chi-restraints excluded: chain L5 residue 12 ILE Chi-restraints excluded: chain L5 residue 49 LYS Chi-restraints excluded: chain L5 residue 97 ASN Chi-restraints excluded: chain L6 residue 6 ILE Chi-restraints excluded: chain L6 residue 17 SER Chi-restraints excluded: chain L6 residue 28 ASP Chi-restraints excluded: chain L6 residue 29 VAL Chi-restraints excluded: chain L6 residue 34 ASN Chi-restraints excluded: chain L6 residue 42 VAL Chi-restraints excluded: chain L6 residue 50 VAL Chi-restraints excluded: chain L7 residue 8 ASN Chi-restraints excluded: chain L7 residue 26 THR Chi-restraints excluded: chain L7 residue 63 ILE Chi-restraints excluded: chain L7 residue 65 VAL Chi-restraints excluded: chain L8 residue 38 ASN Chi-restraints excluded: chain L8 residue 46 VAL Chi-restraints excluded: chain L8 residue 60 VAL Chi-restraints excluded: chain L8 residue 70 ILE Chi-restraints excluded: chain L8 residue 92 LEU Chi-restraints excluded: chain L9 residue 67 LEU Chi-restraints excluded: chain L9 residue 72 ASP Chi-restraints excluded: chain LA residue 38 ILE Chi-restraints excluded: chain LB residue 30 PHE Chi-restraints excluded: chain LB residue 32 LEU Chi-restraints excluded: chain LB residue 55 THR Chi-restraints excluded: chain LC residue 15 VAL Chi-restraints excluded: chain LC residue 65 SER Chi-restraints excluded: chain LC residue 115 VAL Chi-restraints excluded: chain LC residue 121 VAL Chi-restraints excluded: chain LC residue 128 GLN Chi-restraints excluded: chain LC residue 152 SER Chi-restraints excluded: chain LC residue 176 THR Chi-restraints excluded: chain LC residue 177 VAL Chi-restraints excluded: chain LD residue 7 THR Chi-restraints excluded: chain LD residue 33 SER Chi-restraints excluded: chain LD residue 36 VAL Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 54 VAL Chi-restraints excluded: chain LD residue 57 GLU Chi-restraints excluded: chain LE residue 3 VAL Chi-restraints excluded: chain LE residue 8 THR Chi-restraints excluded: chain LF residue 16 ASN Chi-restraints excluded: chain LF residue 32 MET Chi-restraints excluded: chain LG residue 24 SER Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LH residue 49 LEU Chi-restraints excluded: chain LH residue 65 LYS Chi-restraints excluded: chain LI residue 16 VAL Chi-restraints excluded: chain LJ residue 7 LEU Chi-restraints excluded: chain LJ residue 70 THR Chi-restraints excluded: chain LJ residue 82 GLN Chi-restraints excluded: chain LJ residue 123 LEU Chi-restraints excluded: chain LJ residue 129 PHE Chi-restraints excluded: chain LJ residue 132 GLU Chi-restraints excluded: chain LJ residue 135 LYS Chi-restraints excluded: chain LJ residue 146 LEU Chi-restraints excluded: chain LJ residue 152 VAL Chi-restraints excluded: chain LJ residue 163 VAL Chi-restraints excluded: chain LJ residue 165 LEU Chi-restraints excluded: chain LJ residue 182 ASN Chi-restraints excluded: chain LJ residue 187 THR Chi-restraints excluded: chain LJ residue 190 ASP Chi-restraints excluded: chain LJ residue 202 VAL Chi-restraints excluded: chain LL residue 4 VAL Chi-restraints excluded: chain LL residue 17 VAL Chi-restraints excluded: chain LL residue 37 LEU Chi-restraints excluded: chain LL residue 41 MET Chi-restraints excluded: chain LL residue 50 ILE Chi-restraints excluded: chain LL residue 68 THR Chi-restraints excluded: chain LL residue 75 MET Chi-restraints excluded: chain LL residue 86 VAL Chi-restraints excluded: chain LL residue 121 ILE Chi-restraints excluded: chain LL residue 124 SER Chi-restraints excluded: chain LM residue 11 ASN Chi-restraints excluded: chain LM residue 12 ILE Chi-restraints excluded: chain LM residue 30 SER Chi-restraints excluded: chain LM residue 46 THR Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 79 SER Chi-restraints excluded: chain LM residue 85 ILE Chi-restraints excluded: chain LM residue 99 GLU Chi-restraints excluded: chain LM residue 105 SER Chi-restraints excluded: chain LM residue 113 THR Chi-restraints excluded: chain LN residue 6 THR Chi-restraints excluded: chain LN residue 42 THR Chi-restraints excluded: chain LN residue 63 VAL Chi-restraints excluded: chain LN residue 85 VAL Chi-restraints excluded: chain LN residue 89 ASP Chi-restraints excluded: chain LN residue 96 THR Chi-restraints excluded: chain LN residue 116 SER Chi-restraints excluded: chain LN residue 117 LEU Chi-restraints excluded: chain LO residue 23 VAL Chi-restraints excluded: chain LO residue 42 SER Chi-restraints excluded: chain LO residue 46 VAL Chi-restraints excluded: chain LO residue 145 VAL Chi-restraints excluded: chain LP residue 7 VAL Chi-restraints excluded: chain LP residue 37 THR Chi-restraints excluded: chain LP residue 68 ILE Chi-restraints excluded: chain LP residue 120 LEU Chi-restraints excluded: chain LQ residue 11 ASP Chi-restraints excluded: chain LQ residue 42 SER Chi-restraints excluded: chain LQ residue 44 VAL Chi-restraints excluded: chain LQ residue 95 GLU Chi-restraints excluded: chain LR residue 45 ILE Chi-restraints excluded: chain LR residue 63 ILE Chi-restraints excluded: chain LR residue 89 ILE Chi-restraints excluded: chain LR residue 113 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 834 random chunks: chunk 405 optimal weight: 10.0000 chunk 525 optimal weight: 10.0000 chunk 704 optimal weight: 0.9980 chunk 202 optimal weight: 20.0000 chunk 610 optimal weight: 0.4980 chunk 97 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 662 optimal weight: 0.4980 chunk 277 optimal weight: 10.0000 chunk 680 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S3 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S7 41 ASN ** L5 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LL 147 ASN LM 11 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.170990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.151980 restraints weight = 191917.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.144666 restraints weight = 220437.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.141184 restraints weight = 258045.841| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.185 137622 Z= 0.282 Angle : 0.798 59.200 207462 Z= 0.406 Chirality : 0.041 0.385 26811 Planarity : 0.006 0.074 10019 Dihedral : 24.299 179.765 72301 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 13.86 % Favored : 86.11 % Rotamer: Outliers : 5.41 % Allowed : 17.51 % Favored : 77.08 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.12), residues: 4076 helix: -2.76 (0.15), residues: 906 sheet: -1.87 (0.19), residues: 757 loop : -2.82 (0.11), residues: 2413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPL2 213 HIS 0.008 0.002 HISL5 102 PHE 0.020 0.002 PHELO 66 TYR 0.021 0.002 TYRLP 9 ARG 0.014 0.001 ARGSC 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21298.19 seconds wall clock time: 377 minutes 29.94 seconds (22649.94 seconds total)