Starting phenix.real_space_refine on Wed Mar 27 14:27:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agv_15425/03_2024/8agv_15425_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agv_15425/03_2024/8agv_15425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agv_15425/03_2024/8agv_15425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agv_15425/03_2024/8agv_15425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agv_15425/03_2024/8agv_15425_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agv_15425/03_2024/8agv_15425_updated.pdb" } resolution = 2.6 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= 0.021 sd= 0.132 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: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 3643 5.49 5 Mg 13 5.21 5 S 177 5.16 5 C 81320 2.51 5 N 27602 2.21 5 O 38587 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 71": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 151349 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "B" Number of atoms: 1555 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "C" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1416 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "E" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1258 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "F" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "G" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1272 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "I" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "J" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 518 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "M" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "N" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1169 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "P" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 737 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "Q" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "T" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "V" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 645 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 78} Chain: "X" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Z" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 410 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 824 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "d" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 207 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "f" Number of atoms: 68802 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3216, 68782 Classifications: {'RNA': 3216} Modifications used: {'rna2p_pur': 330, 'rna2p_pyr': 220, 'rna3p_pur': 1449, 'rna3p_pyr': 1217} Link IDs: {'rna2p': 550, 'rna3p': 2665} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 3216, 68782 Classifications: {'RNA': 3216} Modifications used: {'rna2p_pur': 330, 'rna2p_pyr': 219, 'rna3p_pur': 1449, 'rna3p_pyr': 1218} Link IDs: {'rna2p': 549, 'rna3p': 2666} Chain breaks: 3 bond proxies already assigned to first conformer: 76966 Chain: "h" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "i" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 14, 'rna3p_pur': 63, 'rna3p_pyr': 66} Link IDs: {'rna2p': 28, 'rna3p': 129} Chain: "j" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1874 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 234} Chain: "k" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2351 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "n" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1307 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 157} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "o" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "p" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1804 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 220} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "q" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1508 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "r" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1764 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "s" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1346 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "t" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "u" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "a" Number of atoms: 6569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6569 Classifications: {'peptide': 848} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 29, 'TRANS': 818} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 324 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 166 Chain: "e" Number of atoms: 11516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1527, 11516 Classifications: {'peptide': 1527} Incomplete info: {'truncation_to_alanine': 269} Link IDs: {'PTRANS': 38, 'TRANS': 1488} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 974 Unresolved non-hydrogen angles: 1242 Unresolved non-hydrogen dihedrals: 810 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 12, 'ASN:plan1': 23, 'TRP:plan': 1, 'ASP:plan': 21, 'PHE:plan': 27, 'GLU:plan': 24, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 562 Chain: "g" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1651 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "w" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1709 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain: "x" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1579 Classifications: {'RNA': 74} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p_pur': 28, 'rna3p_pyr': 31} Link IDs: {'rna2p': 15, 'rna3p': 58} Chain breaks: 1 Chain: "y" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1556 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 30, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 62} Chain breaks: 1 Chain: "z" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 728 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 182 Chain: "0" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "1" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "v" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1085 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 136} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'5CT:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20901 SG CYS T 44 120.446 172.222 212.598 1.00 54.16 S ATOM 20919 SG CYS T 47 122.544 169.569 211.518 1.00 59.61 S ATOM 21191 SG CYS T 84 123.731 172.062 214.331 1.00 57.91 S ATOM 23302 SG CYS W 19 85.069 189.637 170.221 1.00 40.18 S ATOM 23327 SG CYS W 22 83.321 189.701 166.938 1.00 41.00 S ATOM 23427 SG CYS W 34 87.052 189.710 166.984 1.00 38.42 S ATOM 23445 SG CYS W 37 85.081 192.801 168.131 1.00 40.17 S ATOM 25002 SG CYS Z 96 133.510 140.694 76.733 1.00 54.37 S ATOM 25028 SG CYS Z 99 130.889 139.013 78.749 1.00 53.18 S ATOM 25115 SG CYS Z 110 130.764 138.470 75.070 1.00 52.08 S ATOM 25161 SG CYS Z 115 129.699 141.696 76.304 1.00 52.77 S ATOM 25359 SG CYS b 12 132.294 248.291 110.040 1.00 63.95 S ATOM 25394 SG CYS b 17 133.569 251.827 109.130 1.00 72.10 S ATOM 25858 SG CYS b 74 135.785 249.320 111.268 1.00 60.93 S ATOM 25880 SG CYS b 77 132.684 251.159 112.440 1.00 66.15 S ATOM 26403 SG CYS c 39 139.098 169.736 205.774 1.00 58.71 S ATOM 26426 SG CYS c 42 138.486 166.762 207.876 1.00 62.48 S ATOM 26535 SG CYS c 57 136.268 167.265 204.883 1.00 55.64 S ATOM 26553 SG CYS c 60 135.843 169.738 207.629 1.00 57.82 S ATOM A0W6Y SG CYS e1527 39.774 126.291 188.706 1.00285.10 S ATOM A0W7I SG CYS e1530 37.333 123.834 187.680 1.00279.23 S ATOM A0WCA SG CYS e1551 37.984 127.010 185.577 1.00286.27 S ATOM A0WCV SG CYS e1554 36.185 127.728 188.656 1.00284.05 S ATOM A0W2W SG CYS e1508 41.620 120.618 178.117 1.00285.58 S ATOM A0W3F SG CYS e1511 41.493 119.254 174.736 1.00284.14 S ATOM A0W98 SG CYS e1538 43.323 122.880 174.991 1.00281.30 S Residues with excluded nonbonded symmetry interactions: 198 residue: pdb=" N AVAL B 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 3 " occ=0.50 residue: pdb=" N AGLU B 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2AGLU B 4 " occ=0.50 residue: pdb=" N APRO B 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD APRO B 5 " occ=0.50 residue: pdb=" N AVAL B 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 6 " occ=0.50 residue: pdb=" N AVAL B 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 7 " occ=0.50 residue: pdb=" N AVAL B 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 8 " occ=0.50 residue: pdb=" N AILE B 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1AILE B 9 " occ=0.50 residue: pdb=" N AASP B 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2AASP B 10 " occ=0.50 residue: pdb=" N AGLY B 11 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLY B 11 " occ=0.50 residue: pdb=" N ALYS B 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ ALYS B 12 " occ=0.50 residue: pdb=" N AGLY B 13 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLY B 13 " occ=0.50 residue: pdb=" N AHIS B 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2AHIS B 14 " occ=0.50 ... (remaining 186 not shown) Time building chain proxies: 81.02, per 1000 atoms: 0.54 Number of scatterers: 151349 At special positions: 0 Unit cell: (232.98, 283.812, 262.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 177 16.00 P 3643 15.00 Mg 13 11.99 O 38587 8.00 N 27602 7.00 C 81320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 56.37 Conformation dependent library (CDL) restraints added in 11.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 47 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 84 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 44 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 22 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 19 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 34 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 37 " pdb=" ZN Z 201 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 99 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 110 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 115 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 96 " pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 12 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 17 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 39 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 57 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 42 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 60 " pdb=" ZN e2001 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1551 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1530 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1554 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1527 " pdb=" ZN e2002 " pdb="ZN ZN e2002 " - pdb=" ND1 HIS e1535 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1508 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1511 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1538 " Number of angles added : 33 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17764 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 368 helices and 88 sheets defined 48.7% alpha, 13.0% beta 1184 base pairs and 2003 stacking pairs defined. Time for finding SS restraints: 87.29 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 4.805A pdb=" N TYR A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LYS A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 34 removed outlier: 3.753A pdb=" N TRP A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASN A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 83 through 88 removed outlier: 3.844A pdb=" N GLN A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLY A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 88' Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 139 through 145 removed outlier: 4.410A pdb=" N ASP A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 153 removed outlier: 5.053A pdb=" N TRP A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N CYS A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 153' Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 186 through 196 Processing helix chain 'B' and resid 15 through 30 removed outlier: 3.689A pdb=" N ALYS B 25 " --> pdb=" O ASER B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 60 removed outlier: 4.078A pdb=" N ALYS B 60 " --> pdb=" O AASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 4.023A pdb=" N AGLY B 69 " --> pdb=" O AASN B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix No H-bonds generated for 'chain 'B' and resid 65 through 70' Processing helix chain 'B' and resid 75 through 89 removed outlier: 3.835A pdb=" N AMET B 87 " --> pdb=" O AALA B 83 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASER B 89 " --> pdb=" O AARG B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 removed outlier: 3.928A pdb=" N AARG B 101 " --> pdb=" O AALA B 97 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALEU B 102 " --> pdb=" O AALA B 98 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ALYS B 103 " --> pdb=" O ALEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 4.914A pdb=" N ALYS B 114 " --> pdb=" O APRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 151 through 186 removed outlier: 3.814A pdb=" N ALYS B 170 " --> pdb=" O AGLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.729A pdb=" N SER C 14 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ALA C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' Processing helix chain 'C' and resid 25 through 37 removed outlier: 3.640A pdb=" N GLU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 Processing helix chain 'C' and resid 84 through 106 Processing helix chain 'C' and resid 169 through 183 Processing helix chain 'C' and resid 70 through 76 removed outlier: 3.764A pdb=" N GLY C 73 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU C 75 " --> pdb=" O GLN C 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 40 Processing helix chain 'D' and resid 42 through 54 removed outlier: 3.961A pdb=" N LYS D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Proline residue: D 60 - end of helix Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.812A pdb=" N GLN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 118 Processing helix chain 'D' and resid 123 through 131 Processing helix chain 'D' and resid 147 through 154 removed outlier: 4.144A pdb=" N ARG D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLY D 154 " --> pdb=" O VAL D 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 147 through 154' Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.908A pdb=" N VAL E 22 " --> pdb=" O GLY E 18 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TRP E 23 " --> pdb=" O LYS E 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 18 through 23' Processing helix chain 'E' and resid 28 through 36 removed outlier: 5.178A pdb=" N ASN E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 48 Processing helix chain 'E' and resid 60 through 73 Processing helix chain 'E' and resid 77 through 82 removed outlier: 3.710A pdb=" N ARG E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LYS E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 77 through 82' Processing helix chain 'E' and resid 84 through 113 Proline residue: E 90 - end of helix removed outlier: 6.827A pdb=" N VAL E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 130 removed outlier: 3.685A pdb=" N VAL E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 157 Processing helix chain 'F' and resid 33 through 49 Processing helix chain 'F' and resid 98 through 114 Processing helix chain 'F' and resid 117 through 122 removed outlier: 5.661A pdb=" N HIS F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 4.880A pdb=" N PHE F 143 " --> pdb=" O TYR F 139 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU F 144 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 32 removed outlier: 4.512A pdb=" N TYR G 30 " --> pdb=" O HIS G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 removed outlier: 4.286A pdb=" N ILE G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LYS G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 92 through 97' Processing helix chain 'G' and resid 99 through 121 removed outlier: 3.891A pdb=" N GLN G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 26 removed outlier: 4.166A pdb=" N ASN H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY H 26 " --> pdb=" O PRO H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 72 through 88 Processing helix chain 'I' and resid 66 through 71 removed outlier: 5.400A pdb=" N LYS I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 127 removed outlier: 3.884A pdb=" N LEU I 125 " --> pdb=" O GLU I 121 " (cutoff:3.500A) Proline residue: I 127 - end of helix Processing helix chain 'I' and resid 128 through 133 Processing helix chain 'J' and resid 33 through 43 Processing helix chain 'J' and resid 45 through 50 removed outlier: 3.562A pdb=" N ILE J 49 " --> pdb=" O ASN J 45 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ALA J 50 " --> pdb=" O PRO J 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 45 through 50' Processing helix chain 'J' and resid 52 through 60 Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.644A pdb=" N ILE K 63 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLU K 64 " --> pdb=" O TYR K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 78 removed outlier: 3.733A pdb=" N LYS K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP K 78 " --> pdb=" O LYS K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 Processing helix chain 'K' and resid 131 through 140 removed outlier: 3.836A pdb=" N ASN K 137 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG K 138 " --> pdb=" O ASP K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 22 Processing helix chain 'L' and resid 23 through 32 removed outlier: 4.028A pdb=" N VAL L 29 " --> pdb=" O SER L 25 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 44 Processing helix chain 'L' and resid 100 through 105 removed outlier: 3.567A pdb=" N LEU L 104 " --> pdb=" O HIS L 100 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL L 105 " --> pdb=" O PRO L 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 100 through 105' Processing helix chain 'L' and resid 112 through 123 Processing helix chain 'M' and resid 58 through 67 removed outlier: 5.380A pdb=" N VAL M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS M 67 " --> pdb=" O ALA M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 81 removed outlier: 3.568A pdb=" N LEU M 80 " --> pdb=" O ASN M 76 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU M 81 " --> pdb=" O TYR M 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 76 through 81' Processing helix chain 'M' and resid 92 through 97 removed outlier: 5.472A pdb=" N SER M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 125 removed outlier: 3.597A pdb=" N VAL M 113 " --> pdb=" O GLU M 109 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLY M 125 " --> pdb=" O ARG M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'N' and resid 2 through 7 removed outlier: 4.161A pdb=" N THR N 6 " --> pdb=" O PRO N 2 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LYS N 7 " --> pdb=" O SER N 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2 through 7' Processing helix chain 'N' and resid 41 through 49 Processing helix chain 'N' and resid 64 through 69 removed outlier: 4.419A pdb=" N PHE N 68 " --> pdb=" O GLN N 64 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TRP N 69 " --> pdb=" O GLN N 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 64 through 69' Processing helix chain 'N' and resid 74 through 83 removed outlier: 4.577A pdb=" N TRP N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N THR N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU N 81 " --> pdb=" O LYS N 77 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Proline residue: N 83 - end of helix Processing helix chain 'N' and resid 86 through 94 removed outlier: 4.083A pdb=" N ALA N 94 " --> pdb=" O TYR N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 108 Processing helix chain 'N' and resid 131 through 142 Processing helix chain 'O' and resid 11 through 20 removed outlier: 4.643A pdb=" N ASN O 19 " --> pdb=" O LYS O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 59 removed outlier: 3.532A pdb=" N ASN O 42 " --> pdb=" O LYS O 38 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS O 45 " --> pdb=" O ARG O 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 26 through 37 Processing helix chain 'P' and resid 49 through 64 Processing helix chain 'P' and resid 73 through 82 removed outlier: 3.829A pdb=" N THR P 79 " --> pdb=" O ASN P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 104 removed outlier: 4.972A pdb=" N LEU P 104 " --> pdb=" O ILE P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 21 removed outlier: 3.856A pdb=" N ARG Q 19 " --> pdb=" O ASN Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 45 Processing helix chain 'Q' and resid 52 through 61 Processing helix chain 'R' and resid 21 through 26 removed outlier: 5.155A pdb=" N HIS R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 78 through 87 removed outlier: 3.852A pdb=" N THR R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU R 85 " --> pdb=" O ASP R 81 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR R 86 " --> pdb=" O LEU R 82 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N MET R 87 " --> pdb=" O GLU R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 4.186A pdb=" N VAL R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 45 removed outlier: 4.452A pdb=" N PHE S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR S 44 " --> pdb=" O ASP S 40 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 66 removed outlier: 3.621A pdb=" N TYR T 62 " --> pdb=" O ARG T 58 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA T 63 " --> pdb=" O PRO T 59 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR T 64 " --> pdb=" O ARG T 60 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER T 66 " --> pdb=" O TYR T 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 58 through 66' Processing helix chain 'T' and resid 81 through 113 removed outlier: 3.752A pdb=" N GLU T 110 " --> pdb=" O LYS T 106 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 12 removed outlier: 4.177A pdb=" N THR U 11 " --> pdb=" O TYR U 7 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS U 12 " --> pdb=" O GLU U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 38 removed outlier: 3.564A pdb=" N GLN U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU U 36 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER U 37 " --> pdb=" O VAL U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 71 removed outlier: 4.591A pdb=" N THR U 46 " --> pdb=" O PRO U 42 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 82 removed outlier: 5.175A pdb=" N ALA U 82 " --> pdb=" O LYS U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 91 Processing helix chain 'U' and resid 93 through 99 Processing helix chain 'U' and resid 101 through 111 Processing helix chain 'V' and resid 25 through 30 removed outlier: 4.459A pdb=" N LYS V 29 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS V 30 " --> pdb=" O ILE V 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 25 through 30' Processing helix chain 'V' and resid 34 through 49 Processing helix chain 'V' and resid 51 through 64 Processing helix chain 'V' and resid 65 through 77 Processing helix chain 'V' and resid 79 through 100 Processing helix chain 'W' and resid 4 through 11 removed outlier: 3.650A pdb=" N GLY W 9 " --> pdb=" O THR W 5 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS W 10 " --> pdb=" O PRO W 6 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG W 11 " --> pdb=" O SER W 7 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 58 Processing helix chain 'W' and resid 65 through 77 removed outlier: 5.840A pdb=" N HIS W 69 " --> pdb=" O ARG W 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL W 70 " --> pdb=" O TYR W 66 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER W 71 " --> pdb=" O LEU W 67 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG W 72 " --> pdb=" O LYS W 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 17 removed outlier: 3.795A pdb=" N ARG X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG X 17 " --> pdb=" O GLU X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 69 Processing helix chain 'Y' and resid 6 through 21 removed outlier: 5.318A pdb=" N ARG Y 21 " --> pdb=" O LYS Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 30 removed outlier: 4.498A pdb=" N ARG Y 28 " --> pdb=" O PRO Y 24 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG Y 30 " --> pdb=" O TRP Y 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 24 through 30' Processing helix chain 'Z' and resid 79 through 91 removed outlier: 3.873A pdb=" N TYR Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 48 Processing helix chain 'c' and resid 19 through 35 removed outlier: 3.577A pdb=" N GLN c 25 " --> pdb=" O SER c 21 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 92 removed outlier: 4.150A pdb=" N GLU c 91 " --> pdb=" O ARG c 87 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA c 92 " --> pdb=" O GLU c 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 25 removed outlier: 5.694A pdb=" N TRP d 8 " --> pdb=" O MET d 4 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 11 removed outlier: 4.394A pdb=" N GLY j 11 " --> pdb=" O ASN j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 39 removed outlier: 5.744A pdb=" N ARG j 37 " --> pdb=" O ASP j 33 " (cutoff:3.500A) Processing helix chain 'j' and resid 103 through 108 removed outlier: 4.097A pdb=" N VAL j 107 " --> pdb=" O PRO j 103 " (cutoff:3.500A) Proline residue: j 108 - end of helix No H-bonds generated for 'chain 'j' and resid 103 through 108' Processing helix chain 'j' and resid 181 through 193 removed outlier: 4.174A pdb=" N LEU j 191 " --> pdb=" O HIS j 187 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS j 192 " --> pdb=" O LYS j 188 " (cutoff:3.500A) Processing helix chain 'j' and resid 200 through 205 removed outlier: 3.826A pdb=" N MET j 204 " --> pdb=" O ARG j 200 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASN j 205 " --> pdb=" O GLY j 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 200 through 205' Processing helix chain 'j' and resid 173 through 178 removed outlier: 3.642A pdb=" N ASP j 176 " --> pdb=" O GLY j 173 " (cutoff:3.500A) Proline residue: j 178 - end of helix Processing helix chain 'k' and resid 111 through 120 removed outlier: 4.414A pdb=" N ARG k 117 " --> pdb=" O GLU k 113 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE k 118 " --> pdb=" O VAL k 114 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR k 119 " --> pdb=" O LYS k 115 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS k 120 " --> pdb=" O ARG k 116 " (cutoff:3.500A) Processing helix chain 'k' and resid 130 through 139 removed outlier: 3.973A pdb=" N ALA k 138 " --> pdb=" O SER k 134 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN k 139 " --> pdb=" O ALA k 135 " (cutoff:3.500A) Processing helix chain 'k' and resid 142 through 154 removed outlier: 4.412A pdb=" N ARG k 146 " --> pdb=" O ALA k 142 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU k 147 " --> pdb=" O GLY k 143 " (cutoff:3.500A) Processing helix chain 'k' and resid 165 through 170 removed outlier: 4.239A pdb=" N THR k 169 " --> pdb=" O GLN k 165 " (cutoff:3.500A) Proline residue: k 170 - end of helix No H-bonds generated for 'chain 'k' and resid 165 through 170' Processing helix chain 'k' and resid 187 through 199 Processing helix chain 'k' and resid 204 through 209 removed outlier: 4.180A pdb=" N VAL k 208 " --> pdb=" O ALA k 204 " (cutoff:3.500A) Processing helix chain 'k' and resid 228 through 233 Processing helix chain 'k' and resid 347 through 352 removed outlier: 6.411A pdb=" N LEU k 351 " --> pdb=" O SER k 347 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU k 352 " --> pdb=" O ARG k 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 347 through 352' Processing helix chain 'k' and resid 372 through 381 Processing helix chain 'l' and resid 31 through 46 removed outlier: 3.786A pdb=" N SER l 41 " --> pdb=" O THR l 37 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS l 44 " --> pdb=" O THR l 40 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN l 45 " --> pdb=" O SER l 41 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS l 46 " --> pdb=" O VAL l 42 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 131 removed outlier: 3.922A pdb=" N ALA l 130 " --> pdb=" O ILE l 126 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL l 131 " --> pdb=" O ALA l 127 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 139 Processing helix chain 'l' and resid 154 through 159 removed outlier: 4.896A pdb=" N SER l 158 " --> pdb=" O THR l 154 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE l 159 " --> pdb=" O ASP l 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 154 through 159' Processing helix chain 'l' and resid 161 through 173 Processing helix chain 'l' and resid 174 through 185 removed outlier: 4.236A pdb=" N LYS l 185 " --> pdb=" O VAL l 181 " (cutoff:3.500A) Processing helix chain 'l' and resid 191 through 196 removed outlier: 3.778A pdb=" N ARG l 195 " --> pdb=" O LYS l 191 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN l 196 " --> pdb=" O GLY l 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 191 through 196' Processing helix chain 'l' and resid 214 through 221 removed outlier: 4.755A pdb=" N ASN l 221 " --> pdb=" O LYS l 217 " (cutoff:3.500A) Processing helix chain 'l' and resid 234 through 240 Proline residue: l 240 - end of helix Processing helix chain 'l' and resid 251 through 262 removed outlier: 4.668A pdb=" N ASP l 259 " --> pdb=" O PHE l 255 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN l 260 " --> pdb=" O THR l 256 " (cutoff:3.500A) Processing helix chain 'l' and resid 285 through 292 Processing helix chain 'l' and resid 293 through 299 removed outlier: 3.687A pdb=" N ALA l 298 " --> pdb=" O GLU l 294 " (cutoff:3.500A) Processing helix chain 'l' and resid 320 through 328 Processing helix chain 'l' and resid 329 through 338 removed outlier: 4.449A pdb=" N VAL l 333 " --> pdb=" O PRO l 329 " (cutoff:3.500A) Processing helix chain 'l' and resid 352 through 361 Processing helix chain 'm' and resid 9 through 16 Processing helix chain 'm' and resid 20 through 26 Processing helix chain 'm' and resid 29 through 37 removed outlier: 3.682A pdb=" N ARG m 35 " --> pdb=" O TYR m 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 79 through 87 removed outlier: 4.613A pdb=" N LEU m 83 " --> pdb=" O TYR m 79 " (cutoff:3.500A) Proline residue: m 84 - end of helix Processing helix chain 'm' and resid 94 through 114 Processing helix chain 'm' and resid 115 through 120 removed outlier: 4.699A pdb=" N TYR m 119 " --> pdb=" O LEU m 115 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS m 120 " --> pdb=" O ASP m 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 115 through 120' Processing helix chain 'm' and resid 157 through 170 removed outlier: 3.763A pdb=" N GLY m 161 " --> pdb=" O ALA m 157 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY m 170 " --> pdb=" O ALA m 166 " (cutoff:3.500A) Processing helix chain 'm' and resid 191 through 201 removed outlier: 3.619A pdb=" N LEU m 195 " --> pdb=" O ASP m 191 " (cutoff:3.500A) Processing helix chain 'm' and resid 202 through 215 removed outlier: 3.709A pdb=" N TYR m 207 " --> pdb=" O HIS m 203 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP m 214 " --> pdb=" O GLU m 210 " (cutoff:3.500A) Processing helix chain 'm' and resid 216 through 223 removed outlier: 4.784A pdb=" N PHE m 223 " --> pdb=" O PHE m 219 " (cutoff:3.500A) Processing helix chain 'm' and resid 224 through 230 Processing helix chain 'm' and resid 234 through 250 removed outlier: 4.368A pdb=" N ASP m 238 " --> pdb=" O ASP m 234 " (cutoff:3.500A) Processing helix chain 'm' and resid 261 through 273 removed outlier: 3.766A pdb=" N GLU m 268 " --> pdb=" O GLN m 264 " (cutoff:3.500A) Processing helix chain 'm' and resid 278 through 294 Processing helix chain 'n' and resid 80 through 85 removed outlier: 3.994A pdb=" N VAL n 84 " --> pdb=" O ASN n 80 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE n 85 " --> pdb=" O ALA n 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 80 through 85' Processing helix chain 'n' and resid 102 through 107 removed outlier: 3.962A pdb=" N PHE n 106 " --> pdb=" O ASN n 102 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA n 107 " --> pdb=" O VAL n 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 102 through 107' Processing helix chain 'n' and resid 131 through 150 removed outlier: 3.875A pdb=" N LYS n 143 " --> pdb=" O LYS n 139 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA n 144 " --> pdb=" O VAL n 140 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA n 147 " --> pdb=" O LYS n 143 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU n 148 " --> pdb=" O ALA n 144 " (cutoff:3.500A) Processing helix chain 'n' and resid 154 through 162 removed outlier: 5.285A pdb=" N SER n 162 " --> pdb=" O TYR n 158 " (cutoff:3.500A) Processing helix chain 'o' and resid 27 through 73 Processing helix chain 'o' and resid 96 through 107 Processing helix chain 'o' and resid 120 through 131 removed outlier: 4.042A pdb=" N LEU o 126 " --> pdb=" O ALA o 122 " (cutoff:3.500A) Processing helix chain 'o' and resid 140 through 151 Processing helix chain 'o' and resid 165 through 173 removed outlier: 4.156A pdb=" N ILE o 169 " --> pdb=" O ASP o 165 " (cutoff:3.500A) Processing helix chain 'o' and resid 180 through 191 removed outlier: 4.171A pdb=" N VAL o 191 " --> pdb=" O GLU o 187 " (cutoff:3.500A) Processing helix chain 'o' and resid 194 through 203 removed outlier: 5.109A pdb=" N TRP o 203 " --> pdb=" O ASN o 199 " (cutoff:3.500A) Processing helix chain 'o' and resid 235 through 244 removed outlier: 3.632A pdb=" N LEU o 239 " --> pdb=" O PHE o 235 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 69 removed outlier: 4.223A pdb=" N LYS p 63 " --> pdb=" O GLN p 59 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE p 67 " --> pdb=" O LYS p 63 " (cutoff:3.500A) Processing helix chain 'p' and resid 72 through 80 removed outlier: 4.847A pdb=" N ALA p 76 " --> pdb=" O PRO p 72 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE p 78 " --> pdb=" O THR p 74 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLN p 79 " --> pdb=" O ILE p 75 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR p 80 " --> pdb=" O ALA p 76 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 98 removed outlier: 4.002A pdb=" N LYS p 96 " --> pdb=" O LYS p 92 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR p 97 " --> pdb=" O LEU p 93 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG p 98 " --> pdb=" O PHE p 94 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 119 Processing helix chain 'p' and resid 135 through 146 Processing helix chain 'p' and resid 159 through 174 removed outlier: 4.605A pdb=" N VAL p 163 " --> pdb=" O PRO p 159 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE p 165 " --> pdb=" O GLU p 161 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU p 166 " --> pdb=" O LEU p 162 " (cutoff:3.500A) Proline residue: p 167 - end of helix Processing helix chain 'p' and resid 182 through 191 Processing helix chain 'p' and resid 204 through 222 removed outlier: 3.675A pdb=" N GLU p 208 " --> pdb=" O ARG p 204 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA p 209 " --> pdb=" O ALA p 205 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA p 210 " --> pdb=" O GLU p 206 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR p 217 " --> pdb=" O LYS p 213 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA p 220 " --> pdb=" O SER p 216 " (cutoff:3.500A) Processing helix chain 'p' and resid 225 through 233 removed outlier: 4.682A pdb=" N LYS p 231 " --> pdb=" O ASP p 227 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS p 232 " --> pdb=" O GLU p 228 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TRP p 233 " --> pdb=" O VAL p 229 " (cutoff:3.500A) Processing helix chain 'p' and resid 239 through 255 removed outlier: 4.215A pdb=" N SER p 255 " --> pdb=" O LYS p 251 " (cutoff:3.500A) Processing helix chain 'q' and resid 61 through 84 removed outlier: 3.641A pdb=" N ARG q 69 " --> pdb=" O VAL q 65 " (cutoff:3.500A) Processing helix chain 'q' and resid 150 through 166 removed outlier: 4.143A pdb=" N CYS q 165 " --> pdb=" O LEU q 161 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG q 166 " --> pdb=" O GLN q 162 " (cutoff:3.500A) Processing helix chain 'q' and resid 171 through 176 removed outlier: 4.108A pdb=" N LEU q 176 " --> pdb=" O ILE q 172 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 10 removed outlier: 4.429A pdb=" N TYR r 9 " --> pdb=" O PRO r 5 " (cutoff:3.500A) Processing helix chain 'r' and resid 42 through 47 removed outlier: 4.412A pdb=" N PHE r 46 " --> pdb=" O THR r 42 " (cutoff:3.500A) Proline residue: r 47 - end of helix No H-bonds generated for 'chain 'r' and resid 42 through 47' Processing helix chain 'r' and resid 61 through 80 Processing helix chain 'r' and resid 107 through 112 removed outlier: 4.664A pdb=" N LEU r 111 " --> pdb=" O GLY r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 144 through 160 removed outlier: 3.558A pdb=" N GLU r 150 " --> pdb=" O ASP r 146 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR r 157 " --> pdb=" O ARG r 153 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS r 158 " --> pdb=" O ARG r 154 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE r 159 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 160 - end of helix Processing helix chain 'r' and resid 177 through 188 removed outlier: 4.306A pdb=" N ALA r 187 " --> pdb=" O LYS r 183 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLY r 188 " --> pdb=" O LYS r 184 " (cutoff:3.500A) Processing helix chain 'r' and resid 205 through 213 removed outlier: 4.577A pdb=" N PHE r 213 " --> pdb=" O ASN r 209 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 219 removed outlier: 4.577A pdb=" N ALA r 219 " --> pdb=" O GLU r 215 " (cutoff:3.500A) Processing helix chain 's' and resid 27 through 42 Processing helix chain 's' and resid 73 through 88 Processing helix chain 's' and resid 108 through 113 removed outlier: 4.451A pdb=" N LEU s 112 " --> pdb=" O GLU s 108 " (cutoff:3.500A) Processing helix chain 's' and resid 136 through 141 removed outlier: 3.837A pdb=" N ARG s 140 " --> pdb=" O ALA s 136 " (cutoff:3.500A) Processing helix chain 's' and resid 155 through 167 removed outlier: 4.922A pdb=" N TYR s 167 " --> pdb=" O PHE s 163 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 22 removed outlier: 4.153A pdb=" N ARG t 21 " --> pdb=" O HIS t 17 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL t 22 " --> pdb=" O TRP t 18 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 17 through 22' Processing helix chain 't' and resid 27 through 47 Processing helix chain 't' and resid 76 through 84 Processing helix chain 't' and resid 86 through 94 Processing helix chain 't' and resid 105 through 123 Processing helix chain 't' and resid 140 through 146 Proline residue: t 146 - end of helix Processing helix chain 't' and resid 165 through 180 removed outlier: 6.292A pdb=" N THR t 169 " --> pdb=" O SER t 165 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU t 170 " --> pdb=" O ALA t 166 " (cutoff:3.500A) Processing helix chain 't' and resid 181 through 193 Processing helix chain 'u' and resid 59 through 64 removed outlier: 4.075A pdb=" N VAL u 63 " --> pdb=" O ASN u 59 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N VAL u 64 " --> pdb=" O LEU u 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 59 through 64' Processing helix chain 'u' and resid 77 through 89 Processing helix chain 'u' and resid 90 through 98 removed outlier: 3.837A pdb=" N SER u 97 " --> pdb=" O LYS u 93 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N SER u 98 " --> pdb=" O TRP u 94 " (cutoff:3.500A) Processing helix chain 'u' and resid 99 through 112 Processing helix chain 'u' and resid 113 through 138 removed outlier: 4.239A pdb=" N ALA u 136 " --> pdb=" O LYS u 132 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS u 137 " --> pdb=" O LYS u 133 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA u 138 " --> pdb=" O ALA u 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 19 removed outlier: 3.878A pdb=" N GLU a 16 " --> pdb=" O LEU a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 84 removed outlier: 3.547A pdb=" N HIS a 83 " --> pdb=" O LYS a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 153 through 160 removed outlier: 5.414A pdb=" N ASN a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 161 through 175 removed outlier: 4.811A pdb=" N GLU a 175 " --> pdb=" O ASN a 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 177 through 206 removed outlier: 3.853A pdb=" N GLY a 206 " --> pdb=" O LEU a 202 " (cutoff:3.500A) Processing helix chain 'a' and resid 219 through 229 Proline residue: a 229 - end of helix Processing helix chain 'a' and resid 232 through 244 Processing helix chain 'a' and resid 250 through 258 removed outlier: 3.533A pdb=" N THR a 258 " --> pdb=" O LEU a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 259 through 278 Processing helix chain 'a' and resid 299 through 305 removed outlier: 4.282A pdb=" N ILE a 305 " --> pdb=" O ASP a 301 " (cutoff:3.500A) Processing helix chain 'a' and resid 317 through 324 removed outlier: 3.577A pdb=" N ASP a 322 " --> pdb=" O GLY a 318 " (cutoff:3.500A) Processing helix chain 'a' and resid 332 through 395 removed outlier: 6.615A pdb=" N THR a 336 " --> pdb=" O PRO a 332 " (cutoff:3.500A) Processing helix chain 'a' and resid 396 through 413 Processing helix chain 'a' and resid 415 through 430 Processing helix chain 'a' and resid 431 through 438 removed outlier: 5.382A pdb=" N ASN a 438 " --> pdb=" O ALA a 434 " (cutoff:3.500A) Processing helix chain 'a' and resid 513 through 527 Processing helix chain 'a' and resid 529 through 543 removed outlier: 4.058A pdb=" N GLY a 540 " --> pdb=" O GLU a 536 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS a 541 " --> pdb=" O LYS a 537 " (cutoff:3.500A) Processing helix chain 'a' and resid 545 through 554 Processing helix chain 'a' and resid 572 through 578 removed outlier: 4.008A pdb=" N LYS a 576 " --> pdb=" O TYR a 572 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR a 577 " --> pdb=" O PHE a 573 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N SER a 578 " --> pdb=" O PHE a 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 572 through 578' Processing helix chain 'a' and resid 593 through 604 Processing helix chain 'a' and resid 631 through 647 Processing helix chain 'a' and resid 661 through 666 removed outlier: 3.877A pdb=" N VAL a 665 " --> pdb=" O PHE a 661 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER a 666 " --> pdb=" O ALA a 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 661 through 666' Processing helix chain 'a' and resid 839 through 851 removed outlier: 3.712A pdb=" N LYS a 843 " --> pdb=" O GLY a 839 " (cutoff:3.500A) Processing helix chain 'a' and resid 855 through 867 Processing helix chain 'a' and resid 868 through 910 removed outlier: 5.229A pdb=" N LYS a 910 " --> pdb=" O LYS a 906 " (cutoff:3.500A) Processing helix chain 'a' and resid 916 through 925 removed outlier: 3.822A pdb=" N HIS a 920 " --> pdb=" O ASN a 916 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LYS a 925 " --> pdb=" O LYS a 921 " (cutoff:3.500A) Processing helix chain 'a' and resid 943 through 951 removed outlier: 4.560A pdb=" N LYS a 949 " --> pdb=" O PRO a 945 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR a 950 " --> pdb=" O ALA a 946 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYS a 951 " --> pdb=" O LEU a 947 " (cutoff:3.500A) Processing helix chain 'a' and resid 962 through 977 removed outlier: 4.077A pdb=" N ARG a 977 " --> pdb=" O TYR a 973 " (cutoff:3.500A) Processing helix chain 'a' and resid 990 through 1001 removed outlier: 5.576A pdb=" N LYS a1001 " --> pdb=" O ILE a 997 " (cutoff:3.500A) Processing helix chain 'a' and resid 1002 through 1010 removed outlier: 3.690A pdb=" N LEU a1007 " --> pdb=" O GLN a1003 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU a1008 " --> pdb=" O ASP a1004 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N CYS a1010 " --> pdb=" O VAL a1006 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 35 through 42 Processing helix chain 'e' and resid 44 through 57 removed outlier: 5.483A pdb=" N ARG e 57 " --> pdb=" O SER e 53 " (cutoff:3.500A) Processing helix chain 'e' and resid 58 through 76 removed outlier: 3.981A pdb=" N PHE e 76 " --> pdb=" O LEU e 72 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 84 removed outlier: 5.216A pdb=" N ASN e 84 " --> pdb=" O GLU e 80 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 99 removed outlier: 3.518A pdb=" N ALA e 96 " --> pdb=" O SER e 92 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS e 97 " --> pdb=" O GLN e 93 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 122 Processing helix chain 'e' and resid 123 through 130 removed outlier: 6.216A pdb=" N LYS e 127 " --> pdb=" O LYS e 123 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N PHE e 128 " --> pdb=" O LYS e 124 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS e 130 " --> pdb=" O SER e 126 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 142 removed outlier: 4.220A pdb=" N LEU e 135 " --> pdb=" O ASP e 131 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU e 142 " --> pdb=" O LEU e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 144 through 160 Proline residue: e 150 - end of helix Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 175 through 186 Processing helix chain 'e' and resid 189 through 195 removed outlier: 4.480A pdb=" N ASP e 195 " --> pdb=" O ASP e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 200 through 227 removed outlier: 3.717A pdb=" N SER e 204 " --> pdb=" O SER e 200 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N PHE e 206 " --> pdb=" O GLU e 202 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS e 227 " --> pdb=" O PHE e 223 " (cutoff:3.500A) Processing helix chain 'e' and resid 228 through 234 Processing helix chain 'e' and resid 235 through 243 Processing helix chain 'e' and resid 244 through 251 removed outlier: 3.751A pdb=" N LEU e 249 " --> pdb=" O SER e 245 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU e 250 " --> pdb=" O ILE e 246 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN e 251 " --> pdb=" O TRP e 247 " (cutoff:3.500A) Processing helix chain 'e' and resid 257 through 275 removed outlier: 4.620A pdb=" N TYR e 261 " --> pdb=" O ASN e 257 " (cutoff:3.500A) Processing helix chain 'e' and resid 276 through 281 removed outlier: 4.149A pdb=" N LYS e 281 " --> pdb=" O MET e 277 " (cutoff:3.500A) Processing helix chain 'e' and resid 282 through 298 removed outlier: 3.627A pdb=" N THR e 296 " --> pdb=" O LEU e 292 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE e 298 " --> pdb=" O SER e 294 " (cutoff:3.500A) Processing helix chain 'e' and resid 302 through 311 Proline residue: e 308 - end of helix Proline residue: e 311 - end of helix Processing helix chain 'e' and resid 312 through 325 removed outlier: 3.646A pdb=" N TYR e 323 " --> pdb=" O THR e 319 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU e 324 " --> pdb=" O LEU e 320 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP e 325 " --> pdb=" O ASP e 321 " (cutoff:3.500A) Processing helix chain 'e' and resid 326 through 333 removed outlier: 3.567A pdb=" N SER e 330 " --> pdb=" O GLY e 326 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP e 332 " --> pdb=" O ILE e 328 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LYS e 333 " --> pdb=" O TRP e 329 " (cutoff:3.500A) Processing helix chain 'e' and resid 334 through 350 removed outlier: 3.973A pdb=" N THR e 348 " --> pdb=" O SER e 344 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER e 349 " --> pdb=" O VAL e 345 " (cutoff:3.500A) Proline residue: e 350 - end of helix Processing helix chain 'e' and resid 353 through 369 removed outlier: 4.497A pdb=" N ARG e 367 " --> pdb=" O SER e 363 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS e 368 " --> pdb=" O SER e 364 " (cutoff:3.500A) Processing helix chain 'e' and resid 375 through 392 Proline residue: e 379 - end of helix Processing helix chain 'e' and resid 397 through 417 removed outlier: 3.631A pdb=" N ASP e 415 " --> pdb=" O LYS e 411 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER e 416 " --> pdb=" O PHE e 412 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER e 417 " --> pdb=" O ALA e 413 " (cutoff:3.500A) Processing helix chain 'e' and resid 418 through 436 Processing helix chain 'e' and resid 438 through 443 removed outlier: 4.877A pdb=" N THR e 443 " --> pdb=" O LEU e 439 " (cutoff:3.500A) Processing helix chain 'e' and resid 444 through 450 removed outlier: 3.571A pdb=" N SER e 450 " --> pdb=" O ASN e 446 " (cutoff:3.500A) Processing helix chain 'e' and resid 454 through 468 removed outlier: 3.608A pdb=" N TRP e 458 " --> pdb=" O PRO e 454 " (cutoff:3.500A) Processing helix chain 'e' and resid 469 through 477 removed outlier: 5.140A pdb=" N VAL e 477 " --> pdb=" O ARG e 473 " (cutoff:3.500A) Processing helix chain 'e' and resid 478 through 490 Processing helix chain 'e' and resid 493 through 512 Proline residue: e 512 - end of helix Processing helix chain 'e' and resid 514 through 520 removed outlier: 3.676A pdb=" N TYR e 519 " --> pdb=" O VAL e 515 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP e 520 " --> pdb=" O PHE e 516 " (cutoff:3.500A) Processing helix chain 'e' and resid 521 through 533 removed outlier: 4.835A pdb=" N ASP e 533 " --> pdb=" O PHE e 529 " (cutoff:3.500A) Processing helix chain 'e' and resid 534 through 552 removed outlier: 4.502A pdb=" N GLY e 539 " --> pdb=" O ILE e 535 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LYS e 540 " --> pdb=" O PHE e 536 " (cutoff:3.500A) Proline residue: e 549 - end of helix Processing helix chain 'e' and resid 556 through 571 removed outlier: 3.717A pdb=" N ILE e 563 " --> pdb=" O ASN e 559 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS e 571 " --> pdb=" O TYR e 567 " (cutoff:3.500A) Processing helix chain 'e' and resid 572 through 577 removed outlier: 5.365A pdb=" N THR e 577 " --> pdb=" O PHE e 573 " (cutoff:3.500A) Processing helix chain 'e' and resid 578 through 594 removed outlier: 4.978A pdb=" N ASN e 594 " --> pdb=" O ALA e 590 " (cutoff:3.500A) Processing helix chain 'e' and resid 596 through 608 removed outlier: 5.285A pdb=" N ASP e 608 " --> pdb=" O MET e 604 " (cutoff:3.500A) Processing helix chain 'e' and resid 609 through 619 removed outlier: 5.366A pdb=" N ASP e 619 " --> pdb=" O LEU e 615 " (cutoff:3.500A) Processing helix chain 'e' and resid 622 through 634 Processing helix chain 'e' and resid 640 through 646 removed outlier: 4.438A pdb=" N ASN e 646 " --> pdb=" O ILE e 642 " (cutoff:3.500A) Processing helix chain 'e' and resid 651 through 666 Processing helix chain 'e' and resid 667 through 679 removed outlier: 4.834A pdb=" N ASP e 679 " --> pdb=" O LEU e 675 " (cutoff:3.500A) Processing helix chain 'e' and resid 680 through 690 Processing helix chain 'e' and resid 691 through 698 removed outlier: 5.335A pdb=" N TYR e 698 " --> pdb=" O SER e 694 " (cutoff:3.500A) Processing helix chain 'e' and resid 701 through 720 removed outlier: 4.386A pdb=" N SER e 720 " --> pdb=" O ALA e 716 " (cutoff:3.500A) Processing helix chain 'e' and resid 721 through 737 Processing helix chain 'e' and resid 742 through 758 removed outlier: 4.316A pdb=" N TYR e 746 " --> pdb=" O ALA e 742 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU e 752 " --> pdb=" O THR e 748 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU e 753 " --> pdb=" O HIS e 749 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN e 758 " --> pdb=" O ILE e 754 " (cutoff:3.500A) Processing helix chain 'e' and resid 759 through 765 removed outlier: 3.907A pdb=" N ILE e 763 " --> pdb=" O ASP e 759 " (cutoff:3.500A) Processing helix chain 'e' and resid 768 through 777 removed outlier: 3.982A pdb=" N VAL e 772 " --> pdb=" O ASN e 768 " (cutoff:3.500A) Processing helix chain 'e' and resid 781 through 788 removed outlier: 4.186A pdb=" N SER e 785 " --> pdb=" O ASP e 781 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU e 786 " --> pdb=" O TYR e 782 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL e 787 " --> pdb=" O ARG e 783 " (cutoff:3.500A) Processing helix chain 'e' and resid 792 through 798 removed outlier: 4.581A pdb=" N LEU e 796 " --> pdb=" O THR e 792 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU e 797 " --> pdb=" O ASN e 793 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU e 798 " --> pdb=" O THR e 794 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 792 through 798' Processing helix chain 'e' and resid 805 through 827 Proline residue: e 827 - end of helix Processing helix chain 'e' and resid 831 through 852 Processing helix chain 'e' and resid 856 through 861 removed outlier: 4.285A pdb=" N TYR e 860 " --> pdb=" O ASN e 856 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP e 861 " --> pdb=" O ASP e 857 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 856 through 861' Processing helix chain 'e' and resid 875 through 886 Proline residue: e 886 - end of helix Processing helix chain 'e' and resid 895 through 903 removed outlier: 3.558A pdb=" N SER e 901 " --> pdb=" O ASP e 897 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN e 902 " --> pdb=" O ILE e 898 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N SER e 903 " --> pdb=" O ALA e 899 " (cutoff:3.500A) Processing helix chain 'e' and resid 904 through 921 Processing helix chain 'e' and resid 927 through 947 removed outlier: 3.638A pdb=" N SER e 935 " --> pdb=" O GLY e 931 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLN e 947 " --> pdb=" O THR e 943 " (cutoff:3.500A) Processing helix chain 'e' and resid 950 through 969 removed outlier: 4.726A pdb=" N ARG e 966 " --> pdb=" O LEU e 962 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N SER e 967 " --> pdb=" O MET e 963 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER e 969 " --> pdb=" O ASN e 965 " (cutoff:3.500A) Processing helix chain 'e' and resid 970 through 986 removed outlier: 3.835A pdb=" N THR e 974 " --> pdb=" O LYS e 970 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY e 986 " --> pdb=" O SER e 982 " (cutoff:3.500A) Processing helix chain 'e' and resid 988 through 995 Processing helix chain 'e' and resid 996 through 1008 Processing helix chain 'e' and resid 1020 through 1037 Processing helix chain 'e' and resid 1044 through 1063 removed outlier: 4.387A pdb=" N VAL e1048 " --> pdb=" O SER e1044 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE e1062 " --> pdb=" O LYS e1058 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU e1063 " --> pdb=" O LEU e1059 " (cutoff:3.500A) Processing helix chain 'e' and resid 1064 through 1069 removed outlier: 3.791A pdb=" N GLY e1069 " --> pdb=" O VAL e1065 " (cutoff:3.500A) Processing helix chain 'e' and resid 1070 through 1090 removed outlier: 3.515A pdb=" N LEU e1075 " --> pdb=" O THR e1071 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP e1090 " --> pdb=" O MET e1086 " (cutoff:3.500A) Processing helix chain 'e' and resid 1094 through 1111 Processing helix chain 'e' and resid 1123 through 1137 removed outlier: 3.702A pdb=" N MET e1135 " --> pdb=" O LEU e1131 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE e1136 " --> pdb=" O ILE e1132 " (cutoff:3.500A) Processing helix chain 'e' and resid 1145 through 1163 removed outlier: 3.651A pdb=" N THR e1149 " --> pdb=" O ASN e1145 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N GLU e1163 " --> pdb=" O ILE e1159 " (cutoff:3.500A) Processing helix chain 'e' and resid 1164 through 1172 removed outlier: 3.587A pdb=" N SER e1169 " --> pdb=" O LYS e1165 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN e1170 " --> pdb=" O LYS e1166 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LYS e1172 " --> pdb=" O GLU e1168 " (cutoff:3.500A) Processing helix chain 'e' and resid 1173 through 1181 removed outlier: 4.571A pdb=" N ASP e1181 " --> pdb=" O VAL e1177 " (cutoff:3.500A) Processing helix chain 'e' and resid 1182 through 1188 removed outlier: 4.689A pdb=" N ASN e1187 " --> pdb=" O ASP e1183 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE e1188 " --> pdb=" O ILE e1184 " (cutoff:3.500A) Processing helix chain 'e' and resid 1189 through 1217 removed outlier: 3.628A pdb=" N ASP e1208 " --> pdb=" O LYS e1204 " (cutoff:3.500A) Processing helix chain 'e' and resid 1235 through 1240 removed outlier: 3.727A pdb=" N LYS e1239 " --> pdb=" O ASN e1235 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU e1240 " --> pdb=" O SER e1236 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 1235 through 1240' Processing helix chain 'e' and resid 1241 through 1251 Processing helix chain 'e' and resid 1261 through 1281 removed outlier: 3.543A pdb=" N TYR e1278 " --> pdb=" O LEU e1274 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE e1279 " --> pdb=" O ILE e1275 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP e1281 " --> pdb=" O MET e1277 " (cutoff:3.500A) Processing helix chain 'e' and resid 1283 through 1298 removed outlier: 3.505A pdb=" N ILE e1289 " --> pdb=" O ASN e1285 " (cutoff:3.500A) Processing helix chain 'e' and resid 1299 through 1312 removed outlier: 5.364A pdb=" N ASP e1312 " --> pdb=" O THR e1308 " (cutoff:3.500A) Processing helix chain 'e' and resid 1315 through 1323 removed outlier: 3.984A pdb=" N TRP e1319 " --> pdb=" O ASP e1315 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASP e1323 " --> pdb=" O TRP e1319 " (cutoff:3.500A) Processing helix chain 'e' and resid 1324 through 1329 Processing helix chain 'e' and resid 1341 through 1363 Processing helix chain 'e' and resid 1364 through 1374 removed outlier: 4.948A pdb=" N SER e1368 " --> pdb=" O GLY e1364 " (cutoff:3.500A) Processing helix chain 'e' and resid 1376 through 1390 Processing helix chain 'e' and resid 1391 through 1411 removed outlier: 4.599A pdb=" N ASP e1408 " --> pdb=" O ASN e1404 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG e1409 " --> pdb=" O SER e1405 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU e1410 " --> pdb=" O LYS e1406 " (cutoff:3.500A) Processing helix chain 'e' and resid 1465 through 1481 Processing helix chain 'e' and resid 1486 through 1503 Processing helix chain 'e' and resid 1535 through 1547 removed outlier: 4.304A pdb=" N GLY e1547 " --> pdb=" O PHE e1543 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 17 removed outlier: 4.233A pdb=" N PHE g 16 " --> pdb=" O GLU g 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 42 removed outlier: 3.829A pdb=" N PHE g 38 " --> pdb=" O PHE g 34 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 63 removed outlier: 4.796A pdb=" N MET g 62 " --> pdb=" O ILE g 58 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 88 Processing helix chain 'g' and resid 103 through 108 Processing helix chain 'g' and resid 122 through 133 Processing helix chain 'g' and resid 147 through 152 Processing helix chain 'g' and resid 166 through 178 Processing helix chain 'g' and resid 192 through 197 Processing helix chain 'g' and resid 211 through 223 Processing helix chain 'w' and resid 5 through 21 Processing helix chain 'w' and resid 70 through 81 removed outlier: 3.729A pdb=" N SER w 79 " --> pdb=" O ASP w 75 " (cutoff:3.500A) Processing helix chain 'w' and resid 86 through 94 removed outlier: 3.660A pdb=" N ASN w 94 " --> pdb=" O LEU w 90 " (cutoff:3.500A) Processing helix chain 'w' and resid 96 through 108 removed outlier: 4.878A pdb=" N ASN w 108 " --> pdb=" O SER w 104 " (cutoff:3.500A) Processing helix chain 'w' and resid 113 through 124 removed outlier: 4.556A pdb=" N LYS w 118 " --> pdb=" O GLU w 114 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLN w 119 " --> pdb=" O VAL w 115 " (cutoff:3.500A) Proline residue: w 121 - end of helix Processing helix chain 'w' and resid 126 through 132 Processing helix chain 'w' and resid 143 through 154 Processing helix chain 'w' and resid 175 through 195 removed outlier: 5.072A pdb=" N LYS w 195 " --> pdb=" O VAL w 191 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 37 Proline residue: z 34 - end of helix Processing helix chain 'z' and resid 39 through 52 removed outlier: 3.683A pdb=" N GLU z 52 " --> pdb=" O LYS z 48 " (cutoff:3.500A) Processing helix chain 'z' and resid 77 through 87 removed outlier: 5.035A pdb=" N GLU z 87 " --> pdb=" O THR z 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 106 through 118 Processing helix chain 'z' and resid 125 through 138 removed outlier: 4.663A pdb=" N SER z 138 " --> pdb=" O GLY z 134 " (cutoff:3.500A) Processing helix chain 'z' and resid 151 through 156 removed outlier: 5.016A pdb=" N ASN z 156 " --> pdb=" O ILE z 152 " (cutoff:3.500A) Processing helix chain 'z' and resid 158 through 163 Proline residue: z 163 - end of helix Processing helix chain '0' and resid 3 through 23 removed outlier: 4.981A pdb=" N LYS 0 23 " --> pdb=" O LEU 0 19 " (cutoff:3.500A) Processing helix chain '0' and resid 34 through 46 Processing helix chain '0' and resid 55 through 71 removed outlier: 4.923A pdb=" N SER 0 68 " --> pdb=" O ARG 0 64 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP 0 69 " --> pdb=" O GLY 0 65 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU 0 70 " --> pdb=" O PHE 0 66 " (cutoff:3.500A) Proline residue: 0 71 - end of helix Processing helix chain '0' and resid 72 through 81 removed outlier: 4.429A pdb=" N LEU 0 76 " --> pdb=" O ASP 0 72 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU 0 77 " --> pdb=" O PHE 0 73 " (cutoff:3.500A) Proline residue: 0 78 - end of helix removed outlier: 4.205A pdb=" N LYS 0 81 " --> pdb=" O LEU 0 77 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 72 through 81' Processing helix chain '0' and resid 93 through 103 Processing helix chain 'v' and resid 22 through 27 removed outlier: 5.217A pdb=" N ARG v 27 " --> pdb=" O CYS v 23 " (cutoff:3.500A) Processing helix chain 'v' and resid 118 through 131 Processing sheet with id= 1, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.466A pdb=" N VAL A 35 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 61 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY A 58 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A 133 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 117 through 121 removed outlier: 3.635A pdb=" N ASN A 117 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N TYR A 129 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 6 through 10 Processing sheet with id= 4, first strand: chain 'C' and resid 16 through 20 Processing sheet with id= 5, first strand: chain 'C' and resid 57 through 60 removed outlier: 5.436A pdb=" N LYS C 80 " --> pdb=" O PHE C 60 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 124 through 131 No H-bonds generated for sheet with id= 6 Processing sheet with id= 7, first strand: chain 'D' and resid 119 through 122 removed outlier: 4.878A pdb=" N THR D 100 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'F' and resid 24 through 31 removed outlier: 6.706A pdb=" N ILE F 10 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 87 through 96 removed outlier: 5.101A pdb=" N ASN F 74 " --> pdb=" O ILE F 129 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 6 through 10 removed outlier: 4.567A pdb=" N GLU F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 38 through 43 removed outlier: 4.577A pdb=" N ASP G 38 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS G 60 " --> pdb=" O ILE G 42 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 54 through 58 removed outlier: 6.171A pdb=" N ASN H 101 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 79 through 82 removed outlier: 3.921A pdb=" N ALA I 82 " --> pdb=" O ASP I 97 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP I 97 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN I 98 " --> pdb=" O ILE I 22 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA I 21 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N MET I 59 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP I 56 " --> pdb=" O VAL I 78 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 84 through 87 removed outlier: 4.506A pdb=" N VAL I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'I' and resid 75 through 78 Processing sheet with id= 16, first strand: chain 'J' and resid 3 through 6 removed outlier: 6.441A pdb=" N GLU J 4 " --> pdb=" O LYS J 12 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS J 12 " --> pdb=" O GLU J 4 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP J 6 " --> pdb=" O GLY J 10 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 18 through 22 Processing sheet with id= 18, first strand: chain 'K' and resid 81 through 86 removed outlier: 3.734A pdb=" N LYS K 120 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR K 119 " --> pdb=" O ARG K 115 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 56 through 59 removed outlier: 4.092A pdb=" N GLN L 66 " --> pdb=" O VAL L 58 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'L' and resid 72 through 75 Processing sheet with id= 21, first strand: chain 'L' and resid 86 through 89 removed outlier: 4.344A pdb=" N ALA L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 8 through 13 removed outlier: 4.145A pdb=" N LYS M 9 " --> pdb=" O ILE M 25 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS M 21 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 27 through 30 removed outlier: 4.643A pdb=" N LYS M 27 " --> pdb=" O LEU M 42 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'N' and resid 99 through 102 Processing sheet with id= 25, first strand: chain 'P' and resid 22 through 25 removed outlier: 6.373A pdb=" N LYS P 22 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU P 41 " --> pdb=" O ILE P 92 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS P 66 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Q' and resid 48 through 51 removed outlier: 4.934A pdb=" N ASP Q 48 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL Q 8 " --> pdb=" O ARG Q 77 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR Q 9 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 71 through 77 Processing sheet with id= 28, first strand: chain 'S' and resid 11 through 15 removed outlier: 6.753A pdb=" N LEU S 29 " --> pdb=" O LEU S 14 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG S 82 " --> pdb=" O THR S 72 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS S 63 " --> pdb=" O ALA S 55 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS S 47 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG S 48 " --> pdb=" O PHE S 101 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'S' and resid 8 through 14 removed outlier: 4.046A pdb=" N ALA S 96 " --> pdb=" O HIS S 13 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'T' and resid 19 through 24 removed outlier: 4.586A pdb=" N LYS T 19 " --> pdb=" O VAL T 35 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'X' and resid 2 through 5 removed outlier: 4.535A pdb=" N VAL X 55 " --> pdb=" O ILE X 5 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR X 22 " --> pdb=" O ARG X 46 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Z' and resid 100 through 103 removed outlier: 4.138A pdb=" N ALA Z 101 " --> pdb=" O CYS Z 96 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS Z 93 " --> pdb=" O LYS Z 124 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLN Z 120 " --> pdb=" O ARG Z 97 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'b' and resid 7 through 10 removed outlier: 4.478A pdb=" N VAL b 68 " --> pdb=" O LEU b 85 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR b 79 " --> pdb=" O CYS b 74 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'c' and resid 47 through 50 removed outlier: 6.879A pdb=" N ILE c 54 " --> pdb=" O GLY c 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLY c 53 " --> pdb=" O GLY c 66 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS c 62 " --> pdb=" O CYS c 57 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'j' and resid 47 through 50 removed outlier: 3.921A pdb=" N GLN j 47 " --> pdb=" O LYS j 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS j 60 " --> pdb=" O LYS j 46 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN j 86 " --> pdb=" O VAL j 45 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'j' and resid 111 through 114 removed outlier: 4.419A pdb=" N THR j 111 " --> pdb=" O ILE j 136 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG j 147 " --> pdb=" O ILE j 137 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'j' and resid 58 through 64 Processing sheet with id= 38, first strand: chain 'j' and resid 145 through 150 removed outlier: 4.405A pdb=" N ALA j 154 " --> pdb=" O LEU j 150 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'k' and resid 41 through 44 removed outlier: 4.889A pdb=" N ALA k 42 " --> pdb=" O ASN k 184 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLN k 182 " --> pdb=" O THR k 44 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N HIS k 177 " --> pdb=" O THR k 164 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU k 161 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS k 201 " --> pdb=" O VAL k 86 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'k' and resid 53 through 59 removed outlier: 6.661A pdb=" N VAL k 78 " --> pdb=" O ALA k 51 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG k 334 " --> pdb=" O LYS k 50 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE k 335 " --> pdb=" O VAL k 220 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL k 220 " --> pdb=" O ILE k 335 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS k 273 " --> pdb=" O THR k 221 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'k' and resid 98 through 101 Processing sheet with id= 42, first strand: chain 'k' and resid 284 through 288 removed outlier: 3.741A pdb=" N GLY k 288 " --> pdb=" O ASN k 319 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN k 319 " --> pdb=" O GLY k 288 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'k' and resid 76 through 80 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'k' and resid 88 through 93 removed outlier: 3.745A pdb=" N GLY k 88 " --> pdb=" O LEU k 161 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'k' and resid 213 through 216 removed outlier: 4.189A pdb=" N GLU k 213 " --> pdb=" O ILE k 282 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'l' and resid 75 through 78 removed outlier: 4.383A pdb=" N GLN l 87 " --> pdb=" O VAL l 77 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'l' and resid 205 through 208 Processing sheet with id= 48, first strand: chain 'm' and resid 72 through 75 removed outlier: 6.834A pdb=" N ILE m 64 " --> pdb=" O LEU m 75 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'n' and resid 37 through 42 removed outlier: 3.956A pdb=" N THR n 38 " --> pdb=" O TYR n 54 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS n 50 " --> pdb=" O LEU n 42 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'o' and resid 133 through 138 removed outlier: 7.864A pdb=" N TYR o 133 " --> pdb=" O ILE o 89 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS o 82 " --> pdb=" O VAL o 119 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER o 113 " --> pdb=" O ARG o 88 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASN o 112 " --> pdb=" O LEU o 207 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'o' and resid 152 through 155 removed outlier: 8.624A pdb=" N GLY o 152 " --> pdb=" O LEU o 163 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'p' and resid 176 through 181 Processing sheet with id= 53, first strand: chain 'q' and resid 5 through 12 removed outlier: 4.945A pdb=" N GLN q 51 " --> pdb=" O VAL q 12 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU q 52 " --> pdb=" O VAL q 48 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'q' and resid 17 through 20 removed outlier: 5.995A pdb=" N ARG q 23 " --> pdb=" O LEU q 38 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 132 through 137 removed outlier: 4.963A pdb=" N GLU q 143 " --> pdb=" O SER q 137 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP q 142 " --> pdb=" O TYR q 92 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'q' and resid 86 through 90 Processing sheet with id= 57, first strand: chain 'r' and resid 34 through 37 removed outlier: 6.337A pdb=" N TYR r 34 " --> pdb=" O VAL r 89 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU r 52 " --> pdb=" O ILE r 135 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN r 133 " --> pdb=" O SER r 54 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'r' and resid 56 through 59 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'r' and resid 189 through 193 removed outlier: 7.659A pdb=" N GLU r 189 " --> pdb=" O LEU r 200 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE r 196 " --> pdb=" O ASP r 193 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'r' and resid 49 through 55 removed outlier: 5.069A pdb=" N CYS r 49 " --> pdb=" O SER r 168 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLN r 162 " --> pdb=" O ASN r 55 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 's' and resid 45 through 49 removed outlier: 5.683A pdb=" N SER s 22 " --> pdb=" O GLY s 124 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLY s 124 " --> pdb=" O SER s 22 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 's' and resid 52 through 55 removed outlier: 7.191A pdb=" N TYR s 52 " --> pdb=" O ARG s 61 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG s 61 " --> pdb=" O TYR s 52 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 's' and resid 89 through 92 removed outlier: 3.627A pdb=" N ASP s 170 " --> pdb=" O TYR s 89 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU s 91 " --> pdb=" O ASP s 170 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 't' and resid 56 through 59 Processing sheet with id= 65, first strand: chain 'u' and resid 19 through 24 removed outlier: 4.472A pdb=" N ARG u 19 " --> pdb=" O ILE u 35 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS u 31 " --> pdb=" O ILE u 23 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'u' and resid 36 through 39 removed outlier: 6.764A pdb=" N LYS u 43 " --> pdb=" O ILE u 39 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'a' and resid 27 through 32 removed outlier: 3.801A pdb=" N ASN a 28 " --> pdb=" O LYS a 42 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLN a 38 " --> pdb=" O ILE a 32 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'a' and resid 91 through 95 removed outlier: 4.127A pdb=" N ALA a 91 " --> pdb=" O GLN a 104 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE a 100 " --> pdb=" O VAL a 95 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG a 99 " --> pdb=" O PHE a 116 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'a' and resid 122 through 125 removed outlier: 6.747A pdb=" N VAL a 122 " --> pdb=" O GLN a 135 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA a 133 " --> pdb=" O LEU a 124 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'a' and resid 307 through 311 removed outlier: 3.548A pdb=" N THR a 308 " --> pdb=" O LEU a 286 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARG a 281 " --> pdb=" O GLY a 331 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'a' and resid 446 through 454 removed outlier: 9.186A pdb=" N ASN a 446 " --> pdb=" O LEU a 510 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU a 502 " --> pdb=" O LEU a 454 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'a' and resid 586 through 590 removed outlier: 3.748A pdb=" N LEU a 587 " --> pdb=" O LYS a 623 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'a' and resid 657 through 660 Processing sheet with id= 74, first strand: chain 'a' and resid 936 through 942 removed outlier: 3.837A pdb=" N ASP a 936 " --> pdb=" O LYS a 706 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE a 703 " --> pdb=" O TYR a 952 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR a 952 " --> pdb=" O PHE a 703 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'e' and resid 1417 through 1423 removed outlier: 5.631A pdb=" N ASN e1426 " --> pdb=" O LEU e1445 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU e1440 " --> pdb=" O VAL e1459 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'g' and resid 23 through 27 Processing sheet with id= 77, first strand: chain 'g' and resid 69 through 73 Processing sheet with id= 78, first strand: chain 'g' and resid 114 through 117 Processing sheet with id= 79, first strand: chain 'g' and resid 158 through 161 Processing sheet with id= 80, first strand: chain 'w' and resid 49 through 53 removed outlier: 7.221A pdb=" N PHE w 49 " --> pdb=" O LEU w 159 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'w' and resid 65 through 68 Processing sheet with id= 82, first strand: chain 'w' and resid 163 through 169 removed outlier: 6.356A pdb=" N LEU w 163 " --> pdb=" O LEU w 38 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL w 32 " --> pdb=" O VAL w 169 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU w 204 " --> pdb=" O LEU w 216 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'z' and resid 11 through 17 removed outlier: 3.526A pdb=" N LYS z 11 " --> pdb=" O GLN z 65 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL z 60 " --> pdb=" O PRO z 75 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain '0' and resid 49 through 53 removed outlier: 3.837A pdb=" N SER 0 24 " --> pdb=" O THR 0 89 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL 0 27 " --> pdb=" O VAL 0 188 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'v' and resid 18 through 21 removed outlier: 3.677A pdb=" N SER v 149 " --> pdb=" O THR v 137 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'v' and resid 30 through 33 removed outlier: 4.740A pdb=" N GLY v 30 " --> pdb=" O ILE v 41 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL v 60 " --> pdb=" O VAL v 42 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'v' and resid 101 through 104 removed outlier: 3.654A pdb=" N ASP v 108 " --> pdb=" O ASN v 104 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'v' and resid 57 through 63 removed outlier: 4.295A pdb=" N LYS v 68 " --> pdb=" O ASP v 63 " (cutoff:3.500A) 3353 hydrogen bonds defined for protein. 9966 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2914 hydrogen bonds 4640 hydrogen bond angles 0 basepair planarities 1184 basepair parallelities 2003 stacking parallelities Total time for adding SS restraints: 239.45 Time building geometry restraints manager: 61.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 18246 1.32 - 1.44: 63684 1.44 - 1.57: 72380 1.57 - 1.69: 7276 1.69 - 1.82: 279 Bond restraints: 161865 Sorted by residual: bond pdb=" CA UNK 1 58 " pdb=" C UNK 1 58 " ideal model delta sigma weight residual 1.525 1.650 -0.125 2.10e-02 2.27e+03 3.55e+01 bond pdb=" O3' U f2416 " pdb=" P U f2417 " ideal model delta sigma weight residual 1.607 1.536 0.071 1.50e-02 4.44e+03 2.24e+01 bond pdb=" N LYS j 221 " pdb=" CA LYS j 221 " ideal model delta sigma weight residual 1.452 1.400 0.052 1.30e-02 5.92e+03 1.61e+01 bond pdb=" CA PHE e 405 " pdb=" C PHE e 405 " ideal model delta sigma weight residual 1.524 1.475 0.049 1.27e-02 6.20e+03 1.47e+01 bond pdb=" CA LEU e1445 " pdb=" C LEU e1445 " ideal model delta sigma weight residual 1.522 1.481 0.041 1.14e-02 7.69e+03 1.29e+01 ... (remaining 161860 not shown) Histogram of bond angle deviations from ideal: 94.26 - 102.72: 6152 102.72 - 111.18: 83745 111.18 - 119.63: 73277 119.63 - 128.09: 67147 128.09 - 136.55: 6130 Bond angle restraints: 236451 Sorted by residual: angle pdb=" N GLY e1364 " pdb=" CA GLY e1364 " pdb=" C GLY e1364 " ideal model delta sigma weight residual 112.49 127.29 -14.80 1.21e+00 6.83e-01 1.50e+02 angle pdb=" N PHE a 116 " pdb=" CA PHE a 116 " pdb=" C PHE a 116 " ideal model delta sigma weight residual 112.88 99.52 13.36 1.29e+00 6.01e-01 1.07e+02 angle pdb=" N SER e1460 " pdb=" CA SER e1460 " pdb=" C SER e1460 " ideal model delta sigma weight residual 111.36 122.27 -10.91 1.09e+00 8.42e-01 1.00e+02 angle pdb=" N ASP e1181 " pdb=" CA ASP e1181 " pdb=" C ASP e1181 " ideal model delta sigma weight residual 111.28 120.93 -9.65 1.09e+00 8.42e-01 7.84e+01 angle pdb=" N GLN e1141 " pdb=" CA GLN e1141 " pdb=" C GLN e1141 " ideal model delta sigma weight residual 111.28 120.83 -9.55 1.09e+00 8.42e-01 7.68e+01 ... (remaining 236446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 93037 35.98 - 71.96: 8368 71.96 - 107.95: 867 107.95 - 143.93: 20 143.93 - 179.91: 56 Dihedral angle restraints: 102348 sinusoidal: 74893 harmonic: 27455 Sorted by residual: dihedral pdb=" CA THR p 30 " pdb=" C THR p 30 " pdb=" N PRO p 31 " pdb=" CA PRO p 31 " ideal model delta harmonic sigma weight residual -180.00 -124.95 -55.05 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA GLY O 20 " pdb=" C GLY O 20 " pdb=" N ILE O 21 " pdb=" CA ILE O 21 " ideal model delta harmonic sigma weight residual -180.00 -132.40 -47.60 0 5.00e+00 4.00e-02 9.06e+01 dihedral pdb=" CA LYS U 83 " pdb=" C LYS U 83 " pdb=" N LYS U 84 " pdb=" CA LYS U 84 " ideal model delta harmonic sigma weight residual -180.00 -133.06 -46.94 0 5.00e+00 4.00e-02 8.81e+01 ... (remaining 102345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 28723 0.149 - 0.298: 746 0.298 - 0.447: 57 0.447 - 0.596: 2 0.596 - 0.745: 1 Chirality restraints: 29529 Sorted by residual: chirality pdb=" CB ILE U 118 " pdb=" CA ILE U 118 " pdb=" CG1 ILE U 118 " pdb=" CG2 ILE U 118 " both_signs ideal model delta sigma weight residual False 2.64 1.90 0.74 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CA ASP p 158 " pdb=" N ASP p 158 " pdb=" C ASP p 158 " pdb=" CB ASP p 158 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.93e+00 chirality pdb=" C3' G f 282 " pdb=" C4' G f 282 " pdb=" O3' G f 282 " pdb=" C2' G f 282 " both_signs ideal model delta sigma weight residual False -2.48 -2.01 -0.47 2.00e-01 2.50e+01 5.47e+00 ... (remaining 29526 not shown) Planarity restraints: 16480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP m 95 " -0.034 2.00e-02 2.50e+03 3.44e-02 2.96e+01 pdb=" CG TRP m 95 " 0.090 2.00e-02 2.50e+03 pdb=" CD1 TRP m 95 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP m 95 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP m 95 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP m 95 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP m 95 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 95 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 95 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP m 95 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG d 5 " -0.024 2.00e-02 2.50e+03 4.76e-02 2.26e+01 pdb=" C ARG d 5 " 0.082 2.00e-02 2.50e+03 pdb=" O ARG d 5 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA d 6 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 60 " 0.014 2.00e-02 2.50e+03 3.10e-02 1.92e+01 pdb=" CG TYR N 60 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR N 60 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR N 60 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR N 60 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR N 60 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR N 60 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR N 60 " -0.006 2.00e-02 2.50e+03 ... (remaining 16477 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 33 2.12 - 2.81: 40791 2.81 - 3.51: 200182 3.51 - 4.20: 468892 4.20 - 4.90: 652006 Nonbonded interactions: 1361904 Sorted by model distance: nonbonded pdb=" O3' A x 76 " pdb=" C UNK 1 58 " model vdw 1.419 3.270 nonbonded pdb=" OD1 ASP a 98 " pdb=" O6 G x 35 " model vdw 1.521 3.040 nonbonded pdb=" OP1 U f1258 " pdb=" NH1 ARG 0 46 " model vdw 1.523 2.520 nonbonded pdb=" CB GLU e 324 " pdb=" OG1 THR e 327 " model vdw 1.547 3.440 nonbonded pdb=" OD1 ASP a 98 " pdb=" C6 G x 35 " model vdw 1.627 3.260 ... (remaining 1361899 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'x' and (resid 1 through 17 or resid 21 through 76)) selection = chain 'y' } 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=0.01 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.880 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: 0.100 Extract box with map and model: 22.420 Check model and map are aligned: 1.650 Set scattering table: 0.980 Process input model: 596.660 Find NCS groups from input model: 3.580 Set up NCS constraints: 0.540 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: 0.030 Load rotamer database and sin/cos tables:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 641.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 : 0.006 0.125 161865 Z= 0.380 Angle : 0.913 16.536 236451 Z= 0.520 Chirality : 0.057 0.745 29529 Planarity : 0.007 0.103 16480 Dihedral : 21.636 179.911 84584 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 1.56 % Allowed : 2.12 % Favored : 96.32 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: 0.07 (0.08), residues: 9312 helix: 1.23 (0.08), residues: 3881 sheet: 0.09 (0.15), residues: 1214 loop : -1.09 (0.09), residues: 4217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.002 TRP m 95 HIS 0.018 0.002 HIS r 123 PHE 0.046 0.002 PHE o 229 TYR 0.067 0.002 TYR N 60 ARG 0.025 0.001 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1198 time to evaluate : 8.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 144 GLN cc_start: 0.8777 (tp-100) cc_final: 0.8451 (tp-100) REVERT: H 25 ASN cc_start: 0.9031 (m-40) cc_final: 0.8414 (m-40) REVERT: I 128 ARG cc_start: 0.8069 (tpp80) cc_final: 0.7789 (tpp80) REVERT: P 38 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8032 (mttp) REVERT: V 88 GLU cc_start: 0.7682 (tp30) cc_final: 0.7248 (tm-30) REVERT: Y 25 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7335 (mm110) REVERT: k 53 MET cc_start: 0.9155 (mtp) cc_final: 0.8767 (mtp) REVERT: q 19 SER cc_start: 0.9057 (m) cc_final: 0.8787 (t) REVERT: q 150 SER cc_start: 0.9006 (t) cc_final: 0.7788 (t) REVERT: r 115 MET cc_start: 0.8985 (mmm) cc_final: 0.8731 (mmp) REVERT: s 15 GLU cc_start: 0.8146 (tt0) cc_final: 0.7614 (tt0) REVERT: s 48 SER cc_start: 0.8420 (m) cc_final: 0.7984 (t) REVERT: s 89 TYR cc_start: 0.8543 (m-80) cc_final: 0.8035 (m-80) REVERT: s 107 ASP cc_start: 0.8704 (m-30) cc_final: 0.7734 (m-30) REVERT: s 108 GLU cc_start: 0.7258 (pm20) cc_final: 0.6591 (pp20) REVERT: s 131 MET cc_start: 0.8670 (mmm) cc_final: 0.7906 (mmm) REVERT: s 132 ASN cc_start: 0.7975 (p0) cc_final: 0.7678 (p0) REVERT: a 114 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9461 (mm) REVERT: a 612 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8020 (tmm) REVERT: a 621 TRP cc_start: 0.7617 (m100) cc_final: 0.7247 (m100) REVERT: a 696 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8467 (pp30) REVERT: a 697 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8420 (mt) REVERT: a 937 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9015 (mt) REVERT: e 258 THR cc_start: 0.8880 (p) cc_final: 0.8560 (t) REVERT: e 267 LEU cc_start: 0.9421 (tp) cc_final: 0.9186 (pp) REVERT: e 309 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8877 (p) REVERT: e 910 SER cc_start: 0.7654 (OUTLIER) cc_final: 0.7437 (p) REVERT: e 1250 ASP cc_start: 0.9267 (m-30) cc_final: 0.8992 (p0) REVERT: e 1474 MET cc_start: 0.9055 (mtp) cc_final: 0.8818 (mtp) REVERT: g 6 GLN cc_start: 0.8717 (mt0) cc_final: 0.8335 (mt0) REVERT: g 16 PHE cc_start: 0.9181 (m-80) cc_final: 0.8717 (m-80) REVERT: g 23 TYR cc_start: 0.8270 (p90) cc_final: 0.7990 (p90) REVERT: g 140 GLN cc_start: 0.8452 (tp40) cc_final: 0.8247 (tm-30) REVERT: g 157 GLN cc_start: 0.8899 (mp10) cc_final: 0.8311 (mt0) REVERT: w 49 PHE cc_start: 0.7074 (p90) cc_final: 0.6858 (p90) REVERT: w 68 PHE cc_start: 0.7416 (m-10) cc_final: 0.7092 (m-10) REVERT: w 76 ARG cc_start: 0.8550 (mtm180) cc_final: 0.8090 (mtt-85) REVERT: 0 6 GLU cc_start: 0.9523 (mm-30) cc_final: 0.9178 (mp0) REVERT: 0 18 TYR cc_start: 0.8952 (m-80) cc_final: 0.8486 (m-80) REVERT: 0 36 GLN cc_start: 0.8548 (tp-100) cc_final: 0.8137 (tp40) REVERT: 0 58 MET cc_start: 0.8878 (tpt) cc_final: 0.8559 (tpp) REVERT: 0 63 ILE cc_start: 0.9179 (mt) cc_final: 0.8841 (mp) REVERT: 0 189 GLN cc_start: 0.6060 (OUTLIER) cc_final: 0.5037 (tm-30) REVERT: v 33 VAL cc_start: 0.8721 (t) cc_final: 0.8509 (t) REVERT: v 37 ARG cc_start: 0.8438 (mmm160) cc_final: 0.8206 (mmm160) REVERT: v 38 PRO cc_start: 0.8022 (Cg_exo) cc_final: 0.7706 (Cg_endo) REVERT: v 105 MET cc_start: 0.7062 (mmp) cc_final: 0.6752 (mpp) REVERT: v 125 GLN cc_start: 0.8834 (tp40) cc_final: 0.8481 (tm-30) REVERT: v 135 MET cc_start: 0.3924 (mmp) cc_final: 0.3683 (mmp) outliers start: 118 outliers final: 26 residues processed: 1300 average time/residue: 2.0643 time to fit residues: 3932.5881 Evaluate side-chains 832 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 798 time to evaluate : 8.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain s residue 17 LEU Chi-restraints excluded: chain u residue 4 ASP Chi-restraints excluded: chain a residue 74 SER Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 293 TYR Chi-restraints excluded: chain a residue 308 THR Chi-restraints excluded: chain a residue 309 PHE Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 612 MET Chi-restraints excluded: chain a residue 649 TRP Chi-restraints excluded: chain a residue 696 GLN Chi-restraints excluded: chain a residue 697 LEU Chi-restraints excluded: chain a residue 705 TRP Chi-restraints excluded: chain a residue 937 ILE Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 309 VAL Chi-restraints excluded: chain e residue 319 THR Chi-restraints excluded: chain e residue 327 THR Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 867 PHE Chi-restraints excluded: chain e residue 904 VAL Chi-restraints excluded: chain e residue 910 SER Chi-restraints excluded: chain e residue 978 THR Chi-restraints excluded: chain e residue 1300 ILE Chi-restraints excluded: chain e residue 1363 VAL Chi-restraints excluded: chain e residue 1480 ILE Chi-restraints excluded: chain 0 residue 52 LEU Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 189 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1083 optimal weight: 30.0000 chunk 972 optimal weight: 8.9990 chunk 539 optimal weight: 10.0000 chunk 332 optimal weight: 8.9990 chunk 655 optimal weight: 10.0000 chunk 519 optimal weight: 10.0000 chunk 1005 optimal weight: 10.0000 chunk 389 optimal weight: 10.0000 chunk 611 optimal weight: 8.9990 chunk 748 optimal weight: 7.9990 chunk 1165 optimal weight: 40.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN A B 122 GLN A C 137 ASN I 98 ASN I 132 ASN L 26 GLN ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 ASN P 75 ASN S 42 GLN W 76 ASN X 76 ASN Y 25 GLN Z 120 GLN l 291 ASN l 361 HIS m 39 GLN o 80 GLN o 146 GLN p 77 GLN p 243 GLN q 125 ASN r 112 GLN r 175 ASN s 68 HIS s 95 ASN ** a 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 385 ASN a 413 GLN a 517 ASN a 599 GLN a 696 GLN a 957 GLN a 994 HIS e 79 ASN e 189 ASN e 233 ASN ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 386 GLN e 714 GLN ** e 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 805 ASN e 833 HIS ** e1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1288 GLN ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e1457 ASN e1477 GLN e1499 HIS ** e1501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 ASN ** w 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 36 GLN ** 0 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 52 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.141 161865 Z= 0.590 Angle : 0.763 14.044 236451 Z= 0.397 Chirality : 0.048 0.400 29529 Planarity : 0.007 0.104 16480 Dihedral : 22.611 179.358 66883 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 2.53 % Allowed : 10.79 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.08), residues: 9312 helix: 1.27 (0.08), residues: 3912 sheet: 0.01 (0.14), residues: 1200 loop : -0.88 (0.09), residues: 4200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP a 658 HIS 0.018 0.002 HIS w 12 PHE 0.031 0.002 PHE o 229 TYR 0.038 0.002 TYR N 60 ARG 0.015 0.001 ARG I 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 810 time to evaluate : 8.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.8281 (ttt90) REVERT: H 28 PHE cc_start: 0.9142 (t80) cc_final: 0.8906 (t80) REVERT: H 49 ASN cc_start: 0.7710 (t0) cc_final: 0.7501 (t0) REVERT: M 106 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8624 (mt0) REVERT: M 123 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8390 (mp10) REVERT: S 31 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8665 (ttmm) REVERT: U 79 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7794 (p0) REVERT: X 10 GLN cc_start: 0.8273 (tp-100) cc_final: 0.7772 (tp-100) REVERT: j 24 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: j 73 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7806 (tp30) REVERT: n 133 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: n 137 ASP cc_start: 0.7938 (m-30) cc_final: 0.7294 (m-30) REVERT: s 107 ASP cc_start: 0.8343 (m-30) cc_final: 0.8030 (m-30) REVERT: s 108 GLU cc_start: 0.7929 (pm20) cc_final: 0.7721 (pp20) REVERT: s 131 MET cc_start: 0.8830 (mmm) cc_final: 0.8344 (mmm) REVERT: s 170 ASP cc_start: 0.8412 (p0) cc_final: 0.7953 (p0) REVERT: a 114 LEU cc_start: 0.9672 (OUTLIER) cc_final: 0.9420 (mm) REVERT: a 156 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7920 (pp) REVERT: a 293 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7391 (t80) REVERT: a 621 TRP cc_start: 0.7761 (m100) cc_final: 0.7479 (m100) REVERT: a 658 TRP cc_start: 0.9063 (p90) cc_final: 0.8796 (p90) REVERT: a 699 MET cc_start: 0.8702 (tpp) cc_final: 0.8489 (tpp) REVERT: a 996 MET cc_start: 0.9474 (ttt) cc_final: 0.9135 (ttm) REVERT: e 223 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8807 (t80) REVERT: e 258 THR cc_start: 0.9026 (p) cc_final: 0.8807 (t) REVERT: e 910 SER cc_start: 0.7712 (OUTLIER) cc_final: 0.7467 (p) REVERT: e 1060 MET cc_start: 0.1945 (OUTLIER) cc_final: 0.1433 (mpt) REVERT: e 1068 MET cc_start: 0.0315 (ptm) cc_final: -0.0300 (ptt) REVERT: e 1162 MET cc_start: 0.2127 (tmt) cc_final: 0.1733 (ppp) REVERT: e 1303 MET cc_start: 0.9366 (tpt) cc_final: 0.8098 (tpt) REVERT: g 6 GLN cc_start: 0.8647 (mt0) cc_final: 0.8308 (mt0) REVERT: g 16 PHE cc_start: 0.9260 (m-80) cc_final: 0.8859 (m-80) REVERT: g 96 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7998 (mtt90) REVERT: g 140 GLN cc_start: 0.8668 (tp40) cc_final: 0.8257 (tm-30) REVERT: g 223 ARG cc_start: 0.9204 (mmm-85) cc_final: 0.8562 (mmm160) REVERT: w 174 MET cc_start: 0.5364 (mpt) cc_final: 0.4856 (mpt) REVERT: 0 6 GLU cc_start: 0.9532 (mm-30) cc_final: 0.9302 (mp0) REVERT: 0 22 TYR cc_start: 0.8618 (m-80) cc_final: 0.8047 (m-80) REVERT: 0 23 LYS cc_start: 0.9176 (mmpt) cc_final: 0.8668 (pptt) REVERT: 0 36 GLN cc_start: 0.8101 (tp40) cc_final: 0.7882 (tp40) REVERT: v 125 GLN cc_start: 0.9030 (tp40) cc_final: 0.8647 (pp30) REVERT: v 136 VAL cc_start: 0.8588 (t) cc_final: 0.8138 (p) outliers start: 191 outliers final: 84 residues processed: 911 average time/residue: 2.1457 time to fit residues: 2870.6495 Evaluate side-chains 847 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 749 time to evaluate : 8.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 18 ASP Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 106 GLN Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain X residue 22 THR Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain b residue 32 LYS Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 59 CYS Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain l residue 133 SER Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain n residue 160 SER Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain p residue 67 ILE Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain r residue 146 ASP Chi-restraints excluded: chain r residue 177 ASP Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 64 LYS Chi-restraints excluded: chain s residue 65 ILE Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 111 ASP Chi-restraints excluded: chain s residue 117 ASP Chi-restraints excluded: chain s residue 122 ILE Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 182 ILE Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 293 TYR Chi-restraints excluded: chain a residue 301 ASP Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 649 TRP Chi-restraints excluded: chain a residue 705 TRP Chi-restraints excluded: chain e residue 105 VAL Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 754 ILE Chi-restraints excluded: chain e residue 867 PHE Chi-restraints excluded: chain e residue 910 SER Chi-restraints excluded: chain e residue 978 THR Chi-restraints excluded: chain e residue 1060 MET Chi-restraints excluded: chain e residue 1300 ILE Chi-restraints excluded: chain e residue 1316 THR Chi-restraints excluded: chain g residue 96 ARG Chi-restraints excluded: chain g residue 146 ILE Chi-restraints excluded: chain w residue 65 ILE Chi-restraints excluded: chain w residue 72 PHE Chi-restraints excluded: chain w residue 187 VAL Chi-restraints excluded: chain 0 residue 25 LEU Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 80 VAL Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 187 VAL Chi-restraints excluded: chain 0 residue 197 PHE Chi-restraints excluded: chain v residue 22 GLN Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 157 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 647 optimal weight: 10.0000 chunk 361 optimal weight: 1.9990 chunk 969 optimal weight: 0.0170 chunk 793 optimal weight: 3.9990 chunk 321 optimal weight: 2.9990 chunk 1167 optimal weight: 30.0000 chunk 1260 optimal weight: 9.9990 chunk 1039 optimal weight: 6.9990 chunk 1157 optimal weight: 7.9990 chunk 397 optimal weight: 10.0000 chunk 936 optimal weight: 7.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN C 55 GLN I 132 ASN L 26 GLN X 10 GLN X 76 ASN j 47 GLN k 319 ASN l 116 ASN p 61 GLN p 77 GLN p 79 GLN r 51 HIS r 112 GLN r 175 ASN s 68 HIS ** s 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 160 GLN u 41 GLN ** a 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 143 ASN ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 412 GLN ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 832 ASN e 995 GLN ** e1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1288 GLN ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 52 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 161865 Z= 0.237 Angle : 0.583 11.535 236451 Z= 0.307 Chirality : 0.037 0.290 29529 Planarity : 0.004 0.091 16480 Dihedral : 22.627 179.419 66845 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.19 % Rotamer: Outliers : 2.55 % Allowed : 12.89 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.49 (0.09), residues: 9312 helix: 1.57 (0.08), residues: 3916 sheet: 0.11 (0.14), residues: 1212 loop : -0.80 (0.09), residues: 4184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 92 HIS 0.007 0.001 HIS w 12 PHE 0.027 0.001 PHE 0 197 TYR 0.026 0.001 TYR H 36 ARG 0.013 0.000 ARG e1302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 812 time to evaluate : 8.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 86 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: E 144 GLN cc_start: 0.8444 (mm-40) cc_final: 0.8062 (tm-30) REVERT: F 104 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: H 24 GLU cc_start: 0.8143 (pp20) cc_final: 0.7930 (pp20) REVERT: H 49 ASN cc_start: 0.7806 (t0) cc_final: 0.7450 (t0) REVERT: H 92 TRP cc_start: 0.8008 (OUTLIER) cc_final: 0.7644 (m-10) REVERT: H 102 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7506 (mt-10) REVERT: K 64 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7519 (mt-10) REVERT: L 74 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: M 106 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8520 (mt0) REVERT: Q 105 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8582 (mt0) REVERT: S 31 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8677 (ttmm) REVERT: X 10 GLN cc_start: 0.8233 (tp40) cc_final: 0.7498 (tp-100) REVERT: Y 25 GLN cc_start: 0.7955 (mm110) cc_final: 0.7461 (mm110) REVERT: Z 126 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8318 (mttp) REVERT: n 99 GLU cc_start: 0.8383 (pm20) cc_final: 0.7925 (pm20) REVERT: n 133 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6860 (tm-30) REVERT: q 19 SER cc_start: 0.9139 (m) cc_final: 0.8867 (t) REVERT: q 51 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8211 (mp-120) REVERT: r 131 ILE cc_start: 0.9159 (mm) cc_final: 0.8900 (mp) REVERT: s 78 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8195 (pp20) REVERT: s 107 ASP cc_start: 0.8380 (m-30) cc_final: 0.8058 (m-30) REVERT: s 131 MET cc_start: 0.8674 (mmm) cc_final: 0.8125 (mmm) REVERT: s 170 ASP cc_start: 0.8261 (p0) cc_final: 0.7676 (p0) REVERT: t 114 GLN cc_start: 0.7906 (tp-100) cc_final: 0.7706 (tp-100) REVERT: a 114 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9400 (mm) REVERT: a 156 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7986 (pp) REVERT: a 293 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7602 (t80) REVERT: a 609 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7695 (t0) REVERT: a 612 MET cc_start: 0.8557 (tmm) cc_final: 0.8296 (tmm) REVERT: a 621 TRP cc_start: 0.8028 (m100) cc_final: 0.7545 (m100) REVERT: a 917 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: a 996 MET cc_start: 0.9502 (ttt) cc_final: 0.9174 (ttm) REVERT: e 116 MET cc_start: 0.9183 (mmm) cc_final: 0.8703 (mpp) REVERT: e 258 THR cc_start: 0.9003 (p) cc_final: 0.8778 (t) REVERT: e 292 LEU cc_start: 0.9573 (mt) cc_final: 0.9261 (pp) REVERT: e 780 ILE cc_start: -0.4930 (OUTLIER) cc_final: -0.5238 (mm) REVERT: e 910 SER cc_start: 0.7596 (OUTLIER) cc_final: 0.7324 (p) REVERT: e 1060 MET cc_start: 0.1763 (OUTLIER) cc_final: 0.1291 (mpt) REVERT: e 1068 MET cc_start: 0.0628 (ptm) cc_final: -0.0823 (ppp) REVERT: e 1135 MET cc_start: 0.5851 (mmp) cc_final: 0.5571 (mpm) REVERT: e 1246 GLN cc_start: 0.9462 (mm-40) cc_final: 0.9261 (mm-40) REVERT: e 1407 MET cc_start: -0.2383 (mmt) cc_final: -0.2599 (mmt) REVERT: g 1 MET cc_start: 0.5034 (ttt) cc_final: 0.4502 (ttt) REVERT: g 6 GLN cc_start: 0.8511 (mt0) cc_final: 0.8218 (mt0) REVERT: g 16 PHE cc_start: 0.9235 (m-80) cc_final: 0.8841 (m-80) REVERT: g 123 ARG cc_start: 0.8386 (tpp-160) cc_final: 0.7925 (mmp80) REVERT: g 139 ARG cc_start: 0.7719 (mtp85) cc_final: 0.7120 (mtp85) REVERT: g 140 GLN cc_start: 0.8698 (tp40) cc_final: 0.8100 (tp-100) REVERT: g 157 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8789 (mt0) REVERT: g 164 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8616 (mm-40) REVERT: g 223 ARG cc_start: 0.9267 (mmm-85) cc_final: 0.8447 (mmm160) REVERT: w 63 MET cc_start: 0.8978 (ppp) cc_final: 0.8742 (ppp) REVERT: w 119 GLN cc_start: 0.7766 (mp-120) cc_final: 0.7074 (mp10) REVERT: w 174 MET cc_start: 0.5410 (mpt) cc_final: 0.4820 (mpt) REVERT: w 210 MET cc_start: 0.5903 (mmp) cc_final: 0.5604 (mmm) REVERT: 0 37 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8134 (tm-30) REVERT: 0 64 ARG cc_start: 0.8275 (mtm-85) cc_final: 0.7874 (mtm-85) REVERT: 0 69 ASP cc_start: 0.9287 (OUTLIER) cc_final: 0.9032 (p0) REVERT: 0 88 PHE cc_start: 0.7896 (m-10) cc_final: 0.7687 (m-10) REVERT: v 21 MET cc_start: 0.8203 (tpp) cc_final: 0.7916 (tmm) REVERT: v 22 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7566 (tm-30) REVERT: v 80 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7604 (pmm) REVERT: v 125 GLN cc_start: 0.9145 (tp40) cc_final: 0.8731 (pp30) REVERT: v 136 VAL cc_start: 0.8664 (t) cc_final: 0.8294 (p) outliers start: 193 outliers final: 79 residues processed: 920 average time/residue: 2.1168 time to fit residues: 2850.9562 Evaluate side-chains 848 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 748 time to evaluate : 8.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 92 TRP Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 64 GLU Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 106 GLN Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 92 ILE Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 83 ILE Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 160 SER Chi-restraints excluded: chain o residue 39 GLU Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 117 ASP Chi-restraints excluded: chain s residue 122 ILE Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 182 ILE Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 25 ARG Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 293 TYR Chi-restraints excluded: chain a residue 301 ASP Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 917 TYR Chi-restraints excluded: chain e residue 319 THR Chi-restraints excluded: chain e residue 770 ILE Chi-restraints excluded: chain e residue 780 ILE Chi-restraints excluded: chain e residue 910 SER Chi-restraints excluded: chain e residue 978 THR Chi-restraints excluded: chain e residue 1060 MET Chi-restraints excluded: chain e residue 1300 ILE Chi-restraints excluded: chain e residue 1316 THR Chi-restraints excluded: chain g residue 95 GLN Chi-restraints excluded: chain w residue 65 ILE Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain w residue 72 PHE Chi-restraints excluded: chain w residue 169 VAL Chi-restraints excluded: chain w residue 187 VAL Chi-restraints excluded: chain 0 residue 16 ARG Chi-restraints excluded: chain 0 residue 25 LEU Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 69 ASP Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 97 LYS Chi-restraints excluded: chain v residue 22 GLN Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 80 MET Chi-restraints excluded: chain v residue 157 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1153 optimal weight: 50.0000 chunk 877 optimal weight: 5.9990 chunk 605 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 557 optimal weight: 30.0000 chunk 783 optimal weight: 10.0000 chunk 1171 optimal weight: 7.9990 chunk 1240 optimal weight: 40.0000 chunk 612 optimal weight: 10.0000 chunk 1110 optimal weight: 9.9990 chunk 334 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 132 ASN L 26 GLN ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN j 97 ASN l 116 ASN o 194 HIS p 77 GLN r 51 HIS r 112 GLN r 175 ASN ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 412 GLN ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1288 GLN ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 75 GLN ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 52 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.147 161865 Z= 0.532 Angle : 0.693 11.204 236451 Z= 0.361 Chirality : 0.046 0.416 29529 Planarity : 0.006 0.096 16480 Dihedral : 22.543 179.694 66834 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.42 % Favored : 95.52 % Rotamer: Outliers : 3.31 % Allowed : 14.19 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.09), residues: 9312 helix: 1.51 (0.08), residues: 3928 sheet: -0.01 (0.14), residues: 1202 loop : -0.75 (0.09), residues: 4182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 92 HIS 0.007 0.001 HIS N 39 PHE 0.029 0.002 PHE o 229 TYR 0.027 0.002 TYR j 189 ARG 0.013 0.001 ARG X 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 759 time to evaluate : 8.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 86 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: F 104 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: H 44 GLU cc_start: 0.7608 (pm20) cc_final: 0.7164 (pm20) REVERT: H 49 ASN cc_start: 0.7976 (t0) cc_final: 0.7487 (t0) REVERT: H 91 ASP cc_start: 0.8697 (p0) cc_final: 0.8117 (p0) REVERT: M 106 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8497 (mt0) REVERT: P 98 SER cc_start: 0.9127 (t) cc_final: 0.8912 (p) REVERT: Q 105 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8733 (mt0) REVERT: R 19 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.7892 (ttp-170) REVERT: S 31 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8697 (ttmm) REVERT: U 79 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.7739 (p0) REVERT: X 10 GLN cc_start: 0.8028 (tp40) cc_final: 0.7634 (tp-100) REVERT: d 4 MET cc_start: 0.8294 (ttm) cc_final: 0.8038 (ttm) REVERT: j 24 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: n 133 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: o 244 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8287 (t0) REVERT: s 90 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7128 (mm-40) REVERT: s 107 ASP cc_start: 0.8445 (m-30) cc_final: 0.8240 (m-30) REVERT: s 131 MET cc_start: 0.8896 (mmm) cc_final: 0.8504 (mmm) REVERT: s 170 ASP cc_start: 0.8327 (p0) cc_final: 0.7632 (p0) REVERT: u 12 TRP cc_start: 0.8383 (OUTLIER) cc_final: 0.7926 (p90) REVERT: a 114 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9358 (mm) REVERT: a 156 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8157 (pp) REVERT: a 293 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7657 (t80) REVERT: a 609 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7594 (t0) REVERT: a 612 MET cc_start: 0.8312 (tmm) cc_final: 0.8083 (tmm) REVERT: a 621 TRP cc_start: 0.8288 (m100) cc_final: 0.7641 (m100) REVERT: a 917 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: a 996 MET cc_start: 0.9554 (ttt) cc_final: 0.9199 (ttm) REVERT: e 116 MET cc_start: 0.9184 (mmm) cc_final: 0.8727 (mpp) REVERT: e 258 THR cc_start: 0.9082 (p) cc_final: 0.8849 (t) REVERT: e 267 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9115 (pp) REVERT: e 292 LEU cc_start: 0.9633 (mt) cc_final: 0.9358 (pp) REVERT: e 780 ILE cc_start: -0.5196 (OUTLIER) cc_final: -0.5414 (mm) REVERT: e 809 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7211 (ppp) REVERT: e 910 SER cc_start: 0.7567 (OUTLIER) cc_final: 0.7287 (p) REVERT: e 1068 MET cc_start: 0.0323 (ptm) cc_final: -0.1103 (ppp) REVERT: e 1135 MET cc_start: 0.5642 (mmp) cc_final: 0.5379 (mpm) REVERT: g 6 GLN cc_start: 0.8556 (mt0) cc_final: 0.8198 (mt0) REVERT: g 16 PHE cc_start: 0.9224 (m-80) cc_final: 0.8844 (m-80) REVERT: g 123 ARG cc_start: 0.8467 (tpp-160) cc_final: 0.8074 (mmp80) REVERT: g 140 GLN cc_start: 0.8734 (tp40) cc_final: 0.8163 (tp-100) REVERT: g 157 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8930 (mm-40) REVERT: w 107 TYR cc_start: 0.7867 (m-80) cc_final: 0.7616 (m-80) REVERT: w 119 GLN cc_start: 0.7942 (mp-120) cc_final: 0.7483 (mp10) REVERT: w 174 MET cc_start: 0.5829 (mpt) cc_final: 0.5250 (mpt) REVERT: 0 37 GLN cc_start: 0.8513 (tm-30) cc_final: 0.7999 (tp-100) REVERT: 0 40 GLU cc_start: 0.8087 (pp20) cc_final: 0.7545 (pp20) REVERT: 0 44 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8951 (pp20) REVERT: v 80 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7789 (pmm) REVERT: v 125 GLN cc_start: 0.9208 (tp40) cc_final: 0.8822 (tm-30) REVERT: v 136 VAL cc_start: 0.8770 (t) cc_final: 0.8467 (p) outliers start: 250 outliers final: 121 residues processed: 917 average time/residue: 2.0701 time to fit residues: 2815.3885 Evaluate side-chains 877 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 735 time to evaluate : 7.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 106 GLN Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 93 SER Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain X residue 22 THR Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 59 CYS Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 103 THR Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 125 VAL Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 160 SER Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain o residue 244 ASN Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 177 ASP Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 122 ILE Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 182 ILE Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 293 TYR Chi-restraints excluded: chain a residue 301 ASP Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 917 TYR Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain e residue 267 LEU Chi-restraints excluded: chain e residue 319 THR Chi-restraints excluded: chain e residue 770 ILE Chi-restraints excluded: chain e residue 780 ILE Chi-restraints excluded: chain e residue 809 MET Chi-restraints excluded: chain e residue 910 SER Chi-restraints excluded: chain e residue 978 THR Chi-restraints excluded: chain e residue 1300 ILE Chi-restraints excluded: chain e residue 1316 THR Chi-restraints excluded: chain g residue 95 GLN Chi-restraints excluded: chain w residue 65 ILE Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain w residue 72 PHE Chi-restraints excluded: chain w residue 169 VAL Chi-restraints excluded: chain w residue 187 VAL Chi-restraints excluded: chain 0 residue 25 LEU Chi-restraints excluded: chain 0 residue 27 VAL Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 31 ASP Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 94 THR Chi-restraints excluded: chain 0 residue 96 ILE Chi-restraints excluded: chain 0 residue 97 LYS Chi-restraints excluded: chain v residue 22 GLN Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 42 VAL Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 80 MET Chi-restraints excluded: chain v residue 157 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1032 optimal weight: 4.9990 chunk 703 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 923 optimal weight: 2.9990 chunk 511 optimal weight: 5.9990 chunk 1058 optimal weight: 40.0000 chunk 857 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 633 optimal weight: 10.0000 chunk 1113 optimal weight: 10.0000 chunk 312 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 132 ASN L 26 GLN U 16 GLN X 76 ASN l 116 ASN p 77 GLN ** p 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 240 ASN q 157 ASN r 51 HIS r 112 GLN r 133 GLN r 175 ASN ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 160 GLN ** a 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 687 ASN ** e 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 795 HIS e 831 ASN e1455 GLN g 75 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 161865 Z= 0.199 Angle : 0.569 14.003 236451 Z= 0.299 Chirality : 0.036 0.302 29529 Planarity : 0.004 0.089 16480 Dihedral : 22.572 179.963 66834 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 2.80 % Allowed : 15.47 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.09), residues: 9312 helix: 1.71 (0.08), residues: 3918 sheet: 0.07 (0.15), residues: 1198 loop : -0.71 (0.09), residues: 4196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP a 658 HIS 0.008 0.001 HIS w 12 PHE 0.021 0.001 PHE w 68 TYR 0.019 0.001 TYR P 27 ARG 0.022 0.000 ARG 0 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 790 time to evaluate : 8.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 86 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: F 104 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: H 44 GLU cc_start: 0.7591 (pm20) cc_final: 0.7348 (pm20) REVERT: H 49 ASN cc_start: 0.8023 (t0) cc_final: 0.7556 (t0) REVERT: H 92 TRP cc_start: 0.7856 (OUTLIER) cc_final: 0.7251 (m-90) REVERT: L 74 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.8246 (m-80) REVERT: M 95 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.9045 (p) REVERT: M 106 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8372 (mt0) REVERT: Q 105 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8636 (mt0) REVERT: S 31 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8692 (ttmm) REVERT: X 10 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7486 (tp-100) REVERT: j 143 GLU cc_start: 0.8185 (pp20) cc_final: 0.7836 (pp20) REVERT: m 158 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7888 (ptt-90) REVERT: n 133 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: q 51 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8100 (mp-120) REVERT: s 78 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8117 (pp20) REVERT: s 90 GLN cc_start: 0.7451 (mm-40) cc_final: 0.6791 (mm-40) REVERT: s 131 MET cc_start: 0.8849 (mmm) cc_final: 0.8526 (mmm) REVERT: s 170 ASP cc_start: 0.8381 (p0) cc_final: 0.7776 (p0) REVERT: u 12 TRP cc_start: 0.8327 (OUTLIER) cc_final: 0.7672 (p90) REVERT: a 114 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9357 (mm) REVERT: a 156 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8146 (pp) REVERT: a 293 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.7728 (t80) REVERT: a 609 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7598 (t0) REVERT: a 621 TRP cc_start: 0.8274 (m100) cc_final: 0.7554 (m100) REVERT: a 996 MET cc_start: 0.9544 (ttt) cc_final: 0.9080 (ttt) REVERT: e 116 MET cc_start: 0.9204 (mmm) cc_final: 0.8768 (mpp) REVERT: e 258 THR cc_start: 0.9057 (p) cc_final: 0.8800 (t) REVERT: e 292 LEU cc_start: 0.9604 (mt) cc_final: 0.9317 (pp) REVERT: e 809 MET cc_start: 0.7553 (ppp) cc_final: 0.7201 (ppp) REVERT: e 910 SER cc_start: 0.7630 (OUTLIER) cc_final: 0.7328 (p) REVERT: e 1060 MET cc_start: 0.1878 (mpt) cc_final: 0.1419 (mpt) REVERT: e 1068 MET cc_start: 0.0458 (ptm) cc_final: -0.1010 (ppp) REVERT: e 1135 MET cc_start: 0.5668 (mmp) cc_final: 0.5426 (mpm) REVERT: g 6 GLN cc_start: 0.8403 (mt0) cc_final: 0.8126 (mt0) REVERT: g 16 PHE cc_start: 0.9200 (m-80) cc_final: 0.8824 (m-80) REVERT: g 123 ARG cc_start: 0.8510 (tpp-160) cc_final: 0.8217 (mmp80) REVERT: g 140 GLN cc_start: 0.8761 (tp40) cc_final: 0.8190 (tp-100) REVERT: g 157 GLN cc_start: 0.9233 (mm-40) cc_final: 0.8905 (mm-40) REVERT: w 63 MET cc_start: 0.9018 (ppp) cc_final: 0.8492 (ppp) REVERT: w 89 ASP cc_start: 0.9307 (OUTLIER) cc_final: 0.8866 (m-30) REVERT: w 108 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8453 (p0) REVERT: w 119 GLN cc_start: 0.7991 (mp-120) cc_final: 0.7459 (mp10) REVERT: w 174 MET cc_start: 0.5637 (mpt) cc_final: 0.4565 (mpt) REVERT: w 210 MET cc_start: 0.6589 (mmp) cc_final: 0.6323 (mmm) REVERT: 0 31 ASP cc_start: 0.9150 (t0) cc_final: 0.8500 (OUTLIER) REVERT: 0 32 ASN cc_start: 0.9197 (m-40) cc_final: 0.8455 (p0) REVERT: 0 44 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8976 (pp20) REVERT: v 27 ARG cc_start: 0.8532 (tpp80) cc_final: 0.8206 (mmm-85) REVERT: v 125 GLN cc_start: 0.9251 (tp40) cc_final: 0.8830 (pp30) REVERT: v 136 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8522 (p) outliers start: 212 outliers final: 110 residues processed: 926 average time/residue: 2.1289 time to fit residues: 2902.7336 Evaluate side-chains 886 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 756 time to evaluate : 8.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 92 TRP Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 106 GLN Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 10 GLN Chi-restraints excluded: chain X residue 22 THR Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 83 ILE Chi-restraints excluded: chain c residue 89 MET Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 236 LEU Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 155 LEU Chi-restraints excluded: chain n residue 160 SER Chi-restraints excluded: chain o residue 39 GLU Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain p residue 240 ASN Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 177 ASP Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 117 ASP Chi-restraints excluded: chain s residue 122 ILE Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain t residue 182 ILE Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 293 TYR Chi-restraints excluded: chain a residue 301 ASP Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 917 TYR Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain e residue 319 THR Chi-restraints excluded: chain e residue 770 ILE Chi-restraints excluded: chain e residue 910 SER Chi-restraints excluded: chain e residue 978 THR Chi-restraints excluded: chain e residue 1300 ILE Chi-restraints excluded: chain e residue 1359 LEU Chi-restraints excluded: chain e residue 1363 VAL Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain w residue 72 PHE Chi-restraints excluded: chain w residue 89 ASP Chi-restraints excluded: chain w residue 108 ASN Chi-restraints excluded: chain w residue 111 ILE Chi-restraints excluded: chain w residue 169 VAL Chi-restraints excluded: chain w residue 187 VAL Chi-restraints excluded: chain 0 residue 25 LEU Chi-restraints excluded: chain 0 residue 34 SER Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 97 LYS Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 52 HIS Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 136 VAL Chi-restraints excluded: chain v residue 157 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 417 optimal weight: 10.0000 chunk 1116 optimal weight: 20.0000 chunk 245 optimal weight: 10.0000 chunk 728 optimal weight: 9.9990 chunk 306 optimal weight: 9.9990 chunk 1241 optimal weight: 30.0000 chunk 1030 optimal weight: 30.0000 chunk 574 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 410 optimal weight: 10.0000 chunk 651 optimal weight: 10.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN D 45 ASN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 132 ASN L 26 GLN L 120 GLN ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 81 HIS p 77 GLN ** p 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 9 GLN r 51 HIS ** s 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 505 ASN ** e 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 75 GLN w 199 GLN v 52 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.162 161865 Z= 0.607 Angle : 0.729 13.359 236451 Z= 0.377 Chirality : 0.047 0.435 29529 Planarity : 0.006 0.096 16480 Dihedral : 22.511 179.260 66834 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.60 % Favored : 95.35 % Rotamer: Outliers : 3.44 % Allowed : 15.63 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.09), residues: 9312 helix: 1.56 (0.08), residues: 3921 sheet: -0.05 (0.14), residues: 1201 loop : -0.76 (0.09), residues: 4190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP a 658 HIS 0.016 0.002 HIS w 12 PHE 0.030 0.002 PHE o 229 TYR 0.033 0.002 TYR H 36 ARG 0.015 0.001 ARG w 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 753 time to evaluate : 8.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 86 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: F 104 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7510 (tm-30) REVERT: H 44 GLU cc_start: 0.7583 (pm20) cc_final: 0.7319 (pm20) REVERT: H 49 ASN cc_start: 0.8166 (t0) cc_final: 0.7600 (t0) REVERT: I 66 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7929 (mtpp) REVERT: M 95 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.9116 (p) REVERT: M 106 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8291 (mt0) REVERT: P 98 SER cc_start: 0.9137 (t) cc_final: 0.8925 (p) REVERT: S 31 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8683 (ttmm) REVERT: T 107 GLU cc_start: 0.8957 (pp20) cc_final: 0.8734 (pp20) REVERT: U 79 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7725 (p0) REVERT: W 14 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8725 (mttp) REVERT: W 24 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7789 (tpt-90) REVERT: X 10 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7614 (tp-100) REVERT: d 15 ARG cc_start: 0.6715 (ttt180) cc_final: 0.6397 (ttt180) REVERT: j 24 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: j 143 GLU cc_start: 0.8225 (pp20) cc_final: 0.7943 (pp20) REVERT: k 369 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7947 (mtp85) REVERT: m 158 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7957 (ptt-90) REVERT: m 232 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7595 (p0) REVERT: n 133 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7223 (tm-30) REVERT: n 137 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.6885 (m-30) REVERT: o 244 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8364 (t0) REVERT: s 90 GLN cc_start: 0.7359 (mm-40) cc_final: 0.6664 (mm-40) REVERT: s 131 MET cc_start: 0.8700 (mmm) cc_final: 0.8431 (mmm) REVERT: s 170 ASP cc_start: 0.8465 (p0) cc_final: 0.7709 (p0) REVERT: u 12 TRP cc_start: 0.8578 (OUTLIER) cc_final: 0.7917 (p90) REVERT: a 114 LEU cc_start: 0.9628 (OUTLIER) cc_final: 0.9357 (mm) REVERT: a 156 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8151 (pp) REVERT: a 293 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7712 (t80) REVERT: a 609 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7781 (t0) REVERT: a 621 TRP cc_start: 0.8496 (m100) cc_final: 0.7843 (m100) REVERT: a 996 MET cc_start: 0.9516 (ttt) cc_final: 0.9087 (ttt) REVERT: e 223 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8737 (t80) REVERT: e 258 THR cc_start: 0.9124 (p) cc_final: 0.8840 (t) REVERT: e 292 LEU cc_start: 0.9617 (mt) cc_final: 0.9362 (pp) REVERT: e 809 MET cc_start: 0.7391 (ppp) cc_final: 0.7040 (ppp) REVERT: e 910 SER cc_start: 0.7677 (OUTLIER) cc_final: 0.7361 (p) REVERT: e 1060 MET cc_start: 0.2033 (mpt) cc_final: 0.1581 (mpt) REVERT: e 1068 MET cc_start: 0.0477 (ptm) cc_final: -0.1055 (ppp) REVERT: e 1136 PHE cc_start: 0.8608 (m-80) cc_final: 0.8212 (m-10) REVERT: g 6 GLN cc_start: 0.8451 (mt0) cc_final: 0.8187 (mt0) REVERT: g 113 TYR cc_start: 0.8711 (m-80) cc_final: 0.8466 (m-80) REVERT: g 123 ARG cc_start: 0.8582 (tpp-160) cc_final: 0.8333 (mmp80) REVERT: g 140 GLN cc_start: 0.8756 (tp40) cc_final: 0.8176 (tp-100) REVERT: w 89 ASP cc_start: 0.9419 (OUTLIER) cc_final: 0.9182 (m-30) REVERT: w 119 GLN cc_start: 0.8121 (mp-120) cc_final: 0.7775 (mp10) REVERT: w 174 MET cc_start: 0.5699 (mpt) cc_final: 0.4643 (mpt) REVERT: w 210 MET cc_start: 0.7317 (mmp) cc_final: 0.7019 (mmm) REVERT: 0 31 ASP cc_start: 0.9233 (t0) cc_final: 0.8482 (OUTLIER) REVERT: 0 32 ASN cc_start: 0.9142 (m-40) cc_final: 0.8501 (p0) REVERT: 0 44 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8915 (pp20) REVERT: 0 97 LYS cc_start: 0.9658 (OUTLIER) cc_final: 0.9163 (pttp) REVERT: v 27 ARG cc_start: 0.8629 (tpp80) cc_final: 0.8304 (mmm-85) REVERT: v 125 GLN cc_start: 0.9201 (tp40) cc_final: 0.8715 (tp40) REVERT: v 136 VAL cc_start: 0.8822 (t) cc_final: 0.8598 (p) outliers start: 260 outliers final: 146 residues processed: 921 average time/residue: 2.1095 time to fit residues: 2880.9270 Evaluate side-chains 908 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 737 time to evaluate : 7.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 106 GLN Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain W residue 14 LYS Chi-restraints excluded: chain W residue 24 ARG Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 10 GLN Chi-restraints excluded: chain X residue 22 THR Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 59 CYS Chi-restraints excluded: chain c residue 89 MET Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 103 THR Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 369 ARG Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 232 ASP Chi-restraints excluded: chain m residue 236 LEU Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain n residue 137 ASP Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 160 SER Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain o residue 244 ASN Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 6 THR Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 147 VAL Chi-restraints excluded: chain r residue 177 ASP Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 30 LEU Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 65 ILE Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 122 ILE Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain t residue 182 ILE Chi-restraints excluded: chain u residue 7 VAL Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 293 TYR Chi-restraints excluded: chain a residue 301 ASP Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain e residue 216 VAL Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 229 VAL Chi-restraints excluded: chain e residue 309 VAL Chi-restraints excluded: chain e residue 319 THR Chi-restraints excluded: chain e residue 770 ILE Chi-restraints excluded: chain e residue 910 SER Chi-restraints excluded: chain e residue 978 THR Chi-restraints excluded: chain e residue 1300 ILE Chi-restraints excluded: chain e residue 1359 LEU Chi-restraints excluded: chain g residue 95 GLN Chi-restraints excluded: chain g residue 206 THR Chi-restraints excluded: chain w residue 65 ILE Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain w residue 72 PHE Chi-restraints excluded: chain w residue 89 ASP Chi-restraints excluded: chain w residue 108 ASN Chi-restraints excluded: chain w residue 111 ILE Chi-restraints excluded: chain w residue 141 ASN Chi-restraints excluded: chain w residue 169 VAL Chi-restraints excluded: chain 0 residue 25 LEU Chi-restraints excluded: chain 0 residue 34 SER Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 97 LYS Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 188 VAL Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 42 VAL Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 157 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1196 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 707 optimal weight: 7.9990 chunk 906 optimal weight: 0.2980 chunk 702 optimal weight: 4.9990 chunk 1044 optimal weight: 9.9990 chunk 693 optimal weight: 8.9990 chunk 1236 optimal weight: 40.0000 chunk 773 optimal weight: 1.9990 chunk 753 optimal weight: 5.9990 chunk 570 optimal weight: 4.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 132 ASN L 26 GLN Y 33 ASN p 77 GLN p 79 GLN p 240 ASN q 9 GLN r 51 HIS ** s 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 160 GLN a 121 ASN e 233 ASN ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 75 GLN ** w 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 161865 Z= 0.238 Angle : 0.595 14.606 236451 Z= 0.310 Chirality : 0.037 0.300 29529 Planarity : 0.004 0.090 16480 Dihedral : 22.572 179.984 66834 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 2.68 % Allowed : 16.87 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 9312 helix: 1.70 (0.08), residues: 3910 sheet: 0.01 (0.14), residues: 1206 loop : -0.72 (0.09), residues: 4196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP a 658 HIS 0.012 0.001 HIS H 40 PHE 0.021 0.001 PHE Q 39 TYR 0.028 0.001 TYR 0 22 ARG 0.015 0.000 ARG 0 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 780 time to evaluate : 8.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 86 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: F 104 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: H 44 GLU cc_start: 0.7564 (pm20) cc_final: 0.7342 (pm20) REVERT: H 49 ASN cc_start: 0.8139 (t0) cc_final: 0.7584 (t0) REVERT: H 91 ASP cc_start: 0.8852 (p0) cc_final: 0.8553 (p0) REVERT: H 92 TRP cc_start: 0.7956 (OUTLIER) cc_final: 0.7325 (m-90) REVERT: L 74 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.8215 (m-80) REVERT: M 95 VAL cc_start: 0.9266 (OUTLIER) cc_final: 0.9060 (p) REVERT: M 106 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8167 (mt0) REVERT: X 10 GLN cc_start: 0.8031 (tp40) cc_final: 0.7478 (tp-100) REVERT: X 13 GLU cc_start: 0.7618 (pp20) cc_final: 0.7402 (pp20) REVERT: j 24 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8013 (mt0) REVERT: j 143 GLU cc_start: 0.8300 (pp20) cc_final: 0.7924 (pp20) REVERT: k 102 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8389 (pt) REVERT: m 158 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7927 (ptt-90) REVERT: m 232 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7583 (p0) REVERT: n 133 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7135 (tm-30) REVERT: q 51 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8210 (mp-120) REVERT: u 12 TRP cc_start: 0.8553 (OUTLIER) cc_final: 0.7800 (p90) REVERT: a 114 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9391 (mm) REVERT: a 156 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8098 (pp) REVERT: a 293 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7833 (t80) REVERT: a 609 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7611 (t0) REVERT: a 621 TRP cc_start: 0.8451 (m100) cc_final: 0.7748 (m100) REVERT: a 996 MET cc_start: 0.9520 (ttt) cc_final: 0.9078 (ttt) REVERT: e 116 MET cc_start: 0.9214 (mmm) cc_final: 0.8957 (mpp) REVERT: e 258 THR cc_start: 0.9114 (p) cc_final: 0.8830 (t) REVERT: e 292 LEU cc_start: 0.9603 (mt) cc_final: 0.9343 (pp) REVERT: e 809 MET cc_start: 0.7408 (ppp) cc_final: 0.7078 (ppp) REVERT: e 910 SER cc_start: 0.7746 (OUTLIER) cc_final: 0.7424 (p) REVERT: e 1068 MET cc_start: 0.0424 (ptm) cc_final: -0.1084 (ppp) REVERT: e 1136 PHE cc_start: 0.8574 (m-80) cc_final: 0.8189 (m-10) REVERT: e 1410 LEU cc_start: 0.8226 (mm) cc_final: 0.7840 (pp) REVERT: g 6 GLN cc_start: 0.8363 (mt0) cc_final: 0.8104 (mt0) REVERT: g 16 PHE cc_start: 0.9178 (m-80) cc_final: 0.8848 (m-80) REVERT: g 123 ARG cc_start: 0.8576 (tpp-160) cc_final: 0.8317 (mmp80) REVERT: g 140 GLN cc_start: 0.8794 (tp40) cc_final: 0.8217 (tp-100) REVERT: g 157 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8645 (mt0) REVERT: g 164 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8497 (mm-40) REVERT: w 119 GLN cc_start: 0.8034 (mp-120) cc_final: 0.7667 (mp10) REVERT: w 174 MET cc_start: 0.5583 (mpt) cc_final: 0.4514 (mpt) REVERT: w 210 MET cc_start: 0.7415 (mmp) cc_final: 0.6909 (mmm) REVERT: 0 18 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.8068 (t80) REVERT: 0 31 ASP cc_start: 0.9197 (t0) cc_final: 0.8370 (t0) REVERT: 0 32 ASN cc_start: 0.9084 (m-40) cc_final: 0.8443 (p0) REVERT: 0 44 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8858 (pp20) REVERT: 0 53 MET cc_start: 0.8691 (mmm) cc_final: 0.8213 (mmm) REVERT: v 27 ARG cc_start: 0.8640 (tpp80) cc_final: 0.8292 (mmm-85) REVERT: v 125 GLN cc_start: 0.9220 (tp40) cc_final: 0.8684 (tp40) outliers start: 203 outliers final: 127 residues processed: 908 average time/residue: 2.1110 time to fit residues: 2843.1342 Evaluate side-chains 912 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 766 time to evaluate : 7.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 92 TRP Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 106 GLN Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 22 THR Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 25 GLN Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 102 LEU Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain m residue 118 THR Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 232 ASP Chi-restraints excluded: chain m residue 236 LEU Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 160 SER Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain p residue 240 ASN Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 51 GLN Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 177 ASP Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 14 ILE Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 88 GLU Chi-restraints excluded: chain s residue 117 ASP Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain t residue 182 ILE Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 293 TYR Chi-restraints excluded: chain a residue 301 ASP Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 633 ASN Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain e residue 309 VAL Chi-restraints excluded: chain e residue 319 THR Chi-restraints excluded: chain e residue 770 ILE Chi-restraints excluded: chain e residue 910 SER Chi-restraints excluded: chain e residue 978 THR Chi-restraints excluded: chain e residue 1300 ILE Chi-restraints excluded: chain e residue 1359 LEU Chi-restraints excluded: chain e residue 1419 ILE Chi-restraints excluded: chain g residue 146 ILE Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain w residue 72 PHE Chi-restraints excluded: chain w residue 111 ILE Chi-restraints excluded: chain w residue 136 THR Chi-restraints excluded: chain w residue 141 ASN Chi-restraints excluded: chain 0 residue 16 ARG Chi-restraints excluded: chain 0 residue 18 TYR Chi-restraints excluded: chain 0 residue 25 LEU Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 97 LYS Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 188 VAL Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 42 VAL Chi-restraints excluded: chain v residue 52 HIS Chi-restraints excluded: chain v residue 54 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 765 optimal weight: 20.0000 chunk 493 optimal weight: 10.0000 chunk 738 optimal weight: 6.9990 chunk 372 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 chunk 239 optimal weight: 10.0000 chunk 786 optimal weight: 9.9990 chunk 842 optimal weight: 3.9990 chunk 611 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 972 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 132 ASN L 26 GLN p 77 GLN p 240 ASN q 9 GLN r 51 HIS ** s 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 407 GLN ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 75 GLN ** w 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.133 161865 Z= 0.456 Angle : 0.665 19.983 236451 Z= 0.345 Chirality : 0.043 0.378 29529 Planarity : 0.005 0.093 16480 Dihedral : 22.503 179.972 66834 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.46 % Favored : 95.49 % Rotamer: Outliers : 2.83 % Allowed : 17.19 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.09), residues: 9312 helix: 1.59 (0.08), residues: 3929 sheet: -0.04 (0.14), residues: 1208 loop : -0.76 (0.09), residues: 4175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP a 658 HIS 0.008 0.001 HIS w 12 PHE 0.026 0.002 PHE o 229 TYR 0.025 0.002 TYR s 89 ARG 0.017 0.001 ARG X 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 762 time to evaluate : 8.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 86 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: E 144 GLN cc_start: 0.8366 (mm-40) cc_final: 0.7962 (tm-30) REVERT: F 104 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: H 39 ASP cc_start: 0.8379 (p0) cc_final: 0.8141 (p0) REVERT: H 44 GLU cc_start: 0.7568 (pm20) cc_final: 0.7356 (pm20) REVERT: H 49 ASN cc_start: 0.8176 (t0) cc_final: 0.7579 (t0) REVERT: I 32 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7411 (mtp85) REVERT: I 98 ASN cc_start: 0.8975 (OUTLIER) cc_final: 0.8761 (m110) REVERT: M 95 VAL cc_start: 0.9277 (OUTLIER) cc_final: 0.9069 (p) REVERT: P 98 SER cc_start: 0.9139 (t) cc_final: 0.8931 (p) REVERT: Q 105 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8746 (mt0) REVERT: W 24 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7825 (tpt-90) REVERT: X 10 GLN cc_start: 0.8076 (tp40) cc_final: 0.7360 (tp-100) REVERT: X 13 GLU cc_start: 0.7736 (pp20) cc_final: 0.7535 (pp20) REVERT: j 24 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8115 (mt0) REVERT: j 143 GLU cc_start: 0.8225 (pp20) cc_final: 0.7882 (pp20) REVERT: k 102 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8476 (pt) REVERT: l 285 ASP cc_start: 0.8064 (t0) cc_final: 0.7643 (t0) REVERT: m 158 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.7988 (ptt-90) REVERT: m 232 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7617 (p0) REVERT: n 133 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7095 (tm-30) REVERT: o 244 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8453 (t0) REVERT: s 81 GLU cc_start: 0.8245 (tp30) cc_final: 0.8041 (tp30) REVERT: s 90 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7080 (mm110) REVERT: s 170 ASP cc_start: 0.8457 (p0) cc_final: 0.8008 (p0) REVERT: u 5 SER cc_start: 0.9028 (m) cc_final: 0.8770 (m) REVERT: u 12 TRP cc_start: 0.8650 (OUTLIER) cc_final: 0.7872 (p90) REVERT: a 114 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9415 (mm) REVERT: a 156 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8121 (pp) REVERT: a 293 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7881 (t80) REVERT: a 543 MET cc_start: 0.9414 (mmt) cc_final: 0.9205 (mmm) REVERT: a 621 TRP cc_start: 0.8515 (m100) cc_final: 0.7903 (m100) REVERT: a 633 ASN cc_start: 0.9659 (OUTLIER) cc_final: 0.9369 (t0) REVERT: a 659 TRP cc_start: 0.9370 (p90) cc_final: 0.9049 (p-90) REVERT: e 116 MET cc_start: 0.9257 (mmm) cc_final: 0.8995 (mpp) REVERT: e 223 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8805 (t80) REVERT: e 258 THR cc_start: 0.9088 (p) cc_final: 0.8811 (t) REVERT: e 292 LEU cc_start: 0.9616 (mt) cc_final: 0.9361 (pp) REVERT: e 809 MET cc_start: 0.7376 (ppp) cc_final: 0.7039 (ppp) REVERT: e 910 SER cc_start: 0.7715 (OUTLIER) cc_final: 0.7402 (p) REVERT: e 963 MET cc_start: 0.1290 (ptt) cc_final: 0.0933 (pmm) REVERT: e 1068 MET cc_start: 0.0470 (ptm) cc_final: -0.1175 (ppp) REVERT: e 1136 PHE cc_start: 0.8537 (m-80) cc_final: 0.8147 (m-10) REVERT: e 1300 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9092 (mt) REVERT: e 1303 MET cc_start: 0.9275 (ttm) cc_final: 0.8917 (ppp) REVERT: e 1410 LEU cc_start: 0.8262 (mm) cc_final: 0.7891 (pp) REVERT: g 1 MET cc_start: 0.5024 (ttt) cc_final: 0.2475 (mtt) REVERT: g 6 GLN cc_start: 0.8343 (mt0) cc_final: 0.8076 (mt0) REVERT: g 123 ARG cc_start: 0.8623 (tpp-160) cc_final: 0.8337 (mmp80) REVERT: g 140 GLN cc_start: 0.8805 (tp40) cc_final: 0.8220 (tp-100) REVERT: g 157 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8631 (mt0) REVERT: w 119 GLN cc_start: 0.8137 (mp-120) cc_final: 0.7915 (mp10) REVERT: w 174 MET cc_start: 0.5772 (mpt) cc_final: 0.4686 (mpt) REVERT: 0 31 ASP cc_start: 0.9182 (t0) cc_final: 0.8317 (OUTLIER) REVERT: 0 32 ASN cc_start: 0.9141 (m-40) cc_final: 0.8500 (p0) REVERT: 0 64 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7811 (mtm110) REVERT: 0 97 LYS cc_start: 0.9659 (OUTLIER) cc_final: 0.9132 (pttp) REVERT: v 21 MET cc_start: 0.8253 (tpt) cc_final: 0.7927 (tpt) REVERT: v 27 ARG cc_start: 0.8687 (tpp80) cc_final: 0.8328 (mmt90) REVERT: v 80 MET cc_start: 0.8482 (pmm) cc_final: 0.8161 (pmm) REVERT: v 89 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8319 (mm-30) REVERT: v 125 GLN cc_start: 0.9224 (tp40) cc_final: 0.8688 (tp40) outliers start: 214 outliers final: 139 residues processed: 908 average time/residue: 2.0828 time to fit residues: 2793.2241 Evaluate side-chains 910 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 750 time to evaluate : 8.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain I residue 32 ARG Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain R residue 115 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 47 ILE Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain W residue 24 ARG Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 22 THR Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 102 LEU Chi-restraints excluded: chain k residue 103 THR Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain m residue 118 THR Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 232 ASP Chi-restraints excluded: chain m residue 236 LEU Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 160 SER Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain o residue 244 ASN Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain p residue 217 THR Chi-restraints excluded: chain p residue 240 ASN Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 147 VAL Chi-restraints excluded: chain r residue 177 ASP Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 14 ILE Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 88 GLU Chi-restraints excluded: chain s residue 117 ASP Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain t residue 182 ILE Chi-restraints excluded: chain u residue 7 VAL Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 293 TYR Chi-restraints excluded: chain a residue 301 ASP Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 633 ASN Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain e residue 45 ASN Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 229 VAL Chi-restraints excluded: chain e residue 309 VAL Chi-restraints excluded: chain e residue 319 THR Chi-restraints excluded: chain e residue 770 ILE Chi-restraints excluded: chain e residue 910 SER Chi-restraints excluded: chain e residue 978 THR Chi-restraints excluded: chain e residue 1300 ILE Chi-restraints excluded: chain e residue 1365 CYS Chi-restraints excluded: chain e residue 1419 ILE Chi-restraints excluded: chain g residue 146 ILE Chi-restraints excluded: chain g residue 206 THR Chi-restraints excluded: chain w residue 65 ILE Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain w residue 72 PHE Chi-restraints excluded: chain w residue 111 ILE Chi-restraints excluded: chain w residue 136 THR Chi-restraints excluded: chain w residue 141 ASN Chi-restraints excluded: chain 0 residue 16 ARG Chi-restraints excluded: chain 0 residue 25 LEU Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 94 THR Chi-restraints excluded: chain 0 residue 97 LYS Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 188 VAL Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 42 VAL Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 52 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1124 optimal weight: 50.0000 chunk 1184 optimal weight: 8.9990 chunk 1080 optimal weight: 50.0000 chunk 1152 optimal weight: 40.0000 chunk 693 optimal weight: 0.0070 chunk 502 optimal weight: 10.0000 chunk 904 optimal weight: 7.9990 chunk 353 optimal weight: 6.9990 chunk 1041 optimal weight: 8.9990 chunk 1089 optimal weight: 10.0000 chunk 1148 optimal weight: 40.0000 overall best weight: 6.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN C 120 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 132 ASN L 26 GLN L 120 GLN p 77 GLN r 51 HIS ** s 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 530 GLN ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 75 GLN ** w 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 161865 Z= 0.429 Angle : 0.662 19.394 236451 Z= 0.344 Chirality : 0.042 0.385 29529 Planarity : 0.005 0.092 16480 Dihedral : 22.528 179.997 66832 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.35 % Favored : 95.61 % Rotamer: Outliers : 2.75 % Allowed : 17.56 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.09), residues: 9312 helix: 1.55 (0.08), residues: 3934 sheet: -0.01 (0.14), residues: 1209 loop : -0.80 (0.09), residues: 4169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP a 658 HIS 0.010 0.001 HIS H 40 PHE 0.026 0.002 PHE v 99 TYR 0.056 0.002 TYR s 89 ARG 0.016 0.001 ARG c 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 771 time to evaluate : 7.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 86 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: E 144 GLN cc_start: 0.8367 (mm-40) cc_final: 0.7987 (tm-30) REVERT: F 104 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: H 39 ASP cc_start: 0.8447 (p0) cc_final: 0.8098 (p0) REVERT: H 49 ASN cc_start: 0.8181 (t0) cc_final: 0.7460 (t0) REVERT: I 98 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8746 (m110) REVERT: Q 105 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8736 (mt0) REVERT: U 79 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7708 (p0) REVERT: W 24 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7821 (tpt-90) REVERT: X 10 GLN cc_start: 0.8098 (tp40) cc_final: 0.7319 (tp-100) REVERT: j 24 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: j 143 GLU cc_start: 0.8237 (pp20) cc_final: 0.7941 (pp20) REVERT: k 102 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8470 (pt) REVERT: m 158 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.7954 (ptt-90) REVERT: m 232 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7696 (p0) REVERT: n 97 ASN cc_start: 0.8059 (t0) cc_final: 0.7825 (t0) REVERT: n 133 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7170 (tm-30) REVERT: o 244 ASN cc_start: 0.8932 (OUTLIER) cc_final: 0.8442 (t0) REVERT: s 81 GLU cc_start: 0.8257 (tp30) cc_final: 0.7986 (tp30) REVERT: u 5 SER cc_start: 0.9026 (m) cc_final: 0.8764 (m) REVERT: u 12 TRP cc_start: 0.8661 (OUTLIER) cc_final: 0.7743 (p90) REVERT: a 114 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9433 (mm) REVERT: a 156 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8093 (pp) REVERT: a 293 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7833 (t80) REVERT: a 543 MET cc_start: 0.9394 (mmt) cc_final: 0.9184 (mmm) REVERT: a 621 TRP cc_start: 0.8603 (m100) cc_final: 0.8015 (m100) REVERT: a 659 TRP cc_start: 0.9413 (p90) cc_final: 0.9138 (p-90) REVERT: a 994 HIS cc_start: 0.9095 (OUTLIER) cc_final: 0.8827 (m90) REVERT: e 116 MET cc_start: 0.9255 (mmm) cc_final: 0.9030 (mpp) REVERT: e 258 THR cc_start: 0.9169 (p) cc_final: 0.8902 (t) REVERT: e 267 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9167 (pp) REVERT: e 277 MET cc_start: 0.5417 (OUTLIER) cc_final: 0.3387 (ppp) REVERT: e 292 LEU cc_start: 0.9606 (mt) cc_final: 0.9348 (pp) REVERT: e 809 MET cc_start: 0.7350 (ppp) cc_final: 0.7015 (ppp) REVERT: e 910 SER cc_start: 0.7760 (OUTLIER) cc_final: 0.7418 (p) REVERT: e 1068 MET cc_start: 0.0272 (ptm) cc_final: -0.1339 (ppp) REVERT: e 1136 PHE cc_start: 0.8543 (m-80) cc_final: 0.8197 (m-10) REVERT: e 1300 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9009 (mt) REVERT: e 1303 MET cc_start: 0.9246 (ttm) cc_final: 0.8984 (pp-130) REVERT: e 1410 LEU cc_start: 0.8260 (mm) cc_final: 0.7928 (pp) REVERT: g 6 GLN cc_start: 0.8380 (mt0) cc_final: 0.8094 (mt0) REVERT: g 123 ARG cc_start: 0.8638 (tpp-160) cc_final: 0.8361 (mmp80) REVERT: g 140 GLN cc_start: 0.8813 (tp40) cc_final: 0.8236 (tp-100) REVERT: g 157 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8658 (mt0) REVERT: g 164 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8643 (mm-40) REVERT: w 10 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7721 (mmm-85) REVERT: w 60 ARG cc_start: 0.8890 (ptm160) cc_final: 0.8582 (ptm160) REVERT: w 114 GLU cc_start: 0.8591 (pm20) cc_final: 0.8371 (pm20) REVERT: w 174 MET cc_start: 0.6022 (mpt) cc_final: 0.4697 (mpt) REVERT: w 210 MET cc_start: 0.7875 (mmp) cc_final: 0.7304 (mmm) REVERT: 0 31 ASP cc_start: 0.9205 (t0) cc_final: 0.8338 (OUTLIER) REVERT: 0 32 ASN cc_start: 0.9100 (m-40) cc_final: 0.8532 (p0) REVERT: 0 97 LYS cc_start: 0.9662 (OUTLIER) cc_final: 0.9194 (pttt) REVERT: v 21 MET cc_start: 0.8254 (tpt) cc_final: 0.8038 (tpt) REVERT: v 125 GLN cc_start: 0.9258 (tp40) cc_final: 0.8810 (tp40) outliers start: 208 outliers final: 142 residues processed: 905 average time/residue: 2.0957 time to fit residues: 2793.3218 Evaluate side-chains 917 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 754 time to evaluate : 8.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain W residue 24 ARG Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 22 THR Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 59 CYS Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 102 LEU Chi-restraints excluded: chain k residue 103 THR Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain m residue 118 THR Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 232 ASP Chi-restraints excluded: chain m residue 236 LEU Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 133 GLU Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 160 SER Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain o residue 244 ASN Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 76 MET Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 147 VAL Chi-restraints excluded: chain r residue 167 LEU Chi-restraints excluded: chain r residue 177 ASP Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 14 ILE Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 117 ASP Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain t residue 182 ILE Chi-restraints excluded: chain u residue 7 VAL Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 293 TYR Chi-restraints excluded: chain a residue 301 ASP Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 994 HIS Chi-restraints excluded: chain e residue 45 ASN Chi-restraints excluded: chain e residue 229 VAL Chi-restraints excluded: chain e residue 267 LEU Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 309 VAL Chi-restraints excluded: chain e residue 319 THR Chi-restraints excluded: chain e residue 770 ILE Chi-restraints excluded: chain e residue 910 SER Chi-restraints excluded: chain e residue 1300 ILE Chi-restraints excluded: chain e residue 1365 CYS Chi-restraints excluded: chain e residue 1419 ILE Chi-restraints excluded: chain g residue 146 ILE Chi-restraints excluded: chain g residue 206 THR Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain w residue 72 PHE Chi-restraints excluded: chain w residue 136 THR Chi-restraints excluded: chain w residue 141 ASN Chi-restraints excluded: chain 0 residue 16 ARG Chi-restraints excluded: chain 0 residue 25 LEU Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 97 LYS Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 188 VAL Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 42 VAL Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 52 HIS Chi-restraints excluded: chain v residue 73 LEU Chi-restraints excluded: chain v residue 150 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 756 optimal weight: 7.9990 chunk 1218 optimal weight: 9.9990 chunk 743 optimal weight: 5.9990 chunk 578 optimal weight: 10.0000 chunk 847 optimal weight: 0.5980 chunk 1278 optimal weight: 8.9990 chunk 1176 optimal weight: 7.9990 chunk 1017 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 786 optimal weight: 5.9990 chunk 624 optimal weight: 10.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN C 120 ASN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 132 ASN L 26 GLN p 77 GLN p 240 ASN ** s 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 832 ASN g 75 GLN ** w 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 161865 Z= 0.333 Angle : 0.635 19.432 236451 Z= 0.330 Chirality : 0.040 0.344 29529 Planarity : 0.005 0.091 16480 Dihedral : 22.529 179.854 66831 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.36 % Favored : 95.60 % Rotamer: Outliers : 2.47 % Allowed : 17.99 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.09), residues: 9312 helix: 1.58 (0.08), residues: 3938 sheet: -0.03 (0.14), residues: 1211 loop : -0.75 (0.09), residues: 4163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP a 658 HIS 0.021 0.001 HIS H 40 PHE 0.030 0.002 PHE e 30 TYR 0.028 0.002 TYR P 27 ARG 0.019 0.001 ARG w 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 769 time to evaluate : 7.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 86 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: E 144 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7971 (tm-30) REVERT: F 104 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: H 39 ASP cc_start: 0.8306 (p0) cc_final: 0.8006 (p0) REVERT: I 32 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7372 (mtp85) REVERT: I 98 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8734 (m110) REVERT: L 74 TYR cc_start: 0.8655 (OUTLIER) cc_final: 0.8258 (m-80) REVERT: Q 105 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8716 (mt0) REVERT: W 24 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7855 (tpt-90) REVERT: X 10 GLN cc_start: 0.8087 (tp40) cc_final: 0.7570 (tp-100) REVERT: X 13 GLU cc_start: 0.7706 (pp20) cc_final: 0.7469 (pp20) REVERT: d 15 ARG cc_start: 0.6800 (ttt180) cc_final: 0.6453 (ttt180) REVERT: j 24 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8088 (mt0) REVERT: j 143 GLU cc_start: 0.8252 (pp20) cc_final: 0.7994 (pp20) REVERT: k 102 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8432 (pt) REVERT: m 158 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7989 (ptt-90) REVERT: m 232 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7700 (p0) REVERT: n 97 ASN cc_start: 0.8051 (t0) cc_final: 0.7803 (t0) REVERT: n 136 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7538 (mp0) REVERT: o 244 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8461 (t0) REVERT: u 5 SER cc_start: 0.9012 (m) cc_final: 0.8757 (m) REVERT: u 12 TRP cc_start: 0.8628 (OUTLIER) cc_final: 0.7730 (p90) REVERT: a 114 LEU cc_start: 0.9671 (OUTLIER) cc_final: 0.9451 (mm) REVERT: a 156 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8079 (pp) REVERT: a 293 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7838 (t80) REVERT: a 543 MET cc_start: 0.9320 (mmt) cc_final: 0.9115 (mmm) REVERT: a 621 TRP cc_start: 0.8628 (m100) cc_final: 0.8062 (m100) REVERT: a 659 TRP cc_start: 0.9410 (p90) cc_final: 0.9159 (OUTLIER) REVERT: a 994 HIS cc_start: 0.9072 (OUTLIER) cc_final: 0.8809 (m-70) REVERT: e 116 MET cc_start: 0.9241 (mmm) cc_final: 0.8968 (mpp) REVERT: e 267 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9173 (pp) REVERT: e 292 LEU cc_start: 0.9599 (mt) cc_final: 0.9323 (pp) REVERT: e 809 MET cc_start: 0.7333 (ppp) cc_final: 0.7002 (ppp) REVERT: e 910 SER cc_start: 0.7989 (OUTLIER) cc_final: 0.7671 (p) REVERT: e 1068 MET cc_start: 0.0202 (ptm) cc_final: -0.1268 (ppp) REVERT: e 1136 PHE cc_start: 0.8593 (m-80) cc_final: 0.8272 (m-10) REVERT: e 1300 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9114 (mt) REVERT: e 1303 MET cc_start: 0.9310 (OUTLIER) cc_final: 0.9018 (pp-130) REVERT: e 1410 LEU cc_start: 0.8301 (mm) cc_final: 0.7942 (pp) REVERT: g 1 MET cc_start: 0.5011 (ttt) cc_final: 0.3679 (tpp) REVERT: g 123 ARG cc_start: 0.8617 (tpp-160) cc_final: 0.8354 (mmp80) REVERT: g 140 GLN cc_start: 0.8818 (tp40) cc_final: 0.8254 (tp-100) REVERT: g 157 GLN cc_start: 0.9257 (mm-40) cc_final: 0.8665 (mt0) REVERT: w 10 ARG cc_start: 0.8220 (mmm-85) cc_final: 0.7734 (mmm-85) REVERT: w 60 ARG cc_start: 0.8993 (ptm160) cc_final: 0.8681 (ptm160) REVERT: w 114 GLU cc_start: 0.8599 (pm20) cc_final: 0.8312 (pm20) REVERT: w 174 MET cc_start: 0.6059 (mpt) cc_final: 0.5339 (mpt) REVERT: w 210 MET cc_start: 0.7900 (mmp) cc_final: 0.7420 (mmm) REVERT: 0 31 ASP cc_start: 0.9193 (t0) cc_final: 0.8319 (OUTLIER) REVERT: 0 32 ASN cc_start: 0.9087 (m-40) cc_final: 0.8527 (p0) REVERT: v 21 MET cc_start: 0.8240 (tpt) cc_final: 0.8015 (tpt) REVERT: v 88 ASN cc_start: 0.9076 (m-40) cc_final: 0.8728 (m-40) REVERT: v 125 GLN cc_start: 0.9262 (tp40) cc_final: 0.8745 (tp40) outliers start: 187 outliers final: 141 residues processed: 894 average time/residue: 2.1189 time to fit residues: 2818.3011 Evaluate side-chains 913 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 753 time to evaluate : 8.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 106 LEU Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain I residue 32 ARG Chi-restraints excluded: chain I residue 98 ASN Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 30 ASP Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 132 SER Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 109 VAL Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain T residue 94 LEU Chi-restraints excluded: chain T residue 95 ILE Chi-restraints excluded: chain U residue 118 ILE Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain W residue 24 ARG Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 22 THR Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 59 CYS Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 102 LEU Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain m residue 118 THR Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 232 ASP Chi-restraints excluded: chain m residue 236 LEU Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 160 SER Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain o residue 244 ASN Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain p residue 217 THR Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 76 MET Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 147 VAL Chi-restraints excluded: chain r residue 167 LEU Chi-restraints excluded: chain r residue 177 ASP Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 14 ILE Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 88 GLU Chi-restraints excluded: chain s residue 117 ASP Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain t residue 182 ILE Chi-restraints excluded: chain u residue 7 VAL Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 64 VAL Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 90 THR Chi-restraints excluded: chain a residue 102 VAL Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 156 LEU Chi-restraints excluded: chain a residue 293 TYR Chi-restraints excluded: chain a residue 301 ASP Chi-restraints excluded: chain a residue 580 PHE Chi-restraints excluded: chain a residue 933 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 994 HIS Chi-restraints excluded: chain e residue 45 ASN Chi-restraints excluded: chain e residue 216 VAL Chi-restraints excluded: chain e residue 229 VAL Chi-restraints excluded: chain e residue 267 LEU Chi-restraints excluded: chain e residue 309 VAL Chi-restraints excluded: chain e residue 319 THR Chi-restraints excluded: chain e residue 910 SER Chi-restraints excluded: chain e residue 1300 ILE Chi-restraints excluded: chain e residue 1303 MET Chi-restraints excluded: chain e residue 1365 CYS Chi-restraints excluded: chain e residue 1419 ILE Chi-restraints excluded: chain g residue 146 ILE Chi-restraints excluded: chain g residue 206 THR Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain w residue 72 PHE Chi-restraints excluded: chain w residue 89 ASP Chi-restraints excluded: chain w residue 136 THR Chi-restraints excluded: chain w residue 141 ASN Chi-restraints excluded: chain 0 residue 16 ARG Chi-restraints excluded: chain 0 residue 25 LEU Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 76 LEU Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 188 VAL Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 42 VAL Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 52 HIS Chi-restraints excluded: chain v residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 808 optimal weight: 1.9990 chunk 1084 optimal weight: 20.0000 chunk 311 optimal weight: 8.9990 chunk 938 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 282 optimal weight: 1.9990 chunk 1019 optimal weight: 20.0000 chunk 426 optimal weight: 10.0000 chunk 1046 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 132 ASN L 26 GLN p 77 GLN ** s 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 6 GLN g 75 GLN ** g 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 171 ASN ** 0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.068966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.042273 restraints weight = 525913.809| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 1.74 r_work: 0.2591 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2494 r_free = 0.2494 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2493 r_free = 0.2493 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 161865 Z= 0.305 Angle : 0.622 19.156 236451 Z= 0.324 Chirality : 0.039 0.321 29529 Planarity : 0.005 0.091 16480 Dihedral : 22.508 179.696 66831 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.21 % Favored : 95.75 % Rotamer: Outliers : 2.39 % Allowed : 18.24 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.09), residues: 9312 helix: 1.61 (0.08), residues: 3943 sheet: -0.01 (0.14), residues: 1195 loop : -0.74 (0.09), residues: 4174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP a 990 HIS 0.007 0.001 HIS w 12 PHE 0.026 0.001 PHE e 30 TYR 0.029 0.001 TYR e 276 ARG 0.014 0.000 ARG k 300 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49746.57 seconds wall clock time: 865 minutes 32.81 seconds (51932.81 seconds total)