Starting phenix.real_space_refine on Sat Mar 2 20:05:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ot7_3852/03_2024/5ot7_3852_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ot7_3852/03_2024/5ot7_3852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ot7_3852/03_2024/5ot7_3852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ot7_3852/03_2024/5ot7_3852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ot7_3852/03_2024/5ot7_3852_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ot7_3852/03_2024/5ot7_3852_updated.pdb" } resolution = 3.8 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= 0.001 sd= 0.014 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 3 6.06 5 P 4611 5.49 5 Mg 462 5.21 5 S 145 5.16 5 C 78819 2.51 5 N 29043 2.21 5 O 41582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "6 ARG 31": "NH1" <-> "NH2" Residue "6 ARG 81": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "P ARG 68": "NH1" <-> "NH2" Residue "P ARG 70": "NH1" <-> "NH2" Residue "Q ARG 72": "NH1" <-> "NH2" Residue "T ARG 7": "NH1" <-> "NH2" Residue "U ARG 354": "NH1" <-> "NH2" Residue "U ARG 357": "NH1" <-> "NH2" Residue "U ARG 396": "NH1" <-> "NH2" Residue "U ARG 484": "NH1" <-> "NH2" Residue "U ARG 499": "NH1" <-> "NH2" Residue "U ARG 504": "NH1" <-> "NH2" Residue "U ARG 519": "NH1" <-> "NH2" Residue "U ARG 607": "NH1" <-> "NH2" Residue "U ARG 660": "NH1" <-> "NH2" Residue "V ARG 11": "NH1" <-> "NH2" Residue "V ARG 72": "NH1" <-> "NH2" Residue "g ARG 157": "NH1" <-> "NH2" Residue "k ARG 170": "NH1" <-> "NH2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q ARG 55": "NH1" <-> "NH2" Residue "q TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 3": "NH1" <-> "NH2" Residue "u ARG 64": "NH1" <-> "NH2" Residue "u PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 8": "NH1" <-> "NH2" Residue "z PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 86": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 154665 Number of models: 1 Model: "" Number of chains: 75 Chain: "1" Number of atoms: 32391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1507, 32391 Classifications: {'RNA': 1507} Modifications used: {'5*END': 1, 'rna2p_pur': 120, 'rna2p_pyr': 111, 'rna3p_pur': 735, 'rna3p_pyr': 541} Link IDs: {'rna2p': 231, 'rna3p': 1275} Chain: "2" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 63} Chain: "3" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 214 Classifications: {'RNA': 10} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 6} Chain: "4" Number of atoms: 62476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2901, 62476 Classifications: {'RNA': 2901} Modifications used: {'5*END': 1, 'rna2p_pur': 297, 'rna2p_pyr': 149, 'rna3p_pur': 1401, 'rna3p_pyr': 1054} Link IDs: {'rna2p': 446, 'rna3p': 2454} Chain: "5" Number of atoms: 2551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2551 Classifications: {'RNA': 119} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 62, 'rna3p_pyr': 49} Link IDs: {'rna2p': 8, 'rna3p': 110} Chain: "6" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1418 Classifications: {'peptide': 178} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 161} Chain: "7" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1136 Classifications: {'peptide': 146} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 135} Chain: "A" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1901 Classifications: {'peptide': 235} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 222} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1613 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "D" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1147 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 8, 'TRANS': 142} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "F" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1257 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "G" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "H" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1010 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "I" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 885 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "K" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 938 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "N" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "O" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 701 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 824 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 574 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "R" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 763 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "T" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 209 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 5173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5173 Classifications: {'peptide': 661} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 38, 'TRANS': 622} Chain breaks: 1 Chain: "V" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 617 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "W" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 598 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "Y" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 581 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "a" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 459 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 49} Chain: "b" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 433 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "c" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 419 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "d" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 508 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "e" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 307 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "f" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1735 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 213} Chain: "g" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2145 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 253} Chain: "h" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1564 Classifications: {'peptide': 205} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 187} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "i" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1624 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 11, 'TRANS': 196} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 2 Chain: "j" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1459 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain: "k" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1345 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 16, 'TRANS': 159} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "l" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 654 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'TRANS': 129} Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 385 Unresolved non-hydrogen dihedrals: 129 Planarities with less than four sites: {'UNK:plan-1': 128} Unresolved non-hydrogen planarities: 128 Chain: "m" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 701 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'TRANS': 139} Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 140 Planarities with less than four sites: {'UNK:plan-1': 139} Unresolved non-hydrogen planarities: 139 Chain: "n" Number of atoms: 356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 356 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'TRANS': 70} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'UNK:plan-1': 70} Unresolved non-hydrogen planarities: 70 Chain: "o" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1105 Classifications: {'peptide': 139} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 126} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "p" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "q" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1145 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 139} Chain: "r" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1122 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "s" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 968 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "t" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 771 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 2 Chain: "u" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1142 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "v" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 958 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 115} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "w" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "x" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 896 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "y" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "z" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 776 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "1" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Unusual residues: {' MG': 126} Classifications: {'undetermined': 126} Link IDs: {None: 125} Chain: "4" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 322 Unusual residues: {' MG': 322} Classifications: {'undetermined': 322} Link IDs: {None: 321} 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: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" 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: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 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: "h" 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: "q" 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': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A045E SG CYS C 9 120.184 43.858 73.292 1.00 77.57 S ATOM A04AH SG CYS C 31 117.940 43.434 68.851 1.00 69.74 S ATOM A0CHB SG CYS M 24 68.881 73.596 101.327 1.00123.88 S ATOM A0CHZ SG CYS M 27 72.498 73.799 101.394 1.00136.27 S ATOM A0CKY SG CYS M 40 69.475 77.342 100.246 1.00122.09 S ATOM A0CLN SG CYS M 43 70.606 74.169 98.219 1.00104.89 S ATOM A0NZ3 SG CYS e 14 148.015 90.850 175.269 1.00 83.36 S ATOM A0O26 SG CYS e 27 150.064 88.293 173.913 1.00 77.24 S Time building chain proxies: 59.88, per 1000 atoms: 0.39 Number of scatterers: 154665 At special positions: 0 Unit cell: (251.37, 270.112, 241.447, 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 3 29.99 S 145 16.00 P 4611 15.00 Mg 462 11.99 O 41582 8.00 N 29043 7.00 C 78819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS a 33 " - pdb=" SG CYS a 36 " distance=2.03 Simple disulfide: pdb=" SG CYS a 33 " - pdb=" SG CYS a 46 " distance=2.11 Simple disulfide: pdb=" SG CYS a 33 " - pdb=" SG CYS a 49 " distance=1.93 Simple disulfide: pdb=" SG CYS a 36 " - pdb=" SG CYS a 46 " distance=1.91 Simple disulfide: pdb=" SG CYS a 36 " - pdb=" SG CYS a 49 " distance=2.10 Simple disulfide: pdb=" SG CYS a 46 " - pdb=" SG CYS a 49 " distance=2.06 Simple disulfide: pdb=" SG CYS z 76 " - pdb=" SG CYS z 79 " distance=2.04 Simple disulfide: pdb=" SG CYS z 76 " - pdb=" SG CYS z 99 " distance=2.05 Simple disulfide: pdb=" SG CYS z 79 " - pdb=" SG CYS z 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 59.79 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 31 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 9 " pdb=" ZN M 101 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 40 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 27 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 24 " pdb="ZN ZN M 101 " - pdb=" SG CYS M 43 " pdb=" ZN e 102 " pdb="ZN ZN e 102 " - pdb=" SG CYS e 27 " pdb="ZN ZN e 102 " - pdb=" SG CYS e 14 " Number of angles added : 6 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12932 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: 184 helices and 72 sheets defined 32.7% alpha, 15.3% beta 1347 base pairs and 2276 stacking pairs defined. Time for finding SS restraints: 78.53 Creating SS restraints... Processing helix chain '6' and resid 14 through 20 removed outlier: 4.965A pdb=" N LEU 6 18 " --> pdb=" O LYS 6 14 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG 6 20 " --> pdb=" O SER 6 16 " (cutoff:3.500A) Processing helix chain '6' and resid 40 through 51 removed outlier: 4.630A pdb=" N GLN 6 50 " --> pdb=" O LYS 6 46 " (cutoff:3.500A) Processing helix chain '7' and resid 22 through 34 removed outlier: 3.944A pdb=" N ASN 7 28 " --> pdb=" O GLY 7 24 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU 7 31 " --> pdb=" O ARG 7 27 " (cutoff:3.500A) Proline residue: 7 32 - end of helix Processing helix chain '7' and resid 40 through 50 removed outlier: 4.122A pdb=" N LEU 7 47 " --> pdb=" O ASN 7 43 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLU 7 48 " --> pdb=" O LEU 7 44 " (cutoff:3.500A) Processing helix chain '7' and resid 52 through 66 removed outlier: 4.357A pdb=" N ARG 7 57 " --> pdb=" O ALA 7 53 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA 7 65 " --> pdb=" O ARG 7 61 " (cutoff:3.500A) Processing helix chain '7' and resid 93 through 105 removed outlier: 4.677A pdb=" N ILE 7 97 " --> pdb=" O THR 7 93 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA 7 98 " --> pdb=" O ALA 7 94 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU 7 99 " --> pdb=" O LYS 7 95 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ALA 7 100 " --> pdb=" O ASP 7 96 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N HIS 7 105 " --> pdb=" O LEU 7 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 16 removed outlier: 3.594A pdb=" N ALA A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N HIS A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 33 removed outlier: 4.470A pdb=" N ALA A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ARG A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 25 through 33' Processing helix chain 'A' and resid 44 through 64 removed outlier: 3.685A pdb=" N ASP A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ARG A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 4.341A pdb=" N ILE A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 87 " --> pdb=" O MET A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 125 removed outlier: 3.930A pdb=" N GLU A 117 " --> pdb=" O HIS A 113 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 132 through 149 removed outlier: 3.832A pdb=" N VAL A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ARG A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 144 " --> pdb=" O HIS A 140 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS A 147 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.618A pdb=" N GLU A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 181 removed outlier: 4.807A pdb=" N GLU A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.938A pdb=" N VAL A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP A 198 " --> pdb=" O PRO A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 193 through 198' Processing helix chain 'A' and resid 207 through 227 removed outlier: 3.650A pdb=" N LEU A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 removed outlier: 5.106A pdb=" N THR B 15 " --> pdb=" O ARG B 11 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARG B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 16' Processing helix chain 'B' and resid 26 through 31 removed outlier: 4.759A pdb=" N ARG B 30 " --> pdb=" O LYS B 26 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N HIS B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 26 through 31' Processing helix chain 'B' and resid 33 through 46 removed outlier: 4.625A pdb=" N GLN B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N ILE B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 removed outlier: 4.304A pdb=" N VAL B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 90 removed outlier: 3.539A pdb=" N LEU B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 5.524A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 removed outlier: 5.878A pdb=" N GLN B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE B 124 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLU B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ARG B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ARG B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 145 removed outlier: 4.272A pdb=" N VAL B 138 " --> pdb=" O ILE B 134 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG B 140 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 16 removed outlier: 4.744A pdb=" N LEU C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N CYS C 12 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG C 13 " --> pdb=" O CYS C 9 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 14 " --> pdb=" O ARG C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 29 removed outlier: 3.575A pdb=" N SER C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 52 through 69 removed outlier: 3.892A pdb=" N ARG C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 86 removed outlier: 4.668A pdb=" N ASN C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU C 78 " --> pdb=" O GLN C 74 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LYS C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 100 removed outlier: 4.548A pdb=" N LEU C 94 " --> pdb=" O GLY C 90 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG C 100 " --> pdb=" O LEU C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 109 removed outlier: 4.122A pdb=" N VAL C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 124 removed outlier: 3.777A pdb=" N GLN C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 155 removed outlier: 4.815A pdb=" N ASN C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 164 removed outlier: 4.521A pdb=" N GLN C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C 163 " --> pdb=" O ARG C 159 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ALA C 164 " --> pdb=" O GLN C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 209 removed outlier: 5.290A pdb=" N VAL C 203 " --> pdb=" O ASN C 199 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE C 204 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU C 205 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N PHE C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 66 removed outlier: 3.785A pdb=" N ALA D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN D 65 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N MET D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 114 removed outlier: 4.566A pdb=" N GLU D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU D 112 " --> pdb=" O ALA D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 142 removed outlier: 3.819A pdb=" N ARG D 140 " --> pdb=" O MET D 136 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN D 141 " --> pdb=" O GLU D 137 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 153 removed outlier: 4.039A pdb=" N VAL D 148 " --> pdb=" O THR D 144 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS D 153 " --> pdb=" O GLU D 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 34 removed outlier: 3.995A pdb=" N ALA E 20 " --> pdb=" O GLN E 16 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ILE E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLN E 27 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.920A pdb=" N ARG E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE E 81 " --> pdb=" O ARG E 77 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG E 82 " --> pdb=" O GLU E 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 32 removed outlier: 3.660A pdb=" N ALA F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG F 32 " --> pdb=" O ASN F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 44 removed outlier: 4.699A pdb=" N ALA F 39 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA F 40 " --> pdb=" O LYS F 36 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ARG F 41 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE F 42 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 51 removed outlier: 4.443A pdb=" N ILE F 50 " --> pdb=" O ALA F 46 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLN F 51 " --> pdb=" O CYS F 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 46 through 51' Processing helix chain 'F' and resid 62 through 68 removed outlier: 3.933A pdb=" N GLU F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN F 68 " --> pdb=" O GLN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 110 removed outlier: 3.640A pdb=" N ALA F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL F 105 " --> pdb=" O LEU F 101 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLN F 106 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA F 107 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASN F 109 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN F 110 " --> pdb=" O GLN F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 130 removed outlier: 5.233A pdb=" N ILE F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ALA F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU F 124 " --> pdb=" O ILE F 120 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N MET F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP F 126 " --> pdb=" O HIS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 145 removed outlier: 4.952A pdb=" N LYS F 136 " --> pdb=" O GLY F 132 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS F 137 " --> pdb=" O GLY F 133 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS F 138 " --> pdb=" O ALA F 134 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU F 139 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU F 142 " --> pdb=" O LYS F 138 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N MET F 144 " --> pdb=" O ASP F 140 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ALA F 145 " --> pdb=" O VAL F 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 20 removed outlier: 3.898A pdb=" N ARG G 18 " --> pdb=" O ARG G 14 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL G 19 " --> pdb=" O ASN G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.932A pdb=" N LEU G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG G 37 " --> pdb=" O GLU G 33 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE G 38 " --> pdb=" O GLU G 34 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU G 39 " --> pdb=" O ILE G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 107 removed outlier: 5.601A pdb=" N GLY G 106 " --> pdb=" O ARG G 102 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU G 107 " --> pdb=" O VAL G 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 102 through 107' Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'H' and resid 32 through 37 removed outlier: 6.451A pdb=" N TYR H 36 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE H 37 " --> pdb=" O PHE H 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 32 through 37' Processing helix chain 'H' and resid 40 through 46 removed outlier: 4.237A pdb=" N VAL H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ALA H 46 " --> pdb=" O ARG H 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 40 through 46' Processing helix chain 'H' and resid 47 through 54 removed outlier: 4.195A pdb=" N VAL H 53 " --> pdb=" O PRO H 49 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP H 54 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 85 removed outlier: 5.428A pdb=" N GLN H 73 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE H 74 " --> pdb=" O LYS H 70 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA H 82 " --> pdb=" O LYS H 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 29 removed outlier: 4.097A pdb=" N SER I 19 " --> pdb=" O THR I 15 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU I 25 " --> pdb=" O GLN I 21 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ARG I 29 " --> pdb=" O GLU I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 87 removed outlier: 4.049A pdb=" N GLU I 83 " --> pdb=" O ARG I 79 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN I 84 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU I 85 " --> pdb=" O THR I 81 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET I 86 " --> pdb=" O ILE I 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 49 removed outlier: 5.335A pdb=" N ILE J 48 " --> pdb=" O SER J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 76 removed outlier: 4.709A pdb=" N ALA J 65 " --> pdb=" O ALA J 61 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ASP J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA J 72 " --> pdb=" O ALA J 68 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA J 74 " --> pdb=" O LYS J 70 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TYR J 75 " --> pdb=" O LYS J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 100 removed outlier: 4.269A pdb=" N ALA J 94 " --> pdb=" O GLY J 90 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU J 98 " --> pdb=" O ALA J 94 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 116 through 121 Processing helix chain 'L' and resid 14 through 22 removed outlier: 3.948A pdb=" N LEU L 19 " --> pdb=" O VAL L 15 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR L 20 " --> pdb=" O ASP L 16 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR L 21 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE L 22 " --> pdb=" O ALA L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 38 removed outlier: 4.471A pdb=" N GLU L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU L 34 " --> pdb=" O ALA L 30 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU L 35 " --> pdb=" O LYS L 31 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS L 36 " --> pdb=" O GLU L 32 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR L 37 " --> pdb=" O ALA L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 49 removed outlier: 5.792A pdb=" N THR L 49 " --> pdb=" O VAL L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 62 removed outlier: 4.161A pdb=" N VAL L 54 " --> pdb=" O GLU L 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU L 56 " --> pdb=" O GLU L 52 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ARG L 57 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLU L 58 " --> pdb=" O VAL L 54 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR L 59 " --> pdb=" O ARG L 55 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU L 61 " --> pdb=" O ARG L 57 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN L 62 " --> pdb=" O GLU L 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 81 removed outlier: 6.720A pdb=" N ARG L 71 " --> pdb=" O GLU L 67 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA L 75 " --> pdb=" O ARG L 71 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS L 79 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 95 removed outlier: 4.113A pdb=" N LEU L 90 " --> pdb=" O CYS L 86 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG L 94 " --> pdb=" O LEU L 90 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY L 95 " --> pdb=" O ARG L 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 12 removed outlier: 3.582A pdb=" N ALA M 10 " --> pdb=" O LEU M 6 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ARG M 12 " --> pdb=" O GLU M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 51 removed outlier: 4.007A pdb=" N ARG M 45 " --> pdb=" O ARG M 41 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N HIS M 49 " --> pdb=" O ARG M 45 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LYS M 50 " --> pdb=" O GLU M 46 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY M 51 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 16 removed outlier: 3.899A pdb=" N LYS N 8 " --> pdb=" O THR N 4 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N VAL N 11 " --> pdb=" O GLU N 7 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N GLN N 13 " --> pdb=" O GLN N 9 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE N 15 " --> pdb=" O VAL N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 47 removed outlier: 3.914A pdb=" N VAL N 29 " --> pdb=" O THR N 25 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA N 30 " --> pdb=" O GLU N 26 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU N 32 " --> pdb=" O GLN N 28 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG N 35 " --> pdb=" O LEU N 31 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU N 41 " --> pdb=" O ASN N 37 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N HIS N 42 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 74 removed outlier: 4.435A pdb=" N ARG N 54 " --> pdb=" O HIS N 50 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY N 55 " --> pdb=" O HIS N 51 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LEU N 56 " --> pdb=" O SER N 52 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU N 66 " --> pdb=" O GLN N 62 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN N 71 " --> pdb=" O LEU N 67 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG N 72 " --> pdb=" O ARG N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 84 removed outlier: 3.997A pdb=" N ILE N 82 " --> pdb=" O TYR N 78 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 63 removed outlier: 3.813A pdb=" N ALA O 56 " --> pdb=" O ASP O 52 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ARG O 57 " --> pdb=" O VAL O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 78 removed outlier: 3.768A pdb=" N LEU O 74 " --> pdb=" O ALA O 70 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA O 77 " --> pdb=" O LEU O 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 99 removed outlier: 4.138A pdb=" N VAL P 85 " --> pdb=" O ARG P 81 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG P 91 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR P 95 " --> pdb=" O ARG P 91 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLU P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N SER P 97 " --> pdb=" O GLN P 93 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU P 98 " --> pdb=" O ASN P 94 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N SER P 99 " --> pdb=" O TYR P 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 26 removed outlier: 5.006A pdb=" N THR Q 25 " --> pdb=" O LYS Q 21 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU Q 26 " --> pdb=" O VAL Q 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 21 through 26' Processing helix chain 'Q' and resid 37 through 44 removed outlier: 4.344A pdb=" N ARG Q 42 " --> pdb=" O GLU Q 38 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE Q 43 " --> pdb=" O VAL Q 39 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU Q 44 " --> pdb=" O LEU Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 57 Processing helix chain 'Q' and resid 59 through 77 removed outlier: 4.560A pdb=" N ARG Q 64 " --> pdb=" O ALA Q 60 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS Q 68 " --> pdb=" O ARG Q 64 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR Q 69 " --> pdb=" O ILE Q 65 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU Q 76 " --> pdb=" O ARG Q 72 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY Q 77 " --> pdb=" O ALA Q 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 26 removed outlier: 4.683A pdb=" N VAL R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU R 20 " --> pdb=" O LEU R 16 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU R 21 " --> pdb=" O GLU R 17 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU R 22 " --> pdb=" O LYS R 18 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN R 23 " --> pdb=" O VAL R 19 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA R 24 " --> pdb=" O LEU R 20 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS R 25 " --> pdb=" O GLU R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 75 removed outlier: 3.999A pdb=" N GLU R 73 " --> pdb=" O LYS R 70 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA R 75 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 47 removed outlier: 3.926A pdb=" N ARG S 17 " --> pdb=" O LEU S 13 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS S 21 " --> pdb=" O ARG S 17 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG S 25 " --> pdb=" O LYS S 21 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA S 28 " --> pdb=" O LEU S 24 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER S 31 " --> pdb=" O LYS S 27 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ALA S 32 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE S 33 " --> pdb=" O LYS S 29 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS S 34 " --> pdb=" O LYS S 30 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU S 43 " --> pdb=" O LYS S 39 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN S 45 " --> pdb=" O ILE S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 70 removed outlier: 4.429A pdb=" N ALA S 52 " --> pdb=" O LYS S 48 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG S 57 " --> pdb=" O LEU S 53 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA S 66 " --> pdb=" O LEU S 62 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS S 68 " --> pdb=" O ASP S 64 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLY S 69 " --> pdb=" O LYS S 65 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER S 70 " --> pdb=" O ALA S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 74 through 96 removed outlier: 3.822A pdb=" N ALA S 78 " --> pdb=" O LYS S 74 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS S 81 " --> pdb=" O ALA S 77 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU S 84 " --> pdb=" O ARG S 80 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG S 89 " --> pdb=" O MET S 85 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN S 90 " --> pdb=" O ARG S 86 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU S 91 " --> pdb=" O LYS S 87 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU S 92 " --> pdb=" O VAL S 88 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU S 93 " --> pdb=" O ARG S 89 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ALA S 94 " --> pdb=" O GLN S 90 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ALA S 95 " --> pdb=" O LEU S 91 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY S 96 " --> pdb=" O LEU S 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 8 through 16 removed outlier: 4.142A pdb=" N LYS T 12 " --> pdb=" O THR T 8 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE T 13 " --> pdb=" O ARG T 9 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG T 15 " --> pdb=" O GLY T 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 37 removed outlier: 4.175A pdb=" N GLU U 30 " --> pdb=" O THR U 26 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG U 31 " --> pdb=" O THR U 27 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR U 35 " --> pdb=" O ARG U 31 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR U 36 " --> pdb=" O ILE U 32 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLY U 37 " --> pdb=" O LEU U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 92 through 102 removed outlier: 4.184A pdb=" N ARG U 96 " --> pdb=" O ILE U 92 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL U 100 " --> pdb=" O ARG U 96 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASP U 102 " --> pdb=" O MET U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 116 through 129 removed outlier: 4.187A pdb=" N THR U 120 " --> pdb=" O PRO U 116 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL U 121 " --> pdb=" O GLN U 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 156 removed outlier: 4.131A pdb=" N VAL U 149 " --> pdb=" O ASP U 145 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLU U 155 " --> pdb=" O ARG U 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 201 through 206 removed outlier: 4.084A pdb=" N TYR U 205 " --> pdb=" O ILE U 201 " (cutoff:3.500A) Processing helix chain 'U' and resid 209 through 225 removed outlier: 4.476A pdb=" N GLU U 214 " --> pdb=" O ARG U 210 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL U 217 " --> pdb=" O HIS U 213 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLU U 218 " --> pdb=" O GLU U 214 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL U 219 " --> pdb=" O LYS U 215 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA U 220 " --> pdb=" O LEU U 216 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP U 222 " --> pdb=" O GLU U 218 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE U 223 " --> pdb=" O VAL U 219 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP U 224 " --> pdb=" O ALA U 220 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N GLU U 225 " --> pdb=" O ALA U 221 " (cutoff:3.500A) Processing helix chain 'U' and resid 226 through 234 removed outlier: 4.046A pdb=" N LYS U 230 " --> pdb=" O ASN U 226 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR U 231 " --> pdb=" O ILE U 227 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU U 232 " --> pdb=" O MET U 228 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLU U 233 " --> pdb=" O LEU U 229 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY U 234 " --> pdb=" O LYS U 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 226 through 234' Processing helix chain 'U' and resid 238 through 253 removed outlier: 3.906A pdb=" N ASP U 252 " --> pdb=" O LYS U 248 " (cutoff:3.500A) Processing helix chain 'U' and resid 268 through 279 removed outlier: 3.946A pdb=" N ASP U 278 " --> pdb=" O ASP U 274 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 436 removed outlier: 4.244A pdb=" N ALA U 429 " --> pdb=" O SER U 425 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG U 430 " --> pdb=" O GLN U 426 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU U 433 " --> pdb=" O ALA U 429 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU U 434 " --> pdb=" O ARG U 430 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASP U 435 " --> pdb=" O LEU U 431 " (cutoff:3.500A) Proline residue: U 436 - end of helix Processing helix chain 'U' and resid 462 through 468 Processing helix chain 'U' and resid 538 through 553 removed outlier: 4.322A pdb=" N VAL U 542 " --> pdb=" O TYR U 538 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN U 543 " --> pdb=" O ILE U 539 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY U 545 " --> pdb=" O ALA U 541 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE U 546 " --> pdb=" O VAL U 542 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA U 549 " --> pdb=" O GLY U 545 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN U 551 " --> pdb=" O GLU U 547 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER U 552 " --> pdb=" O GLU U 548 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLY U 553 " --> pdb=" O ALA U 549 " (cutoff:3.500A) Processing helix chain 'U' and resid 578 through 598 removed outlier: 4.241A pdb=" N MET U 588 " --> pdb=" O ILE U 584 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ALA U 589 " --> pdb=" O ALA U 585 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ILE U 590 " --> pdb=" O GLY U 586 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LYS U 591 " --> pdb=" O SER U 587 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA U 593 " --> pdb=" O ALA U 589 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL U 594 " --> pdb=" O ILE U 590 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLN U 595 " --> pdb=" O LYS U 591 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS U 596 " --> pdb=" O GLU U 592 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY U 597 " --> pdb=" O ALA U 593 " (cutoff:3.500A) Processing helix chain 'U' and resid 616 through 628 removed outlier: 3.677A pdb=" N ILE U 621 " --> pdb=" O MET U 617 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG U 628 " --> pdb=" O LEU U 624 " (cutoff:3.500A) Processing helix chain 'U' and resid 654 through 664 removed outlier: 4.602A pdb=" N ASP U 658 " --> pdb=" O GLY U 654 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG U 660 " --> pdb=" O ALA U 656 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N SER U 661 " --> pdb=" O THR U 657 " (cutoff:3.500A) Processing helix chain 'U' and resid 680 through 687 removed outlier: 3.527A pdb=" N GLU U 685 " --> pdb=" O LYS U 681 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS U 686 " --> pdb=" O GLN U 682 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU U 687 " --> pdb=" O VAL U 683 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 81 removed outlier: 3.589A pdb=" N TYR W 71 " --> pdb=" O ILE W 67 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU W 75 " --> pdb=" O TYR W 71 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG W 76 " --> pdb=" O GLU W 72 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLY W 79 " --> pdb=" O GLU W 75 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LEU W 80 " --> pdb=" O ARG W 76 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYS W 81 " --> pdb=" O ALA W 77 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 94 removed outlier: 4.185A pdb=" N ILE W 90 " --> pdb=" O SER W 86 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LYS W 91 " --> pdb=" O PRO W 87 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS W 92 " --> pdb=" O LYS W 88 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU W 93 " --> pdb=" O GLU W 89 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LEU W 94 " --> pdb=" O ILE W 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 86 through 94' Processing helix chain 'X' and resid 2 through 16 removed outlier: 3.737A pdb=" N VAL X 6 " --> pdb=" O LYS X 2 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG X 7 " --> pdb=" O LEU X 3 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA X 13 " --> pdb=" O GLN X 9 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG X 14 " --> pdb=" O LEU X 10 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LYS X 15 " --> pdb=" O GLU X 11 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU X 16 " --> pdb=" O GLU X 12 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 42 removed outlier: 4.564A pdb=" N LEU X 21 " --> pdb=" O SER X 17 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU X 22 " --> pdb=" O PRO X 18 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS X 23 " --> pdb=" O VAL X 19 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER X 40 " --> pdb=" O ARG X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 47 through 71 removed outlier: 3.965A pdb=" N ARG X 51 " --> pdb=" O ASN X 47 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG X 55 " --> pdb=" O ARG X 51 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR X 62 " --> pdb=" O ALA X 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 removed outlier: 4.486A pdb=" N ALA Y 22 " --> pdb=" O ASP Y 18 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA Y 25 " --> pdb=" O ALA Y 21 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU Y 26 " --> pdb=" O ALA Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.747A pdb=" N LYS Y 49 " --> pdb=" O GLY Y 45 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 22 removed outlier: 4.213A pdb=" N ALA a 18 " --> pdb=" O ALA a 14 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER a 21 " --> pdb=" O ASP a 17 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N HIS a 22 " --> pdb=" O ALA a 18 " (cutoff:3.500A) Processing helix chain 'a' and resid 49 through 54 Processing helix chain 'c' and resid 8 through 16 Processing helix chain 'c' and resid 17 through 25 removed outlier: 4.760A pdb=" N THR c 24 " --> pdb=" O ALA c 20 " (cutoff:3.500A) Proline residue: c 25 - end of helix Processing helix chain 'c' and resid 26 through 38 removed outlier: 4.380A pdb=" N ARG c 35 " --> pdb=" O LEU c 31 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN c 36 " --> pdb=" O LYS c 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 14 Processing helix chain 'd' and resid 37 through 43 Processing helix chain 'd' and resid 51 through 61 removed outlier: 4.909A pdb=" N ALA d 55 " --> pdb=" O ALA d 51 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LYS d 59 " --> pdb=" O ALA d 55 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU d 60 " --> pdb=" O GLU d 56 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU d 61 " --> pdb=" O ARG d 57 " (cutoff:3.500A) Processing helix chain 'f' and resid 5 through 12 removed outlier: 4.090A pdb=" N ARG f 9 " --> pdb=" O GLY f 5 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA f 10 " --> pdb=" O LYS f 6 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU f 11 " --> pdb=" O ARG f 7 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU f 12 " --> pdb=" O TYR f 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 5 through 12' Processing helix chain 'f' and resid 23 through 28 removed outlier: 4.147A pdb=" N ALA f 27 " --> pdb=" O ILE f 23 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 34 removed outlier: 5.156A pdb=" N LEU f 33 " --> pdb=" O LEU f 29 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA f 34 " --> pdb=" O VAL f 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 29 through 34' Processing helix chain 'f' and resid 120 through 125 Processing helix chain 'f' and resid 151 through 160 removed outlier: 5.295A pdb=" N ARG f 155 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU f 156 " --> pdb=" O GLU f 152 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ALA f 159 " --> pdb=" O ARG f 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 182 through 201 removed outlier: 4.394A pdb=" N ASP f 188 " --> pdb=" O GLU f 184 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG f 191 " --> pdb=" O ALA f 187 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA f 192 " --> pdb=" O ASP f 188 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE f 194 " --> pdb=" O ILE f 190 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ARG f 195 " --> pdb=" O ARG f 191 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU f 198 " --> pdb=" O ILE f 194 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYS f 201 " --> pdb=" O LEU f 197 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 17 removed outlier: 5.303A pdb=" N MET g 16 " --> pdb=" O SER g 12 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N THR g 17 " --> pdb=" O ARG g 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 12 through 17' Processing helix chain 'g' and resid 132 through 137 Proline residue: g 137 - end of helix Processing helix chain 'g' and resid 199 through 204 removed outlier: 4.860A pdb=" N ASN g 203 " --> pdb=" O ALA g 199 " (cutoff:3.500A) Processing helix chain 'g' and resid 209 through 216 removed outlier: 3.728A pdb=" N ARG g 213 " --> pdb=" O ALA g 209 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TRP g 214 " --> pdb=" O GLY g 210 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU g 215 " --> pdb=" O ARG g 211 " (cutoff:3.500A) Processing helix chain 'g' and resid 222 through 227 removed outlier: 4.412A pdb=" N MET g 226 " --> pdb=" O ARG g 222 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ASN g 227 " --> pdb=" O GLY g 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 222 through 227' Processing helix chain 'g' and resid 22 through 27 removed outlier: 3.748A pdb=" N THR g 25 " --> pdb=" O SER g 22 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS g 26 " --> pdb=" O GLU g 23 " (cutoff:3.500A) Processing helix chain 'h' and resid 60 through 65 removed outlier: 6.086A pdb=" N LYS h 64 " --> pdb=" O ASN h 60 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLY h 65 " --> pdb=" O ARG h 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 60 through 65' Processing helix chain 'h' and resid 115 through 120 Processing helix chain 'i' and resid 20 through 25 Proline residue: i 25 - end of helix Processing helix chain 'i' and resid 29 through 45 removed outlier: 3.898A pdb=" N LEU i 33 " --> pdb=" O ASN i 29 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL i 36 " --> pdb=" O LEU i 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG i 44 " --> pdb=" O GLN i 40 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG i 45 " --> pdb=" O LEU i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 102 through 121 removed outlier: 4.056A pdb=" N MET i 112 " --> pdb=" O LYS i 108 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL i 114 " --> pdb=" O LEU i 110 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA i 115 " --> pdb=" O ALA i 111 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU i 120 " --> pdb=" O ASP i 116 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY i 121 " --> pdb=" O ARG i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 135 through 147 removed outlier: 4.253A pdb=" N TRP i 142 " --> pdb=" O GLU i 138 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N GLU i 145 " --> pdb=" O ALA i 141 " (cutoff:3.500A) Processing helix chain 'i' and resid 160 through 168 removed outlier: 3.862A pdb=" N ARG i 164 " --> pdb=" O ASN i 160 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG i 165 " --> pdb=" O GLU i 161 " (cutoff:3.500A) Processing helix chain 'i' and resid 182 through 190 removed outlier: 4.251A pdb=" N ILE i 186 " --> pdb=" O ASN i 182 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU i 190 " --> pdb=" O ILE i 186 " (cutoff:3.500A) Processing helix chain 'i' and resid 195 through 207 removed outlier: 4.719A pdb=" N GLY i 207 " --> pdb=" O GLN i 203 " (cutoff:3.500A) Processing helix chain 'j' and resid 7 through 13 Processing helix chain 'j' and resid 15 through 21 removed outlier: 4.347A pdb=" N ILE j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ARG j 21 " --> pdb=" O PRO j 17 " (cutoff:3.500A) Processing helix chain 'j' and resid 54 through 65 removed outlier: 4.446A pdb=" N GLN j 58 " --> pdb=" O GLU j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 96 through 113 removed outlier: 4.210A pdb=" N TRP j 100 " --> pdb=" O ARG j 96 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS j 105 " --> pdb=" O ILE j 101 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN j 108 " --> pdb=" O GLU j 104 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU j 111 " --> pdb=" O LEU j 107 " (cutoff:3.500A) Proline residue: j 112 - end of helix Processing helix chain 'j' and resid 165 through 177 removed outlier: 3.817A pdb=" N LEU j 172 " --> pdb=" O GLU j 168 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU j 174 " --> pdb=" O ARG j 170 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU j 175 " --> pdb=" O ALA j 171 " (cutoff:3.500A) Processing helix chain 'k' and resid 61 through 79 removed outlier: 3.587A pdb=" N HIS k 65 " --> pdb=" O HIS k 61 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY k 66 " --> pdb=" O LYS k 62 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG k 69 " --> pdb=" O HIS k 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE k 72 " --> pdb=" O THR k 68 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA k 75 " --> pdb=" O LEU k 71 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS k 77 " --> pdb=" O ALA k 73 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL k 79 " --> pdb=" O ALA k 75 " (cutoff:3.500A) Processing helix chain 'k' and resid 137 through 153 removed outlier: 3.715A pdb=" N VAL k 144 " --> pdb=" O LYS k 140 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE k 151 " --> pdb=" O ASN k 147 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG k 152 " --> pdb=" O ILE k 148 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS k 153 " --> pdb=" O ARG k 149 " (cutoff:3.500A) Processing helix chain 'k' and resid 3 through 8 removed outlier: 6.373A pdb=" N LEU k 7 " --> pdb=" O ILE k 4 " (cutoff:3.500A) Proline residue: k 8 - end of helix Processing helix chain 'o' and resid 23 through 36 removed outlier: 5.422A pdb=" N ALA o 27 " --> pdb=" O LEU o 23 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS o 29 " --> pdb=" O ARG o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 86 through 94 removed outlier: 4.622A pdb=" N HIS o 94 " --> pdb=" O MET o 90 " (cutoff:3.500A) Processing helix chain 'o' and resid 95 through 107 removed outlier: 4.120A pdb=" N LEU o 99 " --> pdb=" O PRO o 95 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET o 106 " --> pdb=" O ALA o 102 " (cutoff:3.500A) Processing helix chain 'o' and resid 110 through 121 removed outlier: 3.894A pdb=" N LYS o 118 " --> pdb=" O ARG o 114 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG o 119 " --> pdb=" O ARG o 115 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU o 120 " --> pdb=" O LEU o 116 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LYS o 121 " --> pdb=" O PHE o 117 " (cutoff:3.500A) Processing helix chain 'p' and resid 104 through 110 removed outlier: 3.822A pdb=" N GLU p 108 " --> pdb=" O ARG p 104 " (cutoff:3.500A) Processing helix chain 'p' and resid 111 through 119 removed outlier: 4.588A pdb=" N VAL p 115 " --> pdb=" O PHE p 111 " (cutoff:3.500A) Proline residue: p 119 - end of helix Processing helix chain 'q' and resid 37 through 42 removed outlier: 5.287A pdb=" N SER q 42 " --> pdb=" O GLN q 38 " (cutoff:3.500A) Processing helix chain 'q' and resid 57 through 63 removed outlier: 3.525A pdb=" N LEU q 62 " --> pdb=" O THR q 58 " (cutoff:3.500A) Proline residue: q 63 - end of helix Processing helix chain 'q' and resid 84 through 90 removed outlier: 4.066A pdb=" N ALA q 89 " --> pdb=" O LEU q 85 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ARG q 90 " --> pdb=" O LYS q 86 " (cutoff:3.500A) Processing helix chain 'q' and resid 96 through 104 removed outlier: 3.557A pdb=" N LEU q 100 " --> pdb=" O THR q 96 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL q 101 " --> pdb=" O PRO q 97 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG q 102 " --> pdb=" O GLU q 98 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY q 104 " --> pdb=" O LEU q 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 131 through 140 removed outlier: 5.317A pdb=" N GLU q 136 " --> pdb=" O LYS q 132 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA q 140 " --> pdb=" O GLU q 136 " (cutoff:3.500A) Processing helix chain 'r' and resid 43 through 59 removed outlier: 3.613A pdb=" N ALA r 53 " --> pdb=" O ALA r 49 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET r 54 " --> pdb=" O ALA r 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL r 55 " --> pdb=" O ARG r 51 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS r 57 " --> pdb=" O ALA r 53 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG r 59 " --> pdb=" O VAL r 55 " (cutoff:3.500A) Processing helix chain 'r' and resid 111 through 125 removed outlier: 4.078A pdb=" N GLU r 116 " --> pdb=" O GLU r 112 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS r 123 " --> pdb=" O ARG r 119 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS r 124 " --> pdb=" O ILE r 120 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU r 125 " --> pdb=" O ALA r 121 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 32 removed outlier: 3.736A pdb=" N HIS s 31 " --> pdb=" O SER s 27 " (cutoff:3.500A) Processing helix chain 's' and resid 38 through 58 removed outlier: 3.532A pdb=" N GLU s 43 " --> pdb=" O PRO s 39 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLY s 46 " --> pdb=" O LYS s 42 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE s 47 " --> pdb=" O GLU s 43 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS s 50 " --> pdb=" O GLY s 46 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG s 57 " --> pdb=" O HIS s 53 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLY s 58 " --> pdb=" O LEU s 54 " (cutoff:3.500A) Processing helix chain 's' and resid 59 through 70 removed outlier: 6.027A pdb=" N ARG s 63 " --> pdb=" O ASP s 59 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ARG s 64 " --> pdb=" O LEU s 60 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP s 69 " --> pdb=" O LEU s 65 " (cutoff:3.500A) Processing helix chain 's' and resid 72 through 89 removed outlier: 4.050A pdb=" N ALA s 84 " --> pdb=" O PHE s 80 " (cutoff:3.500A) Proline residue: s 85 - end of helix removed outlier: 4.030A pdb=" N ARG s 88 " --> pdb=" O ALA s 84 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ASP s 89 " --> pdb=" O PRO s 85 " (cutoff:3.500A) Processing helix chain 't' and resid 52 through 57 removed outlier: 5.423A pdb=" N LYS t 57 " --> pdb=" O SER t 53 " (cutoff:3.500A) Processing helix chain 't' and resid 63 through 81 removed outlier: 5.208A pdb=" N ARG t 67 " --> pdb=" O THR t 63 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN t 68 " --> pdb=" O GLU t 64 " (cutoff:3.500A) Processing helix chain 't' and resid 15 through 20 removed outlier: 3.840A pdb=" N ILE t 18 " --> pdb=" O ARG t 15 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LYS t 19 " --> pdb=" O ASN t 16 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG t 20 " --> pdb=" O ARG t 17 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 15 through 20' Processing helix chain 'u' and resid 4 through 13 removed outlier: 3.575A pdb=" N VAL u 10 " --> pdb=" O LEU u 6 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU u 11 " --> pdb=" O ILE u 7 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER u 12 " --> pdb=" O LYS u 8 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG u 13 " --> pdb=" O LEU u 9 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 106 removed outlier: 4.030A pdb=" N LEU u 105 " --> pdb=" O PHE u 101 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER u 106 " --> pdb=" O ILE u 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 101 through 106' Processing helix chain 'u' and resid 109 through 115 removed outlier: 3.907A pdb=" N LYS u 113 " --> pdb=" O GLU u 109 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG u 115 " --> pdb=" O ARG u 111 " (cutoff:3.500A) Processing helix chain 'u' and resid 117 through 128 removed outlier: 5.170A pdb=" N ILE u 121 " --> pdb=" O ASP u 117 " (cutoff:3.500A) Processing helix chain 'v' and resid 7 through 22 removed outlier: 4.590A pdb=" N ARG v 11 " --> pdb=" O GLY v 7 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS v 22 " --> pdb=" O LEU v 18 " (cutoff:3.500A) Processing helix chain 'v' and resid 26 through 31 removed outlier: 3.713A pdb=" N LYS v 30 " --> pdb=" O GLY v 26 " (cutoff:3.500A) Processing helix chain 'v' and resid 32 through 37 removed outlier: 3.733A pdb=" N ARG v 36 " --> pdb=" O PHE v 32 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU v 37 " --> pdb=" O ARG v 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 32 through 37' Processing helix chain 'v' and resid 39 through 71 removed outlier: 3.669A pdb=" N ARG v 50 " --> pdb=" O ALA v 46 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS v 54 " --> pdb=" O ARG v 50 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG v 55 " --> pdb=" O LYS v 51 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL v 63 " --> pdb=" O ARG v 59 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG v 70 " --> pdb=" O ASN v 66 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLN v 71 " --> pdb=" O ALA v 67 " (cutoff:3.500A) Processing helix chain 'v' and resid 75 through 86 removed outlier: 3.688A pdb=" N HIS v 81 " --> pdb=" O SER v 77 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY v 82 " --> pdb=" O THR v 78 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU v 83 " --> pdb=" O PHE v 79 " (cutoff:3.500A) Processing helix chain 'v' and resid 95 through 101 removed outlier: 4.205A pdb=" N ALA v 99 " --> pdb=" O LEU v 95 " (cutoff:3.500A) Processing helix chain 'v' and resid 102 through 117 removed outlier: 4.196A pdb=" N PHE v 106 " --> pdb=" O GLU v 102 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU v 108 " --> pdb=" O GLN v 104 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA v 115 " --> pdb=" O GLU v 111 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA v 116 " --> pdb=" O ARG v 112 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN v 117 " --> pdb=" O ALA v 113 " (cutoff:3.500A) Processing helix chain 'x' and resid 13 through 25 removed outlier: 3.615A pdb=" N VAL x 17 " --> pdb=" O SER x 13 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU x 19 " --> pdb=" O ARG x 15 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL x 20 " --> pdb=" O LYS x 16 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU x 23 " --> pdb=" O LEU x 19 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE x 24 " --> pdb=" O VAL x 20 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG x 25 " --> pdb=" O VAL x 21 " (cutoff:3.500A) Processing helix chain 'x' and resid 28 through 39 removed outlier: 3.616A pdb=" N TYR x 38 " --> pdb=" O ASN x 34 " (cutoff:3.500A) Processing helix chain 'x' and resid 41 through 61 removed outlier: 4.626A pdb=" N TYR x 45 " --> pdb=" O LYS x 41 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE x 46 " --> pdb=" O ARG x 42 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS x 49 " --> pdb=" O TYR x 45 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL x 50 " --> pdb=" O PHE x 46 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN x 60 " --> pdb=" O ALA x 56 " (cutoff:3.500A) Processing helix chain 'y' and resid 14 through 24 removed outlier: 4.100A pdb=" N ALA y 22 " --> pdb=" O TYR y 18 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLU y 23 " --> pdb=" O ALA y 19 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY y 24 " --> pdb=" O GLY y 20 " (cutoff:3.500A) Processing helix chain 'y' and resid 35 through 46 removed outlier: 3.821A pdb=" N LYS y 40 " --> pdb=" O LYS y 36 " (cutoff:3.500A) Processing helix chain 'z' and resid 68 through 73 removed outlier: 4.253A pdb=" N VAL z 72 " --> pdb=" O HIS z 68 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ARG z 73 " --> pdb=" O ALA z 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 68 through 73' Processing sheet with id= 1, first strand: chain '6' and resid 125 through 128 removed outlier: 6.088A pdb=" N ILE 6 137 " --> pdb=" O PRO 6 101 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG 6 103 " --> pdb=" O ILE 6 137 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '6' and resid 7 through 10 removed outlier: 3.579A pdb=" N VAL 6 86 " --> pdb=" O PRO 6 25 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL 6 27 " --> pdb=" O VAL 6 86 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR 6 29 " --> pdb=" O PHE 6 88 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN 6 65 " --> pdb=" O LEU 6 61 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '6' and resid 3 through 7 removed outlier: 5.653A pdb=" N VAL 6 58 " --> pdb=" O TYR 6 3 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '7' and resid 2 through 6 removed outlier: 5.395A pdb=" N LYS 7 2 " --> pdb=" O ALA 7 39 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N LEU 7 35 " --> pdb=" O LEU 7 6 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '7' and resid 124 through 129 No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'A' and resid 68 through 72 removed outlier: 3.561A pdb=" N TYR A 199 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 52 through 59 removed outlier: 6.569A pdb=" N LEU B 52 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 71 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARG B 54 " --> pdb=" O HIS B 69 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU B 58 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 100 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL B 66 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL B 68 " --> pdb=" O ASN B 102 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 165 through 170 removed outlier: 4.202A pdb=" N GLU B 166 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL B 153 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA B 168 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B 151 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY B 148 " --> pdb=" O PHE B 203 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N PHE B 203 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LYS B 150 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 152 " --> pdb=" O LYS B 199 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASN B 181 " --> pdb=" O LEU B 204 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 143 through 147 Processing sheet with id= 10, first strand: chain 'D' and resid 7 through 11 removed outlier: 6.494A pdb=" N GLY D 35 " --> pdb=" O GLU D 7 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU D 31 " --> pdb=" O ILE D 11 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG D 18 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG D 27 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 12 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 78 through 83 removed outlier: 8.041A pdb=" N HIS D 78 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA D 94 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP D 117 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 28 through 35 removed outlier: 4.082A pdb=" N ALA D 30 " --> pdb=" O GLY D 46 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY D 46 " --> pdb=" O ALA D 30 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 39 through 44 removed outlier: 4.324A pdb=" N LYS E 39 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE E 60 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 22 through 27 removed outlier: 6.709A pdb=" N GLU G 22 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 63 " --> pdb=" O GLU G 22 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 82 through 86 removed outlier: 3.901A pdb=" N ARG G 84 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU G 136 " --> pdb=" O ARG G 84 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE G 134 " --> pdb=" O ILE G 86 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 13 through 20 removed outlier: 6.776A pdb=" N ARG H 20 " --> pdb=" O ASP H 60 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'I' and resid 33 through 38 removed outlier: 6.230A pdb=" N GLN I 33 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP I 73 " --> pdb=" O SER I 35 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU I 71 " --> pdb=" O PRO I 37 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS I 68 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL I 72 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE I 6 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ILE I 74 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE I 4 " --> pdb=" O ILE I 74 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ARG I 5 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG I 9 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N GLY I 93 " --> pdb=" O PHE I 11 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'I' and resid 40 through 48 removed outlier: 5.450A pdb=" N ASN I 69 " --> pdb=" O PRO I 41 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG I 43 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR I 67 " --> pdb=" O ARG I 43 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU I 65 " --> pdb=" O ARG I 45 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE I 63 " --> pdb=" O PHE I 47 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'J' and resid 18 through 23 removed outlier: 3.878A pdb=" N ARG J 18 " --> pdb=" O THR J 33 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 63 through 70 removed outlier: 4.965A pdb=" N TYR K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS K 54 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS K 57 " --> pdb=" O THR K 38 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ARG K 34 " --> pdb=" O THR K 61 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG K 33 " --> pdb=" O ILE K 85 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'O' and resid 3 through 10 removed outlier: 3.583A pdb=" N THR O 22 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS O 16 " --> pdb=" O PHE O 9 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'P' and resid 5 through 10 removed outlier: 3.666A pdb=" N ASP P 55 " --> pdb=" O VAL P 10 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU P 58 " --> pdb=" O LEU P 74 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'P' and resid 17 through 26 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'R' and resid 30 through 34 removed outlier: 4.320A pdb=" N ILE R 31 " --> pdb=" O THR R 48 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL R 51 " --> pdb=" O VAL R 58 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'U' and resid 68 through 73 removed outlier: 3.583A pdb=" N ALA U 68 " --> pdb=" O ASP U 83 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG U 13 " --> pdb=" O ARG U 78 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE U 15 " --> pdb=" O ASN U 80 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE U 17 " --> pdb=" O ILE U 82 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'U' and resid 165 through 168 removed outlier: 4.849A pdb=" N GLY U 176 " --> pdb=" O ILE U 168 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE U 177 " --> pdb=" O TYR U 186 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS U 184 " --> pdb=" O ASP U 179 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'U' and resid 289 through 293 removed outlier: 4.149A pdb=" N ILE U 289 " --> pdb=" O ILE U 301 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY U 291 " --> pdb=" O VAL U 299 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU U 297 " --> pdb=" O THR U 293 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'U' and resid 315 through 319 removed outlier: 4.007A pdb=" N LYS U 315 " --> pdb=" O PHE U 327 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE U 327 " --> pdb=" O PHE U 314 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU U 309 " --> pdb=" O GLY U 391 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU U 392 " --> pdb=" O TYR U 340 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N TYR U 340 " --> pdb=" O GLU U 392 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG U 348 " --> pdb=" O ASN U 343 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'U' and resid 355 through 358 removed outlier: 4.256A pdb=" N LEU U 355 " --> pdb=" O VAL U 366 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'U' and resid 510 through 516 removed outlier: 3.899A pdb=" N LYS U 513 " --> pdb=" O THR U 566 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR U 566 " --> pdb=" O LYS U 513 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU U 515 " --> pdb=" O LYS U 564 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'U' and resid 633 through 636 removed outlier: 3.768A pdb=" N GLY U 633 " --> pdb=" O ARG U 644 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE U 643 " --> pdb=" O VAL U 610 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL U 610 " --> pdb=" O ILE U 643 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL U 608 " --> pdb=" O ALA U 645 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL U 647 " --> pdb=" O MET U 606 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET U 606 " --> pdb=" O VAL U 647 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'U' and resid 325 through 329 Processing sheet with id= 33, first strand: chain 'V' and resid 51 through 54 removed outlier: 5.258A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'V' and resid 65 through 69 Processing sheet with id= 35, first strand: chain 'W' and resid 12 through 19 removed outlier: 3.810A pdb=" N SER W 38 " --> pdb=" O SER W 17 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'W' and resid 46 through 52 removed outlier: 3.945A pdb=" N VAL W 49 " --> pdb=" O PHE W 60 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'Y' and resid 3 through 9 removed outlier: 7.374A pdb=" N LEU Y 53 " --> pdb=" O VAL Y 9 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'b' and resid 11 through 14 removed outlier: 3.881A pdb=" N LEU b 11 " --> pdb=" O GLU b 24 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N CYS b 13 " --> pdb=" O ALA b 22 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'e' and resid 2 through 5 removed outlier: 3.843A pdb=" N LYS e 2 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG e 35 " --> pdb=" O LYS e 2 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL e 23 " --> pdb=" O GLN e 36 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'f' and resid 42 through 47 removed outlier: 4.861A pdb=" N GLU f 43 " --> pdb=" O THR f 216 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N THR f 216 " --> pdb=" O GLU f 43 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR f 214 " --> pdb=" O HIS f 45 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS f 47 " --> pdb=" O SER f 212 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER f 212 " --> pdb=" O LYS f 47 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'f' and resid 60 through 64 Processing sheet with id= 42, first strand: chain 'g' and resid 74 through 78 removed outlier: 5.115A pdb=" N ILE g 75 " --> pdb=" O ALA g 119 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA g 119 " --> pdb=" O ILE g 75 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL g 117 " --> pdb=" O ALA g 77 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'g' and resid 81 through 84 removed outlier: 3.864A pdb=" N TYR g 97 " --> pdb=" O GLU g 101 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU g 101 " --> pdb=" O TYR g 97 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'g' and resid 163 through 166 removed outlier: 6.272A pdb=" N ILE g 174 " --> pdb=" O GLN g 166 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU g 181 " --> pdb=" O LEU g 177 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'h' and resid 2 through 6 removed outlier: 6.217A pdb=" N LYS h 2 " --> pdb=" O GLU h 200 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'h' and resid 10 through 15 removed outlier: 3.793A pdb=" N GLY h 10 " --> pdb=" O VAL h 25 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP h 174 " --> pdb=" O LEU h 183 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'h' and resid 31 through 34 removed outlier: 7.028A pdb=" N GLN h 48 " --> pdb=" O VAL h 34 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL h 47 " --> pdb=" O ILE h 81 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'h' and resid 100 through 103 removed outlier: 4.790A pdb=" N GLU h 100 " --> pdb=" O VAL h 172 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'i' and resid 122 through 125 removed outlier: 4.085A pdb=" N LEU i 192 " --> pdb=" O LYS i 122 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET i 194 " --> pdb=" O LEU i 124 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG i 191 " --> pdb=" O SER i 153 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR i 158 " --> pdb=" O LEU i 176 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'j' and resid 68 through 72 removed outlier: 5.512A pdb=" N THR j 71 " --> pdb=" O GLY j 89 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU j 90 " --> pdb=" O GLN j 41 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU j 94 " --> pdb=" O VAL j 37 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL j 37 " --> pdb=" O LEU j 94 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS j 36 " --> pdb=" O VAL j 160 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE j 157 " --> pdb=" O LEU j 133 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR j 131 " --> pdb=" O VAL j 159 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLY j 129 " --> pdb=" O THR j 161 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'k' and resid 23 through 27 removed outlier: 3.684A pdb=" N VAL k 26 " --> pdb=" O LEU k 33 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'k' and resid 41 through 45 Processing sheet with id= 53, first strand: chain 'k' and resid 84 through 89 removed outlier: 4.415A pdb=" N LYS k 85 " --> pdb=" O VAL k 133 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N THR k 129 " --> pdb=" O ILE k 89 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'k' and resid 102 through 106 Processing sheet with id= 55, first strand: chain 'o' and resid 12 through 17 Processing sheet with id= 56, first strand: chain 'o' and resid 72 through 76 removed outlier: 3.743A pdb=" N ILE o 85 " --> pdb=" O TYR o 72 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG o 74 " --> pdb=" O LYS o 83 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS o 83 " --> pdb=" O ARG o 74 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLY o 81 " --> pdb=" O SER o 76 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'p' and resid 18 through 21 removed outlier: 3.566A pdb=" N THR p 6 " --> pdb=" O CYS p 21 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ASN p 82 " --> pdb=" O TYR p 7 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'p' and resid 39 through 42 Processing sheet with id= 59, first strand: chain 'p' and resid 66 through 71 removed outlier: 6.127A pdb=" N LYS p 67 " --> pdb=" O PHE p 79 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE p 79 " --> pdb=" O LYS p 67 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER p 75 " --> pdb=" O ARG p 71 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'q' and resid 79 through 83 Processing sheet with id= 61, first strand: chain 'r' and resid 63 through 66 Processing sheet with id= 62, first strand: chain 'r' and resid 100 through 103 removed outlier: 4.167A pdb=" N ARG r 101 " --> pdb=" O ALA r 36 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU r 34 " --> pdb=" O MET r 103 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS r 128 " --> pdb=" O LEU r 37 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 's' and resid 33 through 37 removed outlier: 3.529A pdb=" N LEU s 111 " --> pdb=" O LEU s 100 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL s 117 " --> pdb=" O TYR s 94 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N TYR s 94 " --> pdb=" O VAL s 117 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 't' and resid 35 through 41 removed outlier: 3.605A pdb=" N ARG t 25 " --> pdb=" O ILE t 40 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL t 28 " --> pdb=" O ASP t 88 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'u' and resid 51 through 54 removed outlier: 4.377A pdb=" N ARG u 51 " --> pdb=" O THR u 62 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR u 62 " --> pdb=" O ARG u 51 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR u 62 " --> pdb=" O ILE u 50 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL u 49 " --> pdb=" O GLY u 25 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY u 25 " --> pdb=" O VAL u 49 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'u' and resid 60 through 66 Processing sheet with id= 67, first strand: chain 'w' and resid 11 through 14 removed outlier: 5.392A pdb=" N PHE w 2 " --> pdb=" O GLY w 41 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY w 41 " --> pdb=" O PHE w 2 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL w 37 " --> pdb=" O LYS w 6 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'w' and resid 59 through 63 removed outlier: 4.584A pdb=" N TYR w 81 " --> pdb=" O LYS w 76 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'x' and resid 68 through 71 removed outlier: 9.546A pdb=" N ARG x 68 " --> pdb=" O LYS x 110 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR x 100 " --> pdb=" O GLY x 79 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA x 73 " --> pdb=" O ILE x 106 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'x' and resid 81 through 87 Processing sheet with id= 71, first strand: chain 'y' and resid 25 through 29 removed outlier: 4.697A pdb=" N TYR y 26 " --> pdb=" O VAL y 81 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL y 81 " --> pdb=" O TYR y 26 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS y 72 " --> pdb=" O LYS y 63 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LYS y 63 " --> pdb=" O LYS y 72 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY y 61 " --> pdb=" O PRO y 74 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.447A pdb=" N GLU z 29 " --> pdb=" O ILE z 38 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU z 31 " --> pdb=" O ALA z 36 " (cutoff:3.500A) 1352 hydrogen bonds defined for protein. 3990 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3576 hydrogen bonds 5864 hydrogen bond angles 0 basepair planarities 1347 basepair parallelities 2276 stacking parallelities Total time for adding SS restraints: 258.08 Time building geometry restraints manager: 64.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 33787 1.34 - 1.47: 65930 1.47 - 1.59: 62081 1.59 - 1.72: 4930 1.72 - 1.85: 253 Bond restraints: 166981 Sorted by residual: bond pdb=" CA VAL z 98 " pdb=" C VAL z 98 " ideal model delta sigma weight residual 1.523 1.588 -0.065 1.27e-02 6.20e+03 2.61e+01 bond pdb=" C LEU d 62 " pdb=" N PRO d 63 " ideal model delta sigma weight residual 1.336 1.377 -0.041 9.80e-03 1.04e+04 1.76e+01 bond pdb=" C SER 6 166 " pdb=" N PRO 6 167 " ideal model delta sigma weight residual 1.328 1.380 -0.052 1.25e-02 6.40e+03 1.71e+01 bond pdb=" C LYS K 47 " pdb=" N PRO K 48 " ideal model delta sigma weight residual 1.336 1.385 -0.049 1.23e-02 6.61e+03 1.59e+01 bond pdb=" CA VAL z 98 " pdb=" CB VAL z 98 " ideal model delta sigma weight residual 1.540 1.594 -0.054 1.36e-02 5.41e+03 1.56e+01 ... (remaining 166976 not shown) Histogram of bond angle deviations from ideal: 79.96 - 91.82: 4 91.82 - 103.68: 11473 103.68 - 115.53: 127782 115.53 - 127.39: 99088 127.39 - 139.25: 10265 Bond angle restraints: 248612 Sorted by residual: angle pdb=" O3' A 1 373 " pdb=" P A 1 374 " pdb=" OP1 A 1 374 " ideal model delta sigma weight residual 108.00 79.96 28.04 3.00e+00 1.11e-01 8.74e+01 angle pdb=" O3' G 1 231 " pdb=" P G 1 232 " pdb=" OP1 G 1 232 " ideal model delta sigma weight residual 108.00 80.24 27.76 3.00e+00 1.11e-01 8.56e+01 angle pdb=" C ARG h 61 " pdb=" N PRO h 62 " pdb=" CA PRO h 62 " ideal model delta sigma weight residual 119.84 109.29 10.55 1.25e+00 6.40e-01 7.12e+01 angle pdb=" C LYS 6 78 " pdb=" N ARG 6 79 " pdb=" CA ARG 6 79 " ideal model delta sigma weight residual 121.54 136.33 -14.79 1.91e+00 2.74e-01 6.00e+01 angle pdb=" N THR J 57 " pdb=" CA THR J 57 " pdb=" C THR J 57 " ideal model delta sigma weight residual 109.81 125.65 -15.84 2.21e+00 2.05e-01 5.14e+01 ... (remaining 248607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 94890 35.99 - 71.99: 11481 71.99 - 107.98: 1470 107.98 - 143.98: 13 143.98 - 179.97: 34 Dihedral angle restraints: 107888 sinusoidal: 87770 harmonic: 20118 Sorted by residual: dihedral pdb=" CA LYS 6 14 " pdb=" C LYS 6 14 " pdb=" N PRO 6 15 " pdb=" CA PRO 6 15 " ideal model delta harmonic sigma weight residual -180.00 -121.66 -58.34 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA ARG z 97 " pdb=" C ARG z 97 " pdb=" N VAL z 98 " pdb=" CA VAL z 98 " ideal model delta harmonic sigma weight residual -180.00 -121.74 -58.26 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA LYS z 81 " pdb=" C LYS z 81 " pdb=" N PRO z 82 " pdb=" CA PRO z 82 " ideal model delta harmonic sigma weight residual -180.00 -121.84 -58.16 0 5.00e+00 4.00e-02 1.35e+02 ... (remaining 107885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.425: 31388 0.425 - 0.851: 3 0.851 - 1.276: 0 1.276 - 1.701: 0 1.701 - 2.126: 2 Chirality restraints: 31393 Sorted by residual: chirality pdb=" P A 1 374 " pdb=" OP1 A 1 374 " pdb=" OP2 A 1 374 " pdb=" O5' A 1 374 " both_signs ideal model delta sigma weight residual True 2.41 0.28 2.13 2.00e-01 2.50e+01 1.13e+02 chirality pdb=" P G 1 232 " pdb=" OP1 G 1 232 " pdb=" OP2 G 1 232 " pdb=" O5' G 1 232 " both_signs ideal model delta sigma weight residual True 2.41 0.30 2.11 2.00e-01 2.50e+01 1.11e+02 chirality pdb=" C3' G 41799 " pdb=" C4' G 41799 " pdb=" O3' G 41799 " pdb=" C2' G 41799 " both_signs ideal model delta sigma weight residual False -2.74 -2.19 -0.55 2.00e-01 2.50e+01 7.64e+00 ... (remaining 31390 not shown) Planarity restraints: 14372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG g 244 " 0.088 5.00e-02 4.00e+02 1.34e-01 2.88e+01 pdb=" N PRO g 245 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO g 245 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO g 245 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS Z 40 " 0.079 5.00e-02 4.00e+02 1.21e-01 2.35e+01 pdb=" N PRO Z 41 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO Z 41 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO Z 41 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG h 61 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO h 62 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO h 62 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO h 62 " 0.063 5.00e-02 4.00e+02 ... (remaining 14369 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 40 2.02 - 2.74: 18015 2.74 - 3.46: 196080 3.46 - 4.18: 478575 4.18 - 4.90: 656546 Nonbonded interactions: 1349256 Sorted by model distance: nonbonded pdb=" O UNK m 78 " pdb=" N UNK m 83 " model vdw 1.298 2.520 nonbonded pdb=" O UNK n 85 " pdb=" N UNK n 89 " model vdw 1.301 2.520 nonbonded pdb=" O UNK m 100 " pdb=" N UNK m 105 " model vdw 1.302 2.520 nonbonded pdb=" N2 G 41062 " pdb=" N UNK m 132 " model vdw 1.354 3.200 nonbonded pdb="MG MG 43134 " pdb="MG MG 43213 " model vdw 1.365 1.300 ... (remaining 1349251 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 'l' and (resid 4 through 84 or resid 86 through 133)) selection = (chain 'm' and (resid 11 through 91 or resid 93 through 140)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 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: 0.080 Extract box with map and model: 20.370 Check model and map are aligned: 1.710 Set scattering table: 1.080 Process input model: 584.690 Find NCS groups from input model: 3.270 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 618.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 166981 Z= 0.205 Angle : 0.843 28.041 248612 Z= 0.423 Chirality : 0.043 2.126 31393 Planarity : 0.007 0.134 14372 Dihedral : 23.298 179.972 94929 Min Nonbonded Distance : 1.298 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.50 % Favored : 87.23 % Rotamer: Outliers : 0.49 % Allowed : 8.75 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.08 % Twisted Proline : 3.20 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.45 (0.07), residues: 6592 helix: -4.43 (0.06), residues: 1499 sheet: -2.92 (0.14), residues: 943 loop : -3.67 (0.07), residues: 4150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP i 34 HIS 0.014 0.002 HIS F 122 PHE 0.039 0.002 PHE A 163 TYR 0.028 0.002 TYR J 59 ARG 0.023 0.001 ARG G 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2182 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 2155 time to evaluate : 7.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 6 145 GLU cc_start: 0.6561 (pp20) cc_final: 0.6162 (mp0) REVERT: A 144 ARG cc_start: 0.7580 (tmt90) cc_final: 0.7290 (mmt180) REVERT: A 154 LEU cc_start: 0.4355 (OUTLIER) cc_final: 0.3953 (pt) REVERT: A 189 ASP cc_start: 0.6163 (p0) cc_final: 0.5673 (m-30) REVERT: C 85 LYS cc_start: 0.7595 (mmmm) cc_final: 0.7354 (ttmm) REVERT: C 126 ILE cc_start: 0.8564 (mp) cc_final: 0.8054 (tp) REVERT: D 36 ASP cc_start: 0.7849 (p0) cc_final: 0.7630 (p0) REVERT: E 14 LEU cc_start: 0.3055 (mt) cc_final: 0.2742 (mp) REVERT: F 51 GLN cc_start: 0.5317 (tp40) cc_final: 0.4738 (tp40) REVERT: G 1 MET cc_start: 0.5267 (mtm) cc_final: 0.4619 (tpp) REVERT: G 11 THR cc_start: 0.8131 (m) cc_final: 0.7787 (p) REVERT: I 69 ASN cc_start: 0.3051 (p0) cc_final: 0.2334 (p0) REVERT: K 47 LYS cc_start: 0.7373 (mttm) cc_final: 0.6835 (mttm) REVERT: P 89 LEU cc_start: 0.8516 (mt) cc_final: 0.7566 (mt) REVERT: S 9 ASN cc_start: 0.7737 (t0) cc_final: 0.7365 (p0) REVERT: S 17 ARG cc_start: 0.8376 (mtm110) cc_final: 0.8143 (mtp-110) REVERT: S 48 LYS cc_start: 0.8568 (mmtp) cc_final: 0.8018 (tptt) REVERT: U 356 LEU cc_start: 0.8417 (pt) cc_final: 0.8012 (pt) REVERT: U 550 MET cc_start: 0.3384 (mmt) cc_final: 0.2821 (mtt) REVERT: U 580 MET cc_start: 0.3686 (tmm) cc_final: 0.3424 (tmm) REVERT: U 652 MET cc_start: 0.6676 (tpp) cc_final: 0.6172 (mmt) REVERT: U 673 PHE cc_start: 0.5073 (t80) cc_final: 0.3408 (m-10) REVERT: V 24 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8325 (mmmt) REVERT: V 66 VAL cc_start: 0.8326 (t) cc_final: 0.8123 (m) REVERT: W 92 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7886 (pttt) REVERT: X 45 SER cc_start: 0.8680 (p) cc_final: 0.8385 (t) REVERT: X 55 ARG cc_start: 0.7692 (mpt180) cc_final: 0.7413 (mpt-90) REVERT: Y 11 SER cc_start: 0.8935 (t) cc_final: 0.8708 (t) REVERT: Y 26 LEU cc_start: 0.8544 (mm) cc_final: 0.7933 (mp) REVERT: b 7 ILE cc_start: 0.6640 (mp) cc_final: 0.6306 (mt) REVERT: b 39 TYR cc_start: 0.4674 (t80) cc_final: 0.3789 (t80) REVERT: b 51 GLU cc_start: 0.4923 (mp0) cc_final: 0.4489 (pm20) REVERT: c 23 ARG cc_start: 0.8294 (ptp90) cc_final: 0.7912 (ptp90) REVERT: d 21 LYS cc_start: 0.7712 (mttt) cc_final: 0.7220 (mttp) REVERT: f 9 ARG cc_start: 0.5226 (mtt90) cc_final: 0.4707 (ttp-110) REVERT: g 49 ILE cc_start: 0.8901 (mp) cc_final: 0.8209 (mp) REVERT: g 52 ARG cc_start: 0.8637 (ttp-110) cc_final: 0.8380 (ttp80) REVERT: g 135 PHE cc_start: 0.8914 (m-80) cc_final: 0.8210 (m-80) REVERT: g 186 HIS cc_start: 0.8163 (t70) cc_final: 0.7775 (t70) REVERT: h 100 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7358 (mm-30) REVERT: h 154 LYS cc_start: 0.8708 (tptp) cc_final: 0.8495 (tptp) REVERT: h 167 VAL cc_start: 0.8735 (t) cc_final: 0.8481 (p) REVERT: i 78 ILE cc_start: 0.8674 (mp) cc_final: 0.8411 (mp) REVERT: j 102 PHE cc_start: 0.7329 (t80) cc_final: 0.7024 (t80) REVERT: k 51 ARG cc_start: 0.6725 (mmt90) cc_final: 0.6334 (tpp-160) REVERT: k 72 ILE cc_start: 0.8561 (mm) cc_final: 0.8257 (mm) REVERT: o 14 VAL cc_start: 0.8721 (t) cc_final: 0.8509 (p) REVERT: o 119 ARG cc_start: 0.8213 (mtp180) cc_final: 0.8002 (mtm-85) REVERT: o 123 TYR cc_start: 0.8222 (m-80) cc_final: 0.7999 (m-10) REVERT: p 29 ASN cc_start: 0.7855 (p0) cc_final: 0.7237 (p0) REVERT: p 107 ARG cc_start: 0.6984 (ttm110) cc_final: 0.6701 (mtm-85) REVERT: q 101 VAL cc_start: 0.8257 (m) cc_final: 0.7854 (t) REVERT: r 27 VAL cc_start: 0.7115 (t) cc_final: 0.6806 (m) REVERT: s 11 ASN cc_start: 0.8257 (m-40) cc_final: 0.7879 (m110) REVERT: s 74 LYS cc_start: 0.9026 (mmmt) cc_final: 0.8666 (tttp) REVERT: s 91 GLN cc_start: 0.8020 (tp-100) cc_final: 0.7381 (mp10) REVERT: s 115 GLU cc_start: 0.7624 (pt0) cc_final: 0.7413 (pt0) REVERT: t 17 ARG cc_start: 0.7566 (ptp-110) cc_final: 0.7265 (ptp90) REVERT: t 27 SER cc_start: 0.9052 (t) cc_final: 0.8796 (p) REVERT: u 1 MET cc_start: 0.4724 (tmt) cc_final: 0.4384 (tpt) REVERT: u 125 ARG cc_start: 0.8040 (mmp80) cc_final: 0.7689 (mtm-85) REVERT: v 25 TRP cc_start: 0.7813 (t-100) cc_final: 0.7302 (t-100) REVERT: v 94 ASN cc_start: 0.7953 (t0) cc_final: 0.7114 (t0) REVERT: w 6 LYS cc_start: 0.8786 (tmmm) cc_final: 0.8426 (tttt) REVERT: x 100 THR cc_start: 0.8925 (t) cc_final: 0.8652 (p) outliers start: 27 outliers final: 4 residues processed: 2168 average time/residue: 1.5652 time to fit residues: 5518.5654 Evaluate side-chains 1311 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1305 time to evaluate : 6.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain k residue 11 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 950 optimal weight: 5.9990 chunk 853 optimal weight: 7.9990 chunk 473 optimal weight: 0.0870 chunk 291 optimal weight: 9.9990 chunk 575 optimal weight: 4.9990 chunk 455 optimal weight: 10.0000 chunk 882 optimal weight: 10.0000 chunk 341 optimal weight: 6.9990 chunk 536 optimal weight: 4.9990 chunk 656 optimal weight: 0.9980 chunk 1022 optimal weight: 7.9990 overall best weight: 3.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 28 ASN ** 7 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 40 HIS A 95 GLN B 31 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN D 20 GLN ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 ASN F 106 GLN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN K 75 HIS ** M 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 GLN N 51 HIS ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 ASN ** S 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 165 GLN ** U 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 543 GLN U 625 ASN V 12 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 65 ASN ** X 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 46 HIS c 6 GLN d 35 GLN g 58 HIS g 116 GLN ** g 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 HIS h 132 HIS h 143 ASN h 192 ASN i 67 GLN i 169 ASN j 121 ASN ** k 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 82 ASN q 70 GLN q 81 GLN q 84 ASN r 12 GLN r 141 GLN ** s 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 16 ASN t 95 HIS ** w 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 64 HIS x 34 ASN x 40 ASN ** x 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 102 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 166981 Z= 0.284 Angle : 0.711 27.767 248612 Z= 0.352 Chirality : 0.040 1.977 31393 Planarity : 0.007 0.101 14372 Dihedral : 24.337 179.942 81174 Min Nonbonded Distance : 1.025 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.35 % Favored : 87.41 % Rotamer: Outliers : 5.34 % Allowed : 16.89 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.08 % Twisted Proline : 2.91 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.08), residues: 6592 helix: -3.09 (0.09), residues: 1587 sheet: -2.59 (0.15), residues: 955 loop : -3.35 (0.08), residues: 4050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP y 29 HIS 0.009 0.002 HIS N 53 PHE 0.047 0.002 PHE A 55 TYR 0.031 0.002 TYR C 68 ARG 0.022 0.001 ARG f 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1698 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1401 time to evaluate : 9.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 61 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6407 (mt) REVERT: 6 146 ILE cc_start: 0.3645 (OUTLIER) cc_final: 0.2543 (pt) REVERT: A 68 ILE cc_start: 0.7186 (mm) cc_final: 0.6785 (tt) REVERT: A 144 ARG cc_start: 0.7720 (tmt90) cc_final: 0.7367 (mmt180) REVERT: B 29 TYR cc_start: 0.5928 (t80) cc_final: 0.5199 (t80) REVERT: B 157 ILE cc_start: 0.7690 (mt) cc_final: 0.7450 (mm) REVERT: C 98 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7182 (mm-30) REVERT: C 126 ILE cc_start: 0.8660 (mp) cc_final: 0.8064 (tp) REVERT: D 66 MET cc_start: 0.6913 (mmm) cc_final: 0.6124 (tpp) REVERT: E 4 TYR cc_start: 0.6879 (m-80) cc_final: 0.6549 (m-80) REVERT: E 40 VAL cc_start: 0.7930 (OUTLIER) cc_final: 0.7694 (m) REVERT: F 131 LYS cc_start: 0.2081 (pttp) cc_final: 0.1785 (tttm) REVERT: G 37 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7166 (pmm150) REVERT: G 102 ARG cc_start: 0.6665 (mpt180) cc_final: 0.6296 (mtt180) REVERT: G 116 LYS cc_start: 0.5132 (OUTLIER) cc_final: 0.4664 (mtmm) REVERT: K 47 LYS cc_start: 0.7554 (mttm) cc_final: 0.6830 (mttm) REVERT: L 39 ILE cc_start: -0.0155 (OUTLIER) cc_final: -0.0592 (mt) REVERT: L 66 LEU cc_start: 0.3857 (OUTLIER) cc_final: 0.3580 (tm) REVERT: N 33 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8220 (p) REVERT: N 58 MET cc_start: 0.7288 (mpt) cc_final: 0.6581 (mpt) REVERT: N 59 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7335 (mtp) REVERT: O 58 TYR cc_start: 0.8197 (t80) cc_final: 0.7960 (t80) REVERT: P 52 LYS cc_start: 0.8115 (tppt) cc_final: 0.7893 (mmmt) REVERT: P 93 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8386 (pm20) REVERT: S 9 ASN cc_start: 0.7856 (t0) cc_final: 0.7454 (p0) REVERT: S 17 ARG cc_start: 0.8392 (mtm110) cc_final: 0.8162 (mtp-110) REVERT: S 48 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8149 (tptt) REVERT: S 72 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6402 (tp) REVERT: U 155 GLU cc_start: 0.4640 (mt-10) cc_final: 0.4256 (tt0) REVERT: U 387 ASP cc_start: 0.5998 (t0) cc_final: 0.5395 (t70) REVERT: U 454 MET cc_start: 0.5219 (tpt) cc_final: 0.4767 (tpt) REVERT: U 580 MET cc_start: 0.3591 (tmm) cc_final: 0.3371 (tmm) REVERT: U 634 MET cc_start: 0.6195 (mtp) cc_final: 0.5947 (mtp) REVERT: V 35 ASN cc_start: 0.8887 (m110) cc_final: 0.8665 (m-40) REVERT: V 78 TYR cc_start: 0.8692 (m-80) cc_final: 0.8478 (m-80) REVERT: V 81 VAL cc_start: 0.9295 (t) cc_final: 0.9013 (m) REVERT: X 65 ASN cc_start: 0.8290 (t160) cc_final: 0.8078 (t0) REVERT: Y 11 SER cc_start: 0.8994 (t) cc_final: 0.8763 (t) REVERT: a 51 TYR cc_start: 0.5862 (OUTLIER) cc_final: 0.5040 (t80) REVERT: a 55 ARG cc_start: 0.5337 (tpt-90) cc_final: 0.4266 (tpt-90) REVERT: b 18 ARG cc_start: 0.4979 (ptt90) cc_final: 0.4075 (ppt90) REVERT: c 1 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7227 (pmt) REVERT: c 23 ARG cc_start: 0.8364 (ptp90) cc_final: 0.7798 (ptp90) REVERT: d 26 LYS cc_start: 0.8265 (mttt) cc_final: 0.8054 (mmtp) REVERT: d 39 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7534 (tttp) REVERT: e 20 HIS cc_start: 0.7683 (m90) cc_final: 0.7399 (m90) REVERT: f 9 ARG cc_start: 0.5447 (mtt90) cc_final: 0.4925 (ttp-110) REVERT: f 109 MET cc_start: 0.5070 (ttt) cc_final: 0.4821 (ttp) REVERT: g 73 VAL cc_start: 0.8838 (t) cc_final: 0.8628 (p) REVERT: g 186 HIS cc_start: 0.8216 (t70) cc_final: 0.7877 (t70) REVERT: g 214 TRP cc_start: 0.9031 (m-10) cc_final: 0.8540 (m-10) REVERT: h 9 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8672 (p) REVERT: h 19 ARG cc_start: 0.7475 (mtp-110) cc_final: 0.7203 (ptm160) REVERT: h 47 VAL cc_start: 0.9181 (t) cc_final: 0.8946 (p) REVERT: h 100 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7311 (mm-30) REVERT: h 105 THR cc_start: 0.8580 (m) cc_final: 0.8283 (p) REVERT: i 100 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8670 (p) REVERT: i 169 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.7839 (m110) REVERT: i 194 MET cc_start: 0.7003 (ptt) cc_final: 0.6799 (ptm) REVERT: k 44 VAL cc_start: 0.5780 (OUTLIER) cc_final: 0.5169 (t) REVERT: k 51 ARG cc_start: 0.6777 (mmt90) cc_final: 0.6332 (tpp-160) REVERT: o 38 HIS cc_start: 0.8069 (p-80) cc_final: 0.7371 (p-80) REVERT: o 39 ARG cc_start: 0.8511 (ttm110) cc_final: 0.8247 (ttm110) REVERT: o 48 MET cc_start: 0.7717 (ptm) cc_final: 0.7405 (ptm) REVERT: o 74 ARG cc_start: 0.7857 (ttp-110) cc_final: 0.7007 (ttp80) REVERT: o 119 ARG cc_start: 0.8621 (mtp180) cc_final: 0.8345 (mtm-85) REVERT: o 123 TYR cc_start: 0.8449 (m-80) cc_final: 0.7972 (m-10) REVERT: p 107 ARG cc_start: 0.7297 (ttm110) cc_final: 0.6947 (mtm-85) REVERT: q 76 LYS cc_start: 0.8333 (tttm) cc_final: 0.7063 (tmmt) REVERT: q 101 VAL cc_start: 0.8344 (m) cc_final: 0.7908 (t) REVERT: s 11 ASN cc_start: 0.8852 (m-40) cc_final: 0.8596 (m-40) REVERT: s 26 LYS cc_start: 0.9052 (mtmm) cc_final: 0.8516 (mtmm) REVERT: s 74 LYS cc_start: 0.9056 (mmmt) cc_final: 0.8730 (tttm) REVERT: s 91 GLN cc_start: 0.8003 (tp-100) cc_final: 0.7570 (mp10) REVERT: s 115 GLU cc_start: 0.7848 (pt0) cc_final: 0.7519 (pt0) REVERT: u 125 ARG cc_start: 0.8117 (mmp80) cc_final: 0.7830 (mtt180) REVERT: w 60 GLU cc_start: 0.8238 (pm20) cc_final: 0.7195 (pt0) REVERT: w 93 GLU cc_start: 0.7565 (tp30) cc_final: 0.7356 (mm-30) REVERT: y 60 ARG cc_start: 0.7484 (mtp85) cc_final: 0.7031 (mmm160) REVERT: z 38 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6536 (mp) outliers start: 297 outliers final: 142 residues processed: 1583 average time/residue: 1.5048 time to fit residues: 4028.3099 Evaluate side-chains 1384 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1223 time to evaluate : 6.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 41 LEU Chi-restraints excluded: chain 6 residue 42 VAL Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 61 LEU Chi-restraints excluded: chain 6 residue 67 LEU Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 6 residue 146 ILE Chi-restraints excluded: chain 6 residue 155 LEU Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 109 ILE Chi-restraints excluded: chain 7 residue 114 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 59 MET Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 94 ASN Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain U residue 188 TYR Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 359 HIS Chi-restraints excluded: chain U residue 378 VAL Chi-restraints excluded: chain U residue 668 SER Chi-restraints excluded: chain V residue 12 ASN Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain a residue 19 ARG Chi-restraints excluded: chain a residue 51 TYR Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain d residue 34 TRP Chi-restraints excluded: chain d residue 39 LYS Chi-restraints excluded: chain e residue 26 ILE Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 202 LYS Chi-restraints excluded: chain g residue 204 ILE Chi-restraints excluded: chain g residue 205 VAL Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain g residue 257 LEU Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain i residue 3 GLU Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 114 VAL Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 154 VAL Chi-restraints excluded: chain i residue 155 LEU Chi-restraints excluded: chain i residue 157 VAL Chi-restraints excluded: chain i residue 158 THR Chi-restraints excluded: chain i residue 169 ASN Chi-restraints excluded: chain i residue 175 THR Chi-restraints excluded: chain i residue 181 LEU Chi-restraints excluded: chain i residue 183 VAL Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 149 VAL Chi-restraints excluded: chain k residue 11 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 60 ARG Chi-restraints excluded: chain k residue 64 LEU Chi-restraints excluded: chain k residue 129 THR Chi-restraints excluded: chain k residue 134 SER Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 30 ILE Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 85 ILE Chi-restraints excluded: chain o residue 116 LEU Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 35 VAL Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain p residue 58 VAL Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain q residue 115 LEU Chi-restraints excluded: chain r residue 2 LEU Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 120 ILE Chi-restraints excluded: chain r residue 132 VAL Chi-restraints excluded: chain s residue 38 VAL Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain s residue 73 VAL Chi-restraints excluded: chain s residue 117 VAL Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 36 TYR Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 98 VAL Chi-restraints excluded: chain u residue 9 LEU Chi-restraints excluded: chain u residue 27 THR Chi-restraints excluded: chain u residue 49 VAL Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain u residue 99 LEU Chi-restraints excluded: chain v residue 18 LEU Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 95 LEU Chi-restraints excluded: chain w residue 37 VAL Chi-restraints excluded: chain w residue 45 THR Chi-restraints excluded: chain w residue 51 VAL Chi-restraints excluded: chain x residue 13 SER Chi-restraints excluded: chain x residue 53 SER Chi-restraints excluded: chain x residue 66 GLU Chi-restraints excluded: chain x residue 103 ILE Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain y residue 52 VAL Chi-restraints excluded: chain y residue 80 ILE Chi-restraints excluded: chain z residue 24 VAL Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 38 ILE Chi-restraints excluded: chain z residue 61 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 568 optimal weight: 9.9990 chunk 317 optimal weight: 10.0000 chunk 851 optimal weight: 2.9990 chunk 696 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 1024 optimal weight: 5.9990 chunk 1106 optimal weight: 4.9990 chunk 912 optimal weight: 4.9990 chunk 1015 optimal weight: 0.3980 chunk 349 optimal weight: 8.9990 chunk 821 optimal weight: 0.3980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 HIS B 104 GLN C 43 HIS D 20 GLN F 28 ASN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 ASN ** M 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 HIS ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 ASN S 18 GLN ** S 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 266 ASN U 506 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 38 GLN ** X 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 57 GLN g 201 HIS g 203 ASN ** g 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 192 ASN ** i 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 169 ASN k 143 GLN r 141 GLN ** s 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 166981 Z= 0.233 Angle : 0.652 27.360 248612 Z= 0.325 Chirality : 0.038 1.961 31393 Planarity : 0.006 0.099 14372 Dihedral : 24.288 179.304 81164 Min Nonbonded Distance : 1.134 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.35 % Favored : 87.42 % Rotamer: Outliers : 5.86 % Allowed : 19.48 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.08 % Twisted Proline : 2.62 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.09), residues: 6592 helix: -2.31 (0.11), residues: 1574 sheet: -2.35 (0.15), residues: 977 loop : -3.17 (0.09), residues: 4041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 173 HIS 0.010 0.001 HIS A 19 PHE 0.037 0.002 PHE A 55 TYR 0.035 0.002 TYR j 12 ARG 0.010 0.001 ARG h 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1651 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 1325 time to evaluate : 7.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 98 MET cc_start: 0.7065 (tpp) cc_final: 0.6859 (tpp) REVERT: 6 146 ILE cc_start: 0.4311 (OUTLIER) cc_final: 0.3944 (pt) REVERT: A 68 ILE cc_start: 0.7626 (mm) cc_final: 0.7147 (tt) REVERT: A 105 PHE cc_start: 0.6632 (t80) cc_final: 0.6280 (t80) REVERT: A 144 ARG cc_start: 0.7566 (tmt90) cc_final: 0.7278 (mmt180) REVERT: B 29 TYR cc_start: 0.6218 (t80) cc_final: 0.5572 (t80) REVERT: C 126 ILE cc_start: 0.8461 (mp) cc_final: 0.7987 (tp) REVERT: C 187 ARG cc_start: 0.7512 (ppt170) cc_final: 0.7298 (ppt170) REVERT: C 204 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8162 (pt) REVERT: D 61 TYR cc_start: 0.8619 (m-10) cc_final: 0.8403 (m-10) REVERT: E 40 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7919 (m) REVERT: F 51 GLN cc_start: 0.6008 (tp40) cc_final: 0.5486 (tp40) REVERT: G 102 ARG cc_start: 0.6639 (mpt180) cc_final: 0.6222 (mtt180) REVERT: G 116 LYS cc_start: 0.5651 (OUTLIER) cc_final: 0.5079 (mtmm) REVERT: I 24 VAL cc_start: 0.3107 (t) cc_final: 0.2801 (t) REVERT: I 50 ILE cc_start: 0.6005 (mt) cc_final: 0.5774 (mt) REVERT: I 69 ASN cc_start: 0.5824 (p0) cc_final: 0.5605 (p0) REVERT: K 20 LYS cc_start: 0.6620 (pmmt) cc_final: 0.6211 (pmmt) REVERT: K 114 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.6178 (ptpp) REVERT: L 39 ILE cc_start: -0.0161 (OUTLIER) cc_final: -0.0599 (mt) REVERT: L 66 LEU cc_start: 0.3658 (OUTLIER) cc_final: 0.3336 (tm) REVERT: N 8 LYS cc_start: 0.6910 (ptmt) cc_final: 0.6021 (ptmt) REVERT: N 12 ILE cc_start: 0.7311 (pt) cc_final: 0.6818 (mt) REVERT: N 32 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8158 (mt) REVERT: N 33 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8253 (p) REVERT: N 59 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7284 (ttp) REVERT: N 62 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6921 (tm130) REVERT: O 19 ILE cc_start: 0.8738 (mm) cc_final: 0.8462 (mm) REVERT: O 36 ILE cc_start: 0.7711 (OUTLIER) cc_final: 0.7183 (pt) REVERT: O 58 TYR cc_start: 0.8165 (t80) cc_final: 0.7889 (t80) REVERT: P 36 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7521 (pp) REVERT: P 61 GLU cc_start: 0.6308 (pt0) cc_final: 0.6091 (pt0) REVERT: S 9 ASN cc_start: 0.7873 (t0) cc_final: 0.7464 (p0) REVERT: S 17 ARG cc_start: 0.8362 (mtm110) cc_final: 0.8069 (mtp-110) REVERT: S 45 GLN cc_start: 0.7625 (tm130) cc_final: 0.7118 (pt0) REVERT: S 72 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6343 (tp) REVERT: U 90 PHE cc_start: 0.6021 (OUTLIER) cc_final: 0.5515 (m-80) REVERT: U 155 GLU cc_start: 0.4216 (mt-10) cc_final: 0.3989 (tt0) REVERT: U 212 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.6630 (t80) REVERT: U 454 MET cc_start: 0.4967 (tpt) cc_final: 0.4640 (tpt) REVERT: U 461 ILE cc_start: 0.5197 (OUTLIER) cc_final: 0.4972 (pt) REVERT: U 580 MET cc_start: 0.3270 (tmm) cc_final: 0.3032 (ttm) REVERT: U 634 MET cc_start: 0.5946 (mtp) cc_final: 0.5581 (mtp) REVERT: V 78 TYR cc_start: 0.8662 (m-80) cc_final: 0.8380 (m-80) REVERT: V 81 VAL cc_start: 0.9312 (t) cc_final: 0.9052 (m) REVERT: W 92 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8444 (pptt) REVERT: W 93 GLU cc_start: 0.7398 (mp0) cc_final: 0.6971 (mp0) REVERT: W 94 LEU cc_start: 0.7116 (mt) cc_final: 0.6878 (mp) REVERT: X 12 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8140 (tm-30) REVERT: X 55 ARG cc_start: 0.8008 (mpt-90) cc_final: 0.7597 (mpt-90) REVERT: Y 4 LEU cc_start: 0.8380 (tm) cc_final: 0.8145 (tm) REVERT: Y 26 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8228 (mp) REVERT: a 51 TYR cc_start: 0.5844 (OUTLIER) cc_final: 0.5255 (t80) REVERT: a 55 ARG cc_start: 0.5332 (tpt-90) cc_final: 0.4237 (tpt-90) REVERT: b 39 TYR cc_start: 0.6115 (t80) cc_final: 0.5755 (t80) REVERT: c 1 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7243 (pmt) REVERT: c 22 MET cc_start: 0.8085 (mmm) cc_final: 0.7880 (mmm) REVERT: c 23 ARG cc_start: 0.8338 (ptp90) cc_final: 0.7871 (ptp90) REVERT: d 39 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7535 (tttp) REVERT: f 9 ARG cc_start: 0.5348 (mtt90) cc_final: 0.4834 (ttp-170) REVERT: f 219 MET cc_start: 0.3493 (mmp) cc_final: 0.2900 (mmm) REVERT: g 88 ARG cc_start: 0.8681 (mtm-85) cc_final: 0.8394 (mtm-85) REVERT: g 151 LYS cc_start: 0.8444 (mtmt) cc_final: 0.8066 (mttt) REVERT: g 186 HIS cc_start: 0.8378 (t70) cc_final: 0.8090 (t70) REVERT: g 214 TRP cc_start: 0.9155 (m-10) cc_final: 0.8616 (m-10) REVERT: g 226 MET cc_start: 0.8177 (mmt) cc_final: 0.7971 (mmt) REVERT: h 11 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.7204 (mtm) REVERT: h 24 THR cc_start: 0.9045 (m) cc_final: 0.8421 (m) REVERT: h 47 VAL cc_start: 0.9187 (t) cc_final: 0.8917 (p) REVERT: h 100 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7472 (mm-30) REVERT: h 105 THR cc_start: 0.8538 (m) cc_final: 0.8313 (p) REVERT: h 197 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8407 (pp) REVERT: i 97 TYR cc_start: 0.8632 (m-80) cc_final: 0.8251 (m-10) REVERT: i 100 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8622 (p) REVERT: i 169 ASN cc_start: 0.8470 (t0) cc_final: 0.8073 (m-40) REVERT: j 99 MET cc_start: 0.5766 (mtp) cc_final: 0.5470 (mmm) REVERT: j 148 MET cc_start: 0.5921 (tmm) cc_final: 0.5398 (tpt) REVERT: j 149 VAL cc_start: 0.5176 (OUTLIER) cc_final: 0.4926 (p) REVERT: j 155 MET cc_start: 0.6637 (tmm) cc_final: 0.6259 (tmm) REVERT: j 178 PHE cc_start: 0.4594 (m-80) cc_final: 0.4189 (m-80) REVERT: k 51 ARG cc_start: 0.6761 (mmt90) cc_final: 0.6186 (tpp-160) REVERT: k 57 ASP cc_start: 0.7898 (t0) cc_final: 0.7643 (t0) REVERT: o 48 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7449 (ptm) REVERT: o 85 ILE cc_start: 0.9014 (pt) cc_final: 0.8802 (pt) REVERT: p 66 LYS cc_start: 0.8736 (mtpt) cc_final: 0.8410 (mttt) REVERT: p 107 ARG cc_start: 0.7406 (ttm110) cc_final: 0.7094 (mtm-85) REVERT: p 120 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7268 (tm-30) REVERT: q 76 LYS cc_start: 0.8324 (tttm) cc_final: 0.7013 (tmmt) REVERT: q 101 VAL cc_start: 0.8206 (m) cc_final: 0.7681 (t) REVERT: s 11 ASN cc_start: 0.8841 (m-40) cc_final: 0.8635 (m-40) REVERT: s 74 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8741 (tttm) REVERT: s 91 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7575 (mp10) REVERT: s 115 GLU cc_start: 0.7992 (pt0) cc_final: 0.7658 (pt0) REVERT: t 88 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7634 (p0) REVERT: t 95 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.6968 (t-170) REVERT: u 125 ARG cc_start: 0.8245 (mmp80) cc_final: 0.7768 (mtt180) REVERT: v 84 LYS cc_start: 0.8056 (mmtm) cc_final: 0.7350 (mttt) REVERT: w 60 GLU cc_start: 0.8389 (pm20) cc_final: 0.7819 (pm20) REVERT: w 95 LEU cc_start: 0.8997 (mp) cc_final: 0.8703 (pp) REVERT: x 110 LYS cc_start: 0.6850 (OUTLIER) cc_final: 0.6571 (tttm) REVERT: y 60 ARG cc_start: 0.7594 (mtp85) cc_final: 0.7227 (mmp80) REVERT: z 38 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6509 (mp) outliers start: 326 outliers final: 181 residues processed: 1515 average time/residue: 1.4261 time to fit residues: 3665.6803 Evaluate side-chains 1437 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1225 time to evaluate : 7.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 3 TYR Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 6 residue 41 LEU Chi-restraints excluded: chain 6 residue 42 VAL Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 61 LEU Chi-restraints excluded: chain 6 residue 67 LEU Chi-restraints excluded: chain 6 residue 94 GLU Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 6 residue 146 ILE Chi-restraints excluded: chain 6 residue 155 LEU Chi-restraints excluded: chain 6 residue 163 LEU Chi-restraints excluded: chain 7 residue 38 LEU Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 109 ILE Chi-restraints excluded: chain 7 residue 114 LEU Chi-restraints excluded: chain 7 residue 136 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain D residue 13 ILE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 122 HIS Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain H residue 28 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 40 SER Chi-restraints excluded: chain N residue 59 MET Chi-restraints excluded: chain N residue 62 GLN Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 60 ILE Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 152 THR Chi-restraints excluded: chain U residue 188 TYR Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 212 TYR Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain U residue 260 LEU Chi-restraints excluded: chain U residue 292 THR Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 359 HIS Chi-restraints excluded: chain U residue 377 VAL Chi-restraints excluded: chain U residue 378 VAL Chi-restraints excluded: chain U residue 389 LEU Chi-restraints excluded: chain U residue 461 ILE Chi-restraints excluded: chain U residue 668 SER Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain Y residue 18 ASP Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain a residue 19 ARG Chi-restraints excluded: chain a residue 51 TYR Chi-restraints excluded: chain b residue 16 CYS Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 34 TRP Chi-restraints excluded: chain d residue 39 LYS Chi-restraints excluded: chain e residue 26 ILE Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 155 LEU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 201 HIS Chi-restraints excluded: chain g residue 202 LYS Chi-restraints excluded: chain g residue 204 ILE Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain g residue 257 LEU Chi-restraints excluded: chain h residue 11 MET Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 128 SER Chi-restraints excluded: chain h residue 171 GLU Chi-restraints excluded: chain h residue 197 ILE Chi-restraints excluded: chain i residue 3 GLU Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 157 VAL Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain i residue 175 THR Chi-restraints excluded: chain i residue 181 LEU Chi-restraints excluded: chain i residue 197 ASP Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 92 VAL Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 149 VAL Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain k residue 11 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 60 ARG Chi-restraints excluded: chain k residue 64 LEU Chi-restraints excluded: chain k residue 129 THR Chi-restraints excluded: chain o residue 5 VAL Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 30 ILE Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 48 MET Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 71 ILE Chi-restraints excluded: chain o residue 76 SER Chi-restraints excluded: chain o residue 88 GLU Chi-restraints excluded: chain o residue 133 GLN Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 29 ASN Chi-restraints excluded: chain p residue 58 VAL Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain q residue 106 LEU Chi-restraints excluded: chain q residue 115 LEU Chi-restraints excluded: chain r residue 75 THR Chi-restraints excluded: chain r residue 120 ILE Chi-restraints excluded: chain r residue 132 VAL Chi-restraints excluded: chain s residue 3 HIS Chi-restraints excluded: chain s residue 38 VAL Chi-restraints excluded: chain s residue 73 VAL Chi-restraints excluded: chain s residue 117 VAL Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain t residue 36 TYR Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 88 ASP Chi-restraints excluded: chain t residue 95 HIS Chi-restraints excluded: chain t residue 98 VAL Chi-restraints excluded: chain u residue 6 LEU Chi-restraints excluded: chain u residue 27 THR Chi-restraints excluded: chain u residue 49 VAL Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain u residue 99 LEU Chi-restraints excluded: chain u residue 107 ASP Chi-restraints excluded: chain u residue 123 GLN Chi-restraints excluded: chain v residue 16 LYS Chi-restraints excluded: chain v residue 18 LEU Chi-restraints excluded: chain v residue 29 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 95 LEU Chi-restraints excluded: chain w residue 22 VAL Chi-restraints excluded: chain w residue 37 VAL Chi-restraints excluded: chain w residue 45 THR Chi-restraints excluded: chain x residue 13 SER Chi-restraints excluded: chain x residue 53 SER Chi-restraints excluded: chain x residue 66 GLU Chi-restraints excluded: chain x residue 76 VAL Chi-restraints excluded: chain x residue 100 THR Chi-restraints excluded: chain x residue 103 ILE Chi-restraints excluded: chain x residue 110 LYS Chi-restraints excluded: chain y residue 7 VAL Chi-restraints excluded: chain y residue 12 VAL Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain y residue 52 VAL Chi-restraints excluded: chain z residue 24 VAL Chi-restraints excluded: chain z residue 35 TYR Chi-restraints excluded: chain z residue 38 ILE Chi-restraints excluded: chain z residue 61 ILE Chi-restraints excluded: chain z residue 75 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 1012 optimal weight: 0.8980 chunk 770 optimal weight: 20.0000 chunk 531 optimal weight: 5.9990 chunk 113 optimal weight: 20.0000 chunk 488 optimal weight: 6.9990 chunk 687 optimal weight: 5.9990 chunk 1028 optimal weight: 0.2980 chunk 1088 optimal weight: 2.9990 chunk 537 optimal weight: 9.9990 chunk 974 optimal weight: 30.0000 chunk 293 optimal weight: 7.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 GLN ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 HIS ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 ASN ** S 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 506 GLN U 664 GLN V 12 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 65 ASN ** Y 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 31 HIS f 57 GLN g 201 HIS g 203 ASN ** g 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 192 ASN ** i 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 79 ASN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 147 ASN o 94 HIS r 141 GLN ** w 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 166981 Z= 0.267 Angle : 0.688 27.424 248612 Z= 0.342 Chirality : 0.040 1.953 31393 Planarity : 0.006 0.100 14372 Dihedral : 24.309 179.924 81164 Min Nonbonded Distance : 1.070 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.38 % Favored : 86.44 % Rotamer: Outliers : 6.79 % Allowed : 20.48 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.08 % Twisted Proline : 2.33 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.09), residues: 6592 helix: -1.93 (0.12), residues: 1576 sheet: -2.21 (0.15), residues: 973 loop : -3.09 (0.09), residues: 4043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 138 HIS 0.056 0.002 HIS g 201 PHE 0.032 0.002 PHE A 163 TYR 0.039 0.002 TYR F 151 ARG 0.015 0.001 ARG G 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1692 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1314 time to evaluate : 7.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 93 ASP cc_start: 0.6816 (OUTLIER) cc_final: 0.6490 (p0) REVERT: 6 99 TYR cc_start: 0.6339 (m-10) cc_final: 0.5889 (m-10) REVERT: A 68 ILE cc_start: 0.7716 (mm) cc_final: 0.7257 (tt) REVERT: A 144 ARG cc_start: 0.7587 (tmt90) cc_final: 0.7294 (mmt180) REVERT: A 215 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6585 (tt) REVERT: B 29 TYR cc_start: 0.6375 (t80) cc_final: 0.5830 (t80) REVERT: B 84 ILE cc_start: 0.4142 (tp) cc_final: 0.3265 (tp) REVERT: C 75 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.7745 (m-80) REVERT: C 187 ARG cc_start: 0.7557 (ppt170) cc_final: 0.7333 (ppt170) REVERT: C 204 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8334 (pt) REVERT: E 41 GLU cc_start: 0.7451 (pm20) cc_final: 0.7116 (pm20) REVERT: F 43 PHE cc_start: 0.4509 (OUTLIER) cc_final: 0.3997 (m-80) REVERT: F 51 GLN cc_start: 0.5963 (tp40) cc_final: 0.5311 (tp40) REVERT: G 102 ARG cc_start: 0.6752 (mpt180) cc_final: 0.6285 (mtt180) REVERT: G 116 LYS cc_start: 0.6041 (OUTLIER) cc_final: 0.5104 (mtpt) REVERT: I 24 VAL cc_start: 0.2966 (t) cc_final: 0.2572 (t) REVERT: J 66 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.7037 (tp) REVERT: K 19 ARG cc_start: 0.7047 (mmp80) cc_final: 0.6640 (tpp80) REVERT: K 20 LYS cc_start: 0.6856 (pmmt) cc_final: 0.6469 (pmmt) REVERT: K 114 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.6190 (ptpp) REVERT: L 21 TYR cc_start: 0.2982 (OUTLIER) cc_final: -0.1014 (m-80) REVERT: L 39 ILE cc_start: -0.0280 (OUTLIER) cc_final: -0.0786 (mp) REVERT: L 66 LEU cc_start: 0.3856 (OUTLIER) cc_final: 0.3565 (tm) REVERT: N 12 ILE cc_start: 0.7237 (pt) cc_final: 0.6847 (mt) REVERT: N 35 ARG cc_start: 0.6801 (ttp80) cc_final: 0.6499 (ttm110) REVERT: N 58 MET cc_start: 0.7164 (mmt) cc_final: 0.6267 (mpp) REVERT: N 59 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7258 (mtp) REVERT: N 62 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7114 (tm130) REVERT: O 19 ILE cc_start: 0.8705 (mm) cc_final: 0.8437 (mm) REVERT: S 9 ASN cc_start: 0.7937 (t0) cc_final: 0.7528 (p0) REVERT: S 17 ARG cc_start: 0.8359 (mtm110) cc_final: 0.8078 (mtp-110) REVERT: S 30 LYS cc_start: 0.8465 (mptt) cc_final: 0.8261 (mptt) REVERT: S 45 GLN cc_start: 0.7529 (tm130) cc_final: 0.6967 (pt0) REVERT: S 72 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6560 (tp) REVERT: U 90 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.5979 (m-80) REVERT: U 177 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6643 (mp) REVERT: U 212 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6645 (t80) REVERT: U 312 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7711 (pt) REVERT: U 387 ASP cc_start: 0.6413 (t0) cc_final: 0.6159 (t0) REVERT: U 634 MET cc_start: 0.5820 (mtp) cc_final: 0.5385 (mtp) REVERT: V 78 TYR cc_start: 0.8705 (m-80) cc_final: 0.8358 (m-80) REVERT: W 50 ARG cc_start: 0.8083 (tpp-160) cc_final: 0.7840 (tpp-160) REVERT: W 92 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8097 (pptt) REVERT: W 93 GLU cc_start: 0.7446 (mp0) cc_final: 0.7179 (mm-30) REVERT: W 94 LEU cc_start: 0.7594 (mt) cc_final: 0.7375 (mp) REVERT: X 12 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8172 (tm-30) REVERT: X 46 GLN cc_start: 0.8849 (mt0) cc_final: 0.8617 (mt0) REVERT: X 55 ARG cc_start: 0.8069 (mpt-90) cc_final: 0.7745 (mpt-90) REVERT: Y 5 LYS cc_start: 0.8442 (ttmm) cc_final: 0.7463 (ttpp) REVERT: Y 26 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8195 (mp) REVERT: a 39 MET cc_start: 0.8055 (mmt) cc_final: 0.7794 (mmp) REVERT: a 51 TYR cc_start: 0.5766 (OUTLIER) cc_final: 0.5308 (t80) REVERT: a 55 ARG cc_start: 0.5641 (tpt-90) cc_final: 0.4770 (tpt-90) REVERT: b 39 TYR cc_start: 0.6288 (t80) cc_final: 0.5673 (t80) REVERT: c 1 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7005 (pmt) REVERT: c 22 MET cc_start: 0.8039 (mmm) cc_final: 0.7618 (tmm) REVERT: c 23 ARG cc_start: 0.8372 (ptp90) cc_final: 0.7816 (ptp90) REVERT: d 39 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7555 (tttp) REVERT: f 9 ARG cc_start: 0.5541 (mtt90) cc_final: 0.5014 (ttp-170) REVERT: f 219 MET cc_start: 0.3469 (mmp) cc_final: 0.2957 (mmm) REVERT: g 31 LYS cc_start: 0.7562 (ptmt) cc_final: 0.6906 (mmtm) REVERT: g 101 GLU cc_start: 0.8692 (tp30) cc_final: 0.8304 (tp30) REVERT: g 115 GLN cc_start: 0.8103 (pm20) cc_final: 0.7883 (pm20) REVERT: g 226 MET cc_start: 0.8034 (mmt) cc_final: 0.7792 (mmt) REVERT: h 47 VAL cc_start: 0.9269 (t) cc_final: 0.9017 (p) REVERT: h 100 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7542 (mm-30) REVERT: h 105 THR cc_start: 0.8711 (m) cc_final: 0.8483 (p) REVERT: h 174 ASP cc_start: 0.8273 (t0) cc_final: 0.8073 (t0) REVERT: h 177 PRO cc_start: 0.8596 (Cg_exo) cc_final: 0.8326 (Cg_endo) REVERT: h 197 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8509 (pp) REVERT: i 97 TYR cc_start: 0.8660 (m-80) cc_final: 0.8297 (m-10) REVERT: i 100 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8725 (p) REVERT: i 112 MET cc_start: 0.7597 (ttm) cc_final: 0.7288 (ttp) REVERT: i 169 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8008 (m-40) REVERT: j 155 MET cc_start: 0.6742 (tmm) cc_final: 0.6225 (tmm) REVERT: j 178 PHE cc_start: 0.4869 (m-80) cc_final: 0.4565 (m-80) REVERT: k 44 VAL cc_start: 0.5820 (OUTLIER) cc_final: 0.5296 (t) REVERT: k 51 ARG cc_start: 0.6790 (mmt90) cc_final: 0.5824 (mmp-170) REVERT: k 137 ASP cc_start: 0.7138 (t70) cc_final: 0.6801 (t0) REVERT: o 38 HIS cc_start: 0.7907 (p-80) cc_final: 0.7440 (p-80) REVERT: o 39 ARG cc_start: 0.8732 (ttm110) cc_final: 0.8142 (ttm110) REVERT: o 48 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7318 (ptp) REVERT: o 109 LYS cc_start: 0.8136 (mmmm) cc_final: 0.7854 (mmmt) REVERT: o 123 TYR cc_start: 0.8551 (m-80) cc_final: 0.8196 (m-80) REVERT: p 6 THR cc_start: 0.8678 (m) cc_final: 0.8428 (m) REVERT: p 66 LYS cc_start: 0.8754 (mtpt) cc_final: 0.8425 (mttt) REVERT: p 107 ARG cc_start: 0.7704 (ttm110) cc_final: 0.6965 (mtt180) REVERT: p 120 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7596 (tm-30) REVERT: q 76 LYS cc_start: 0.8380 (tttm) cc_final: 0.7774 (tppt) REVERT: q 101 VAL cc_start: 0.8344 (m) cc_final: 0.7840 (t) REVERT: s 42 LYS cc_start: 0.8807 (mtpp) cc_final: 0.8564 (mtpm) REVERT: s 91 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7640 (mp10) REVERT: s 115 GLU cc_start: 0.8092 (pt0) cc_final: 0.7786 (pt0) REVERT: t 88 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7438 (p0) REVERT: t 89 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7300 (mtm110) REVERT: u 74 ARG cc_start: 0.8214 (tpt90) cc_final: 0.7716 (ttt-90) REVERT: u 123 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7844 (pm20) REVERT: u 125 ARG cc_start: 0.8306 (mmp80) cc_final: 0.7656 (mtt180) REVERT: v 36 ARG cc_start: 0.9035 (ttp-110) cc_final: 0.8452 (ttp80) REVERT: v 84 LYS cc_start: 0.8191 (mmtm) cc_final: 0.7469 (mttt) REVERT: w 11 GLN cc_start: 0.8178 (pp30) cc_final: 0.7909 (pp30) REVERT: w 60 GLU cc_start: 0.8275 (pm20) cc_final: 0.7988 (pm20) REVERT: x 20 VAL cc_start: 0.8931 (p) cc_final: 0.8627 (t) REVERT: x 110 LYS cc_start: 0.7240 (OUTLIER) cc_final: 0.6556 (tttm) REVERT: y 60 ARG cc_start: 0.7744 (mtp85) cc_final: 0.7516 (mmm-85) REVERT: z 38 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6784 (mp) REVERT: z 84 ARG cc_start: 0.5902 (OUTLIER) cc_final: 0.5610 (mmt180) outliers start: 378 outliers final: 228 residues processed: 1532 average time/residue: 1.4398 time to fit residues: 3738.6216 Evaluate side-chains 1480 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1218 time to evaluate : 7.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 3 TYR Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 6 residue 9 TYR Chi-restraints excluded: chain 6 residue 41 LEU Chi-restraints excluded: chain 6 residue 42 VAL Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 61 LEU Chi-restraints excluded: chain 6 residue 90 VAL Chi-restraints excluded: chain 6 residue 93 ASP Chi-restraints excluded: chain 6 residue 120 ILE Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 6 residue 155 LEU Chi-restraints excluded: chain 6 residue 163 LEU Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 19 VAL Chi-restraints excluded: chain 7 residue 38 LEU Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 109 ILE Chi-restraints excluded: chain 7 residue 114 LEU Chi-restraints excluded: chain 7 residue 123 LEU Chi-restraints excluded: chain 7 residue 136 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain F residue 122 HIS Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 37 ARG Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 128 ARG Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 66 LEU Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 21 TYR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 40 SER Chi-restraints excluded: chain N residue 59 MET Chi-restraints excluded: chain N residue 62 GLN Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 94 ASN Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 81 ILE Chi-restraints excluded: chain U residue 90 PHE Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 177 ILE Chi-restraints excluded: chain U residue 188 TYR Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 212 TYR Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain U residue 260 LEU Chi-restraints excluded: chain U residue 286 ILE Chi-restraints excluded: chain U residue 292 THR Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 312 LEU Chi-restraints excluded: chain U residue 326 THR Chi-restraints excluded: chain U residue 359 HIS Chi-restraints excluded: chain U residue 378 VAL Chi-restraints excluded: chain U residue 383 THR Chi-restraints excluded: chain U residue 389 LEU Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain Y residue 18 ASP Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 19 ARG Chi-restraints excluded: chain a residue 51 TYR Chi-restraints excluded: chain b residue 16 CYS Chi-restraints excluded: chain b residue 20 ASN Chi-restraints excluded: chain c residue 1 MET Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain d residue 34 TRP Chi-restraints excluded: chain d residue 39 LYS Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 26 ILE Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 204 ILE Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain g residue 257 LEU Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 128 SER Chi-restraints excluded: chain h residue 166 THR Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain h residue 197 ILE Chi-restraints excluded: chain i residue 3 GLU Chi-restraints excluded: chain i residue 50 SER Chi-restraints excluded: chain i residue 60 SER Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 154 VAL Chi-restraints excluded: chain i residue 169 ASN Chi-restraints excluded: chain i residue 181 LEU Chi-restraints excluded: chain i residue 183 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 92 VAL Chi-restraints excluded: chain j residue 99 MET Chi-restraints excluded: chain k residue 11 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 60 ARG Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 129 THR Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 30 ILE Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 43 THR Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 48 MET Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 71 ILE Chi-restraints excluded: chain o residue 76 SER Chi-restraints excluded: chain o residue 88 GLU Chi-restraints excluded: chain o residue 116 LEU Chi-restraints excluded: chain o residue 127 ASP Chi-restraints excluded: chain o residue 133 GLN Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 29 ASN Chi-restraints excluded: chain p residue 58 VAL Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 115 VAL Chi-restraints excluded: chain q residue 57 THR Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 67 MET Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain q residue 106 LEU Chi-restraints excluded: chain q residue 115 LEU Chi-restraints excluded: chain r residue 2 LEU Chi-restraints excluded: chain r residue 94 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 120 ILE Chi-restraints excluded: chain r residue 132 VAL Chi-restraints excluded: chain s residue 38 VAL Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain s residue 73 VAL Chi-restraints excluded: chain s residue 117 VAL Chi-restraints excluded: chain t residue 14 VAL Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain t residue 36 TYR Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 88 ASP Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain t residue 98 VAL Chi-restraints excluded: chain u residue 6 LEU Chi-restraints excluded: chain u residue 27 THR Chi-restraints excluded: chain u residue 49 VAL Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain u residue 123 GLN Chi-restraints excluded: chain v residue 16 LYS Chi-restraints excluded: chain v residue 18 LEU Chi-restraints excluded: chain v residue 29 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 104 GLN Chi-restraints excluded: chain w residue 22 VAL Chi-restraints excluded: chain w residue 37 VAL Chi-restraints excluded: chain w residue 45 THR Chi-restraints excluded: chain x residue 6 ILE Chi-restraints excluded: chain x residue 13 SER Chi-restraints excluded: chain x residue 53 SER Chi-restraints excluded: chain x residue 66 GLU Chi-restraints excluded: chain x residue 76 VAL Chi-restraints excluded: chain x residue 78 GLU Chi-restraints excluded: chain x residue 100 THR Chi-restraints excluded: chain x residue 103 ILE Chi-restraints excluded: chain x residue 110 LYS Chi-restraints excluded: chain y residue 7 VAL Chi-restraints excluded: chain y residue 12 VAL Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain y residue 52 VAL Chi-restraints excluded: chain y residue 54 VAL Chi-restraints excluded: chain z residue 24 VAL Chi-restraints excluded: chain z residue 38 ILE Chi-restraints excluded: chain z residue 61 ILE Chi-restraints excluded: chain z residue 75 ILE Chi-restraints excluded: chain z residue 84 ARG Chi-restraints excluded: chain z residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 906 optimal weight: 7.9990 chunk 617 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 810 optimal weight: 0.9980 chunk 449 optimal weight: 10.0000 chunk 928 optimal weight: 6.9990 chunk 752 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 555 optimal weight: 10.0000 chunk 976 optimal weight: 20.0000 chunk 274 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 75 ASN ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN D 20 GLN ** E 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 HIS ** M 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 HIS ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 94 ASN ** S 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 45 GLN ** U 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 506 GLN V 12 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 31 HIS f 140 ASN g 203 ASN ** g 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 129 HIS h 143 ASN h 192 ASN i 8 GLN ** i 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 147 ASN ** p 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 68 GLN r 141 GLN s 50 HIS ** w 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.117 166981 Z= 0.341 Angle : 0.761 27.696 248612 Z= 0.376 Chirality : 0.043 1.947 31393 Planarity : 0.007 0.109 14372 Dihedral : 24.424 179.556 81164 Min Nonbonded Distance : 1.079 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.21 % Favored : 85.54 % Rotamer: Outliers : 7.06 % Allowed : 21.97 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.08 % Twisted Proline : 2.62 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.91 (0.09), residues: 6592 helix: -1.91 (0.12), residues: 1599 sheet: -2.29 (0.15), residues: 989 loop : -3.12 (0.09), residues: 4004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP i 39 HIS 0.009 0.002 HIS i 31 PHE 0.030 0.002 PHE A 105 TYR 0.055 0.002 TYR F 151 ARG 0.013 0.001 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1656 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 393 poor density : 1263 time to evaluate : 7.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 93 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6676 (p0) REVERT: A 68 ILE cc_start: 0.7802 (mm) cc_final: 0.7347 (tt) REVERT: A 97 TRP cc_start: 0.7513 (t-100) cc_final: 0.6853 (t-100) REVERT: A 144 ARG cc_start: 0.7657 (tmt90) cc_final: 0.7397 (mmt180) REVERT: A 215 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6565 (tt) REVERT: B 3 ASN cc_start: 0.4208 (OUTLIER) cc_final: 0.3276 (p0) REVERT: B 29 TYR cc_start: 0.6367 (t80) cc_final: 0.6034 (t80) REVERT: C 75 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: C 126 ILE cc_start: 0.8523 (mp) cc_final: 0.8017 (tp) REVERT: C 204 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8513 (pt) REVERT: D 68 GLU cc_start: 0.8354 (mp0) cc_final: 0.7997 (mp0) REVERT: E 41 GLU cc_start: 0.7350 (pm20) cc_final: 0.7137 (pm20) REVERT: F 43 PHE cc_start: 0.4440 (OUTLIER) cc_final: 0.4033 (m-80) REVERT: F 51 GLN cc_start: 0.5658 (tp40) cc_final: 0.4892 (tp40) REVERT: F 69 VAL cc_start: 0.3313 (OUTLIER) cc_final: 0.3042 (m) REVERT: G 102 ARG cc_start: 0.6963 (mpt180) cc_final: 0.6234 (mtt180) REVERT: H 128 ARG cc_start: 0.0544 (OUTLIER) cc_final: 0.0105 (pmt100) REVERT: I 24 VAL cc_start: 0.3192 (t) cc_final: 0.2797 (t) REVERT: K 19 ARG cc_start: 0.7210 (mmp80) cc_final: 0.6771 (tpp80) REVERT: K 20 LYS cc_start: 0.6949 (OUTLIER) cc_final: 0.6607 (pmmt) REVERT: L 21 TYR cc_start: 0.3146 (OUTLIER) cc_final: -0.0120 (m-80) REVERT: L 59 TYR cc_start: 0.5737 (t80) cc_final: 0.4469 (t80) REVERT: N 59 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7305 (ttp) REVERT: O 50 LYS cc_start: 0.7517 (tmtt) cc_final: 0.7142 (mmtm) REVERT: O 58 TYR cc_start: 0.8139 (t80) cc_final: 0.7856 (t80) REVERT: P 38 ARG cc_start: 0.7764 (mtp85) cc_final: 0.7332 (mtt-85) REVERT: Q 51 LEU cc_start: 0.4076 (mp) cc_final: 0.3832 (mt) REVERT: S 9 ASN cc_start: 0.8019 (t0) cc_final: 0.7632 (p0) REVERT: S 72 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6503 (tp) REVERT: U 128 TYR cc_start: 0.5763 (m-10) cc_final: 0.5509 (m-10) REVERT: U 387 ASP cc_start: 0.6469 (t0) cc_final: 0.6240 (t0) REVERT: U 454 MET cc_start: 0.4695 (tpt) cc_final: 0.4281 (tpt) REVERT: U 634 MET cc_start: 0.5624 (OUTLIER) cc_final: 0.5198 (mtp) REVERT: V 46 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8692 (mttt) REVERT: V 78 TYR cc_start: 0.8678 (m-80) cc_final: 0.8299 (m-80) REVERT: W 92 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8137 (pptt) REVERT: W 93 GLU cc_start: 0.7618 (mp0) cc_final: 0.7334 (mm-30) REVERT: X 12 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8154 (tm-30) REVERT: X 46 GLN cc_start: 0.8914 (mt0) cc_final: 0.8703 (mm-40) REVERT: Y 4 LEU cc_start: 0.8462 (tm) cc_final: 0.8255 (tm) REVERT: a 39 MET cc_start: 0.8013 (mmt) cc_final: 0.7746 (mmp) REVERT: a 51 TYR cc_start: 0.5815 (OUTLIER) cc_final: 0.5340 (t80) REVERT: a 55 ARG cc_start: 0.6015 (tpt-90) cc_final: 0.5108 (tpt-90) REVERT: b 39 TYR cc_start: 0.6817 (t80) cc_final: 0.6112 (t80) REVERT: c 22 MET cc_start: 0.8191 (mmm) cc_final: 0.7719 (tmm) REVERT: c 23 ARG cc_start: 0.8484 (ptp90) cc_final: 0.7924 (ptp90) REVERT: d 39 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7631 (tttp) REVERT: d 62 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7941 (mm) REVERT: f 219 MET cc_start: 0.3716 (mmp) cc_final: 0.3280 (mmm) REVERT: g 31 LYS cc_start: 0.8005 (ptmt) cc_final: 0.7289 (mmtm) REVERT: g 115 GLN cc_start: 0.8154 (pm20) cc_final: 0.7664 (pm20) REVERT: g 151 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8521 (mtmt) REVERT: g 176 ARG cc_start: 0.8435 (ttp-170) cc_final: 0.8204 (ttp80) REVERT: g 226 MET cc_start: 0.8207 (mmt) cc_final: 0.7960 (mmt) REVERT: h 47 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.9008 (p) REVERT: h 100 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7529 (mm-30) REVERT: h 164 ARG cc_start: 0.8305 (ttt90) cc_final: 0.7903 (ttt90) REVERT: h 174 ASP cc_start: 0.8267 (t0) cc_final: 0.8029 (t0) REVERT: h 177 PRO cc_start: 0.8665 (Cg_exo) cc_final: 0.8321 (Cg_endo) REVERT: h 182 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8753 (tt) REVERT: i 100 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8788 (p) REVERT: i 112 MET cc_start: 0.7728 (ttm) cc_final: 0.7419 (ttp) REVERT: j 148 MET cc_start: 0.6628 (tmm) cc_final: 0.6066 (tpt) REVERT: j 155 MET cc_start: 0.7099 (tmm) cc_final: 0.6720 (tmm) REVERT: j 178 PHE cc_start: 0.4817 (m-80) cc_final: 0.4483 (m-80) REVERT: k 44 VAL cc_start: 0.5900 (OUTLIER) cc_final: 0.5368 (t) REVERT: k 51 ARG cc_start: 0.6996 (mmt90) cc_final: 0.5933 (mmp-170) REVERT: o 48 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7369 (ptp) REVERT: o 96 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7971 (mm-30) REVERT: o 123 TYR cc_start: 0.8529 (m-80) cc_final: 0.8324 (m-80) REVERT: p 66 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8473 (mttt) REVERT: p 96 THR cc_start: 0.8434 (m) cc_final: 0.8141 (p) REVERT: p 107 ARG cc_start: 0.7734 (ttm110) cc_final: 0.7380 (mtm-85) REVERT: p 120 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7780 (tm-30) REVERT: r 6 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6530 (ttt90) REVERT: r 7 MET cc_start: 0.7663 (mmm) cc_final: 0.7131 (mmm) REVERT: r 9 TYR cc_start: 0.7670 (m-80) cc_final: 0.7408 (m-10) REVERT: r 22 LYS cc_start: 0.8124 (tmtt) cc_final: 0.7817 (tttp) REVERT: r 115 MET cc_start: 0.8615 (mmm) cc_final: 0.8166 (mmm) REVERT: s 115 GLU cc_start: 0.8152 (pt0) cc_final: 0.7811 (pt0) REVERT: t 88 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7294 (p0) REVERT: t 89 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7236 (mtm110) REVERT: u 123 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7904 (pm20) REVERT: v 84 LYS cc_start: 0.8342 (mmtm) cc_final: 0.7690 (mttt) REVERT: x 20 VAL cc_start: 0.8924 (p) cc_final: 0.8651 (t) REVERT: x 110 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6794 (tttm) REVERT: y 87 GLN cc_start: 0.6234 (OUTLIER) cc_final: 0.5824 (mp10) REVERT: z 38 ILE cc_start: 0.7104 (OUTLIER) cc_final: 0.6739 (mp) REVERT: z 55 TYR cc_start: 0.5029 (OUTLIER) cc_final: 0.3723 (p90) REVERT: z 84 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5827 (mmt180) outliers start: 393 outliers final: 260 residues processed: 1512 average time/residue: 1.3995 time to fit residues: 3613.7954 Evaluate side-chains 1457 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1166 time to evaluate : 7.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 3 TYR Chi-restraints excluded: chain 6 residue 5 LEU Chi-restraints excluded: chain 6 residue 41 LEU Chi-restraints excluded: chain 6 residue 42 VAL Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 61 LEU Chi-restraints excluded: chain 6 residue 93 ASP Chi-restraints excluded: chain 6 residue 120 ILE Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 6 residue 163 LEU Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 19 VAL Chi-restraints excluded: chain 7 residue 38 LEU Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 109 ILE Chi-restraints excluded: chain 7 residue 114 LEU Chi-restraints excluded: chain 7 residue 123 LEU Chi-restraints excluded: chain 7 residue 136 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 97 PHE Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 128 ARG Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 21 TYR Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 40 SER Chi-restraints excluded: chain N residue 59 MET Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain P residue 11 VAL Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain S residue 85 MET Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 81 ILE Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 188 TYR Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 212 TYR Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain U residue 260 LEU Chi-restraints excluded: chain U residue 292 THR Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 326 THR Chi-restraints excluded: chain U residue 348 ARG Chi-restraints excluded: chain U residue 359 HIS Chi-restraints excluded: chain U residue 377 VAL Chi-restraints excluded: chain U residue 378 VAL Chi-restraints excluded: chain U residue 389 LEU Chi-restraints excluded: chain U residue 517 LEU Chi-restraints excluded: chain U residue 612 THR Chi-restraints excluded: chain U residue 634 MET Chi-restraints excluded: chain U residue 668 SER Chi-restraints excluded: chain V residue 12 ASN Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 64 ASP Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Y residue 18 ASP Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 19 ARG Chi-restraints excluded: chain a residue 51 TYR Chi-restraints excluded: chain b residue 7 ILE Chi-restraints excluded: chain b residue 16 CYS Chi-restraints excluded: chain b residue 20 ASN Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain d residue 34 TRP Chi-restraints excluded: chain d residue 39 LYS Chi-restraints excluded: chain d residue 61 LEU Chi-restraints excluded: chain d residue 62 LEU Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 223 VAL Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 201 HIS Chi-restraints excluded: chain g residue 204 ILE Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain g residue 257 LEU Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 128 SER Chi-restraints excluded: chain h residue 166 THR Chi-restraints excluded: chain h residue 171 GLU Chi-restraints excluded: chain h residue 182 LEU Chi-restraints excluded: chain i residue 3 GLU Chi-restraints excluded: chain i residue 50 SER Chi-restraints excluded: chain i residue 60 SER Chi-restraints excluded: chain i residue 82 ILE Chi-restraints excluded: chain i residue 89 VAL Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 154 VAL Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain i residue 181 LEU Chi-restraints excluded: chain i residue 183 VAL Chi-restraints excluded: chain j residue 14 GLU Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 92 VAL Chi-restraints excluded: chain j residue 99 MET Chi-restraints excluded: chain j residue 109 VAL Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain j residue 149 VAL Chi-restraints excluded: chain k residue 7 LEU Chi-restraints excluded: chain k residue 11 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 60 ARG Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 129 THR Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 30 ILE Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 43 THR Chi-restraints excluded: chain o residue 48 MET Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 71 ILE Chi-restraints excluded: chain o residue 88 GLU Chi-restraints excluded: chain o residue 116 LEU Chi-restraints excluded: chain o residue 127 ASP Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 29 ASN Chi-restraints excluded: chain p residue 58 VAL Chi-restraints excluded: chain q residue 60 MET Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 67 MET Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain q residue 115 LEU Chi-restraints excluded: chain r residue 6 ARG Chi-restraints excluded: chain r residue 58 PHE Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain r residue 75 THR Chi-restraints excluded: chain r residue 94 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 120 ILE Chi-restraints excluded: chain r residue 132 VAL Chi-restraints excluded: chain s residue 3 HIS Chi-restraints excluded: chain s residue 38 VAL Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 73 VAL Chi-restraints excluded: chain s residue 117 VAL Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 54 LEU Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 80 LEU Chi-restraints excluded: chain t residue 88 ASP Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain u residue 6 LEU Chi-restraints excluded: chain u residue 27 THR Chi-restraints excluded: chain u residue 43 GLN Chi-restraints excluded: chain u residue 44 ASP Chi-restraints excluded: chain u residue 49 VAL Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain u residue 107 ASP Chi-restraints excluded: chain u residue 123 GLN Chi-restraints excluded: chain v residue 16 LYS Chi-restraints excluded: chain v residue 18 LEU Chi-restraints excluded: chain v residue 29 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain w residue 22 VAL Chi-restraints excluded: chain w residue 37 VAL Chi-restraints excluded: chain w residue 45 THR Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain x residue 6 ILE Chi-restraints excluded: chain x residue 13 SER Chi-restraints excluded: chain x residue 53 SER Chi-restraints excluded: chain x residue 66 GLU Chi-restraints excluded: chain x residue 76 VAL Chi-restraints excluded: chain x residue 78 GLU Chi-restraints excluded: chain x residue 100 THR Chi-restraints excluded: chain x residue 103 ILE Chi-restraints excluded: chain x residue 110 LYS Chi-restraints excluded: chain y residue 7 VAL Chi-restraints excluded: chain y residue 12 VAL Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain y residue 52 VAL Chi-restraints excluded: chain y residue 54 VAL Chi-restraints excluded: chain y residue 87 GLN Chi-restraints excluded: chain z residue 24 VAL Chi-restraints excluded: chain z residue 38 ILE Chi-restraints excluded: chain z residue 55 TYR Chi-restraints excluded: chain z residue 75 ILE Chi-restraints excluded: chain z residue 84 ARG Chi-restraints excluded: chain z residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 366 optimal weight: 5.9990 chunk 980 optimal weight: 30.0000 chunk 215 optimal weight: 6.9990 chunk 639 optimal weight: 10.0000 chunk 268 optimal weight: 20.0000 chunk 1089 optimal weight: 5.9990 chunk 904 optimal weight: 1.9990 chunk 504 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 360 optimal weight: 4.9990 chunk 571 optimal weight: 0.0870 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 55 HIS ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN G 81 HIS ** M 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 HIS N 62 GLN O 16 HIS ** S 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 266 ASN U 506 GLN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 GLN ** X 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 GLN ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 48 GLN ** i 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 141 GLN s 13 HIS ** w 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.152 166981 Z= 0.302 Angle : 0.722 27.590 248612 Z= 0.358 Chirality : 0.041 1.952 31393 Planarity : 0.006 0.111 14372 Dihedral : 24.432 179.731 81164 Min Nonbonded Distance : 1.087 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.02 % Favored : 85.80 % Rotamer: Outliers : 7.28 % Allowed : 22.64 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.08 % Twisted Proline : 2.33 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.09), residues: 6592 helix: -1.74 (0.12), residues: 1592 sheet: -2.26 (0.15), residues: 992 loop : -3.09 (0.09), residues: 4008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP i 39 HIS 0.008 0.001 HIS G 82 PHE 0.028 0.002 PHE A 163 TYR 0.066 0.002 TYR F 151 ARG 0.012 0.001 ARG R 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1630 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 405 poor density : 1225 time to evaluate : 7.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 6 93 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6721 (p0) REVERT: 7 6 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5724 (tt) REVERT: A 68 ILE cc_start: 0.7822 (mm) cc_final: 0.7400 (tt) REVERT: A 97 TRP cc_start: 0.7530 (t-100) cc_final: 0.7067 (t-100) REVERT: A 101 MET cc_start: 0.6192 (mtt) cc_final: 0.5378 (mtt) REVERT: A 215 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6540 (tt) REVERT: B 29 TYR cc_start: 0.6301 (t80) cc_final: 0.6046 (t80) REVERT: C 21 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8085 (pp) REVERT: C 75 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8050 (m-80) REVERT: C 126 ILE cc_start: 0.8586 (mp) cc_final: 0.7960 (tp) REVERT: C 204 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8463 (pt) REVERT: D 68 GLU cc_start: 0.8325 (mp0) cc_final: 0.7943 (mp0) REVERT: F 43 PHE cc_start: 0.4463 (OUTLIER) cc_final: 0.4111 (m-80) REVERT: G 102 ARG cc_start: 0.6999 (mpt180) cc_final: 0.6294 (mtt180) REVERT: G 138 TRP cc_start: 0.7354 (p-90) cc_final: 0.6950 (p-90) REVERT: I 24 VAL cc_start: 0.3287 (t) cc_final: 0.2789 (t) REVERT: K 19 ARG cc_start: 0.7224 (mmp80) cc_final: 0.6813 (tpp80) REVERT: K 20 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6658 (pmmt) REVERT: K 77 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.5717 (mt) REVERT: L 21 TYR cc_start: 0.3236 (OUTLIER) cc_final: -0.0032 (m-80) REVERT: L 39 ILE cc_start: -0.0757 (OUTLIER) cc_final: -0.1318 (mp) REVERT: L 59 TYR cc_start: 0.5834 (t80) cc_final: 0.4547 (t80) REVERT: N 62 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7135 (tm130) REVERT: O 50 LYS cc_start: 0.7551 (tmtt) cc_final: 0.7176 (mmtm) REVERT: P 14 LYS cc_start: 0.7690 (mmmm) cc_final: 0.7185 (tptp) REVERT: S 9 ASN cc_start: 0.7970 (t0) cc_final: 0.7636 (p0) REVERT: S 72 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6447 (tp) REVERT: U 203 GLU cc_start: 0.5926 (mp0) cc_final: 0.5621 (mp0) REVERT: U 385 THR cc_start: 0.8249 (p) cc_final: 0.7982 (p) REVERT: U 634 MET cc_start: 0.5704 (OUTLIER) cc_final: 0.5325 (mtp) REVERT: V 46 LYS cc_start: 0.8975 (mmmm) cc_final: 0.8652 (mttt) REVERT: V 78 TYR cc_start: 0.8659 (m-80) cc_final: 0.8356 (m-80) REVERT: W 92 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8004 (pptt) REVERT: W 93 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: X 12 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8223 (tm-30) REVERT: X 46 GLN cc_start: 0.8902 (mt0) cc_final: 0.8698 (mm-40) REVERT: X 70 GLN cc_start: 0.7190 (tm-30) cc_final: 0.6877 (tm-30) REVERT: Y 44 ARG cc_start: 0.8367 (tpp80) cc_final: 0.7936 (tpp80) REVERT: a 39 MET cc_start: 0.8033 (mmt) cc_final: 0.7774 (mmp) REVERT: a 51 TYR cc_start: 0.5924 (OUTLIER) cc_final: 0.5489 (t80) REVERT: c 22 MET cc_start: 0.8216 (mmm) cc_final: 0.7726 (tmm) REVERT: c 23 ARG cc_start: 0.8493 (ptp90) cc_final: 0.7977 (ptp90) REVERT: d 39 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7641 (tttp) REVERT: g 151 LYS cc_start: 0.8416 (mtmt) cc_final: 0.8192 (mtmt) REVERT: g 203 ASN cc_start: 0.7872 (t160) cc_final: 0.7639 (t0) REVERT: g 226 MET cc_start: 0.8177 (mmt) cc_final: 0.7941 (mmt) REVERT: h 47 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8995 (p) REVERT: h 52 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.6236 (tt) REVERT: h 76 ARG cc_start: 0.7371 (mmt90) cc_final: 0.6885 (mmt180) REVERT: h 100 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7564 (mm-30) REVERT: h 164 ARG cc_start: 0.8268 (ttt90) cc_final: 0.7942 (ttt90) REVERT: h 174 ASP cc_start: 0.8317 (t0) cc_final: 0.8063 (t0) REVERT: h 177 PRO cc_start: 0.8638 (Cg_exo) cc_final: 0.8310 (Cg_endo) REVERT: h 182 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8782 (tt) REVERT: h 192 ASN cc_start: 0.8636 (m-40) cc_final: 0.8292 (m-40) REVERT: i 100 THR cc_start: 0.9031 (OUTLIER) cc_final: 0.8765 (p) REVERT: i 194 MET cc_start: 0.7456 (ptm) cc_final: 0.6645 (ptm) REVERT: j 148 MET cc_start: 0.6891 (tmm) cc_final: 0.6117 (tpt) REVERT: j 178 PHE cc_start: 0.4856 (m-80) cc_final: 0.4509 (m-80) REVERT: k 44 VAL cc_start: 0.5815 (OUTLIER) cc_final: 0.5289 (t) REVERT: k 51 ARG cc_start: 0.7108 (mmt90) cc_final: 0.6026 (mmp-170) REVERT: o 48 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7361 (ptp) REVERT: o 96 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8040 (mm-30) REVERT: o 109 LYS cc_start: 0.8191 (mmmm) cc_final: 0.7931 (mmmt) REVERT: p 96 THR cc_start: 0.8333 (m) cc_final: 0.8011 (p) REVERT: p 97 ARG cc_start: 0.8744 (ttp80) cc_final: 0.8291 (ttp80) REVERT: p 107 ARG cc_start: 0.7933 (ttm110) cc_final: 0.7567 (mtm-85) REVERT: p 120 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: q 21 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8568 (mmt-90) REVERT: r 7 MET cc_start: 0.7397 (mmm) cc_final: 0.6902 (mmm) REVERT: r 22 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7774 (tttp) REVERT: r 103 MET cc_start: 0.8797 (mtm) cc_final: 0.8527 (mtm) REVERT: s 115 GLU cc_start: 0.8198 (pt0) cc_final: 0.7954 (pt0) REVERT: t 88 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7328 (p0) REVERT: t 89 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7418 (mtm110) REVERT: u 123 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7925 (pm20) REVERT: v 84 LYS cc_start: 0.8348 (mmtm) cc_final: 0.7669 (mttt) REVERT: w 60 GLU cc_start: 0.8425 (pm20) cc_final: 0.7633 (pt0) REVERT: x 20 VAL cc_start: 0.8888 (p) cc_final: 0.8643 (t) REVERT: x 110 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6733 (tttm) REVERT: z 26 LYS cc_start: 0.8397 (tppp) cc_final: 0.8191 (mtpt) REVERT: z 38 ILE cc_start: 0.7068 (OUTLIER) cc_final: 0.6655 (mp) REVERT: z 55 TYR cc_start: 0.5153 (OUTLIER) cc_final: 0.3699 (p90) REVERT: z 84 ARG cc_start: 0.6208 (OUTLIER) cc_final: 0.5589 (mmt180) outliers start: 405 outliers final: 288 residues processed: 1479 average time/residue: 1.3997 time to fit residues: 3544.8098 Evaluate side-chains 1490 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1169 time to evaluate : 6.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 3 TYR Chi-restraints excluded: chain 6 residue 41 LEU Chi-restraints excluded: chain 6 residue 42 VAL Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 61 LEU Chi-restraints excluded: chain 6 residue 67 LEU Chi-restraints excluded: chain 6 residue 93 ASP Chi-restraints excluded: chain 6 residue 120 ILE Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 6 residue 163 LEU Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 6 LEU Chi-restraints excluded: chain 7 residue 12 LEU Chi-restraints excluded: chain 7 residue 38 LEU Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 109 ILE Chi-restraints excluded: chain 7 residue 114 LEU Chi-restraints excluded: chain 7 residue 123 LEU Chi-restraints excluded: chain 7 residue 136 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 128 ARG Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 21 TYR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 40 SER Chi-restraints excluded: chain N residue 62 GLN Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 45 GLN Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 81 ILE Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 155 GLU Chi-restraints excluded: chain U residue 160 ARG Chi-restraints excluded: chain U residue 188 TYR Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 212 TYR Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain U residue 260 LEU Chi-restraints excluded: chain U residue 292 THR Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 322 VAL Chi-restraints excluded: chain U residue 331 TYR Chi-restraints excluded: chain U residue 359 HIS Chi-restraints excluded: chain U residue 378 VAL Chi-restraints excluded: chain U residue 389 LEU Chi-restraints excluded: chain U residue 517 LEU Chi-restraints excluded: chain U residue 631 ILE Chi-restraints excluded: chain U residue 634 MET Chi-restraints excluded: chain U residue 668 SER Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 64 ASP Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 LEU Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Y residue 18 ASP Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 19 ARG Chi-restraints excluded: chain a residue 51 TYR Chi-restraints excluded: chain b residue 7 ILE Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 16 CYS Chi-restraints excluded: chain b residue 20 ASN Chi-restraints excluded: chain c residue 9 ARG Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain d residue 34 TRP Chi-restraints excluded: chain d residue 39 LYS Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 12 ASP Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 26 ILE Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 172 ILE Chi-restraints excluded: chain f residue 223 VAL Chi-restraints excluded: chain g residue 10 THR Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 201 HIS Chi-restraints excluded: chain g residue 202 LYS Chi-restraints excluded: chain g residue 204 ILE Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain g residue 257 LEU Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 51 PHE Chi-restraints excluded: chain h residue 52 LEU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 128 SER Chi-restraints excluded: chain h residue 166 THR Chi-restraints excluded: chain h residue 171 GLU Chi-restraints excluded: chain h residue 182 LEU Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain i residue 3 GLU Chi-restraints excluded: chain i residue 50 SER Chi-restraints excluded: chain i residue 60 SER Chi-restraints excluded: chain i residue 89 VAL Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 140 LEU Chi-restraints excluded: chain i residue 154 VAL Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain i residue 181 LEU Chi-restraints excluded: chain j residue 14 GLU Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 92 VAL Chi-restraints excluded: chain j residue 99 MET Chi-restraints excluded: chain j residue 131 TYR Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain j residue 149 VAL Chi-restraints excluded: chain k residue 11 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 60 ARG Chi-restraints excluded: chain k residue 64 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 129 THR Chi-restraints excluded: chain k residue 134 SER Chi-restraints excluded: chain o residue 5 VAL Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 30 ILE Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 43 THR Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 48 MET Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 71 ILE Chi-restraints excluded: chain o residue 88 GLU Chi-restraints excluded: chain o residue 116 LEU Chi-restraints excluded: chain o residue 127 ASP Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 58 VAL Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain p residue 115 VAL Chi-restraints excluded: chain p residue 120 GLU Chi-restraints excluded: chain q residue 21 ARG Chi-restraints excluded: chain q residue 57 THR Chi-restraints excluded: chain q residue 60 MET Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 67 MET Chi-restraints excluded: chain q residue 68 GLN Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 96 THR Chi-restraints excluded: chain q residue 106 LEU Chi-restraints excluded: chain q residue 115 LEU Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain r residue 75 THR Chi-restraints excluded: chain r residue 94 VAL Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 120 ILE Chi-restraints excluded: chain r residue 141 GLN Chi-restraints excluded: chain s residue 3 HIS Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 38 VAL Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 73 VAL Chi-restraints excluded: chain s residue 117 VAL Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 32 LEU Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain t residue 36 TYR Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 88 ASP Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain t residue 103 GLU Chi-restraints excluded: chain u residue 6 LEU Chi-restraints excluded: chain u residue 27 THR Chi-restraints excluded: chain u residue 44 ASP Chi-restraints excluded: chain u residue 49 VAL Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain u residue 107 ASP Chi-restraints excluded: chain u residue 123 GLN Chi-restraints excluded: chain u residue 124 ASP Chi-restraints excluded: chain v residue 16 LYS Chi-restraints excluded: chain v residue 18 LEU Chi-restraints excluded: chain v residue 29 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain v residue 104 GLN Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 22 VAL Chi-restraints excluded: chain w residue 37 VAL Chi-restraints excluded: chain w residue 45 THR Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 88 ARG Chi-restraints excluded: chain x residue 6 ILE Chi-restraints excluded: chain x residue 13 SER Chi-restraints excluded: chain x residue 53 SER Chi-restraints excluded: chain x residue 66 GLU Chi-restraints excluded: chain x residue 76 VAL Chi-restraints excluded: chain x residue 78 GLU Chi-restraints excluded: chain x residue 100 THR Chi-restraints excluded: chain x residue 103 ILE Chi-restraints excluded: chain x residue 110 LYS Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 7 VAL Chi-restraints excluded: chain y residue 9 LEU Chi-restraints excluded: chain y residue 12 VAL Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain y residue 52 VAL Chi-restraints excluded: chain z residue 24 VAL Chi-restraints excluded: chain z residue 38 ILE Chi-restraints excluded: chain z residue 55 TYR Chi-restraints excluded: chain z residue 75 ILE Chi-restraints excluded: chain z residue 84 ARG Chi-restraints excluded: chain z residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 1050 optimal weight: 0.9990 chunk 122 optimal weight: 20.0000 chunk 620 optimal weight: 7.9990 chunk 795 optimal weight: 9.9990 chunk 616 optimal weight: 2.9990 chunk 917 optimal weight: 3.9990 chunk 608 optimal weight: 7.9990 chunk 1085 optimal weight: 7.9990 chunk 679 optimal weight: 0.7980 chunk 661 optimal weight: 8.9990 chunk 501 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN C 201 GLN ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 HIS P 94 ASN ** S 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 266 ASN V 12 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 65 ASN c 36 GLN ** d 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 227 ASN ** g 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 79 ASN ** j 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 143 GLN r 141 GLN ** w 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 166981 Z= 0.273 Angle : 0.706 27.521 248612 Z= 0.350 Chirality : 0.041 1.954 31393 Planarity : 0.006 0.111 14372 Dihedral : 24.435 178.848 81164 Min Nonbonded Distance : 1.097 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 14.17 % Favored : 85.62 % Rotamer: Outliers : 7.24 % Allowed : 23.66 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.08 % Twisted Proline : 2.62 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.09), residues: 6592 helix: -1.62 (0.12), residues: 1582 sheet: -2.22 (0.15), residues: 1009 loop : -3.02 (0.09), residues: 4001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP i 39 HIS 0.008 0.001 HIS G 82 PHE 0.066 0.002 PHE A 55 TYR 0.071 0.002 TYR F 151 ARG 0.010 0.001 ARG v 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1604 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 403 poor density : 1201 time to evaluate : 7.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 93 ASP cc_start: 0.6883 (OUTLIER) cc_final: 0.6597 (p0) REVERT: 7 6 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5680 (tt) REVERT: A 68 ILE cc_start: 0.7816 (mm) cc_final: 0.7438 (tt) REVERT: A 97 TRP cc_start: 0.7513 (t-100) cc_final: 0.6961 (t-100) REVERT: A 101 MET cc_start: 0.6491 (mtt) cc_final: 0.5768 (mtt) REVERT: A 226 ARG cc_start: 0.6161 (ptt-90) cc_final: 0.5776 (ptt-90) REVERT: B 3 ASN cc_start: 0.4142 (OUTLIER) cc_final: 0.3213 (p0) REVERT: C 21 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8120 (pp) REVERT: C 70 ILE cc_start: 0.7314 (mp) cc_final: 0.7032 (mp) REVERT: C 75 PHE cc_start: 0.8425 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: C 116 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.5949 (tp40) REVERT: C 120 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7626 (mm) REVERT: C 126 ILE cc_start: 0.8543 (mp) cc_final: 0.7907 (tp) REVERT: C 204 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8459 (pt) REVERT: D 68 GLU cc_start: 0.8297 (mp0) cc_final: 0.7929 (mp0) REVERT: F 43 PHE cc_start: 0.4466 (OUTLIER) cc_final: 0.4094 (m-80) REVERT: F 69 VAL cc_start: 0.3352 (OUTLIER) cc_final: 0.3143 (m) REVERT: G 102 ARG cc_start: 0.7052 (mpt180) cc_final: 0.6274 (mtt180) REVERT: G 138 TRP cc_start: 0.7387 (p-90) cc_final: 0.7028 (p-90) REVERT: H 128 ARG cc_start: 0.0804 (OUTLIER) cc_final: 0.0595 (pmt100) REVERT: I 24 VAL cc_start: 0.3245 (t) cc_final: 0.2828 (t) REVERT: K 19 ARG cc_start: 0.7263 (mmp80) cc_final: 0.6862 (tpp80) REVERT: K 20 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6643 (pmmt) REVERT: K 111 LYS cc_start: 0.7678 (pptt) cc_final: 0.7454 (pptt) REVERT: K 114 LYS cc_start: 0.6553 (OUTLIER) cc_final: 0.6057 (ptpp) REVERT: L 21 TYR cc_start: 0.3207 (OUTLIER) cc_final: -0.0066 (m-80) REVERT: L 39 ILE cc_start: -0.0814 (OUTLIER) cc_final: -0.1356 (mp) REVERT: L 82 MET cc_start: 0.4541 (ptt) cc_final: 0.4254 (ptt) REVERT: O 50 LYS cc_start: 0.7518 (tmtt) cc_final: 0.7145 (mmtm) REVERT: P 14 LYS cc_start: 0.7693 (mmmm) cc_final: 0.7210 (tptp) REVERT: S 9 ASN cc_start: 0.7908 (t0) cc_final: 0.7600 (p0) REVERT: S 72 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.6533 (tp) REVERT: U 35 TYR cc_start: 0.5436 (OUTLIER) cc_final: 0.5091 (m-80) REVERT: U 203 GLU cc_start: 0.5996 (mp0) cc_final: 0.5739 (mp0) REVERT: U 266 ASN cc_start: 0.6958 (OUTLIER) cc_final: 0.5927 (p0) REVERT: U 385 THR cc_start: 0.8478 (p) cc_final: 0.8222 (p) REVERT: U 610 VAL cc_start: 0.6925 (OUTLIER) cc_final: 0.6686 (p) REVERT: U 634 MET cc_start: 0.5684 (OUTLIER) cc_final: 0.5263 (mtp) REVERT: V 46 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8693 (mttt) REVERT: V 78 TYR cc_start: 0.8599 (m-80) cc_final: 0.8303 (m-80) REVERT: W 57 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7145 (mm-30) REVERT: W 92 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.7949 (pptt) REVERT: W 93 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: X 12 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8138 (tm-30) REVERT: X 55 ARG cc_start: 0.8176 (mpt-90) cc_final: 0.7515 (mpt-90) REVERT: X 70 GLN cc_start: 0.7092 (tm-30) cc_final: 0.6808 (tm-30) REVERT: Y 44 ARG cc_start: 0.8301 (tpp80) cc_final: 0.7843 (tpp80) REVERT: a 39 MET cc_start: 0.8041 (mmt) cc_final: 0.7783 (mmp) REVERT: a 51 TYR cc_start: 0.5949 (OUTLIER) cc_final: 0.5532 (t80) REVERT: c 22 MET cc_start: 0.8200 (mmm) cc_final: 0.7687 (tmm) REVERT: c 23 ARG cc_start: 0.8456 (ptp90) cc_final: 0.7965 (ptp90) REVERT: d 39 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7645 (tttp) REVERT: g 31 LYS cc_start: 0.8129 (ptmt) cc_final: 0.7449 (mmtm) REVERT: g 151 LYS cc_start: 0.8512 (mtmt) cc_final: 0.8269 (mtmt) REVERT: g 176 ARG cc_start: 0.8452 (ttp-170) cc_final: 0.8156 (ttp80) REVERT: g 203 ASN cc_start: 0.7806 (t160) cc_final: 0.7589 (t0) REVERT: g 226 MET cc_start: 0.8203 (mmt) cc_final: 0.7913 (mmt) REVERT: h 47 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.9001 (p) REVERT: h 52 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.5957 (tt) REVERT: h 76 ARG cc_start: 0.7444 (mmt90) cc_final: 0.6960 (mmt180) REVERT: h 100 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7582 (mm-30) REVERT: h 164 ARG cc_start: 0.8266 (ttt90) cc_final: 0.7965 (ttt90) REVERT: h 168 MET cc_start: 0.7897 (mtm) cc_final: 0.7530 (mtp) REVERT: h 174 ASP cc_start: 0.8385 (t0) cc_final: 0.8129 (t0) REVERT: h 182 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8765 (tt) REVERT: h 200 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7080 (tm-30) REVERT: i 35 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: i 100 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8784 (p) REVERT: i 110 LEU cc_start: 0.9537 (tp) cc_final: 0.9226 (tp) REVERT: i 179 GLU cc_start: 0.8390 (pp20) cc_final: 0.7796 (pp20) REVERT: j 148 MET cc_start: 0.7071 (tmm) cc_final: 0.6246 (tpt) REVERT: j 178 PHE cc_start: 0.4832 (m-80) cc_final: 0.4515 (m-80) REVERT: k 44 VAL cc_start: 0.5827 (OUTLIER) cc_final: 0.5283 (t) REVERT: k 51 ARG cc_start: 0.7123 (mmt90) cc_final: 0.6030 (mmp-170) REVERT: k 121 ILE cc_start: 0.8109 (mm) cc_final: 0.7867 (mm) REVERT: o 48 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7377 (ptp) REVERT: o 109 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7902 (mmmt) REVERT: p 12 ASP cc_start: 0.8227 (t70) cc_final: 0.8002 (t70) REVERT: p 18 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8544 (ttpt) REVERT: p 107 ARG cc_start: 0.7891 (ttm110) cc_final: 0.7536 (mtm-85) REVERT: p 120 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7869 (tm-30) REVERT: r 6 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.7051 (tpt90) REVERT: r 22 LYS cc_start: 0.8036 (tmtt) cc_final: 0.7781 (tttp) REVERT: s 115 GLU cc_start: 0.8210 (pt0) cc_final: 0.7976 (pt0) REVERT: t 88 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7325 (p0) REVERT: t 89 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7339 (mtm110) REVERT: t 95 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.6940 (t-170) REVERT: v 84 LYS cc_start: 0.8399 (mmtm) cc_final: 0.7700 (mttt) REVERT: w 60 GLU cc_start: 0.8457 (pm20) cc_final: 0.7807 (pt0) REVERT: x 20 VAL cc_start: 0.8843 (p) cc_final: 0.8551 (t) REVERT: x 110 LYS cc_start: 0.7197 (mtmt) cc_final: 0.6742 (tttt) REVERT: z 38 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.6506 (mp) REVERT: z 55 TYR cc_start: 0.5194 (OUTLIER) cc_final: 0.3794 (p90) REVERT: z 84 ARG cc_start: 0.6164 (OUTLIER) cc_final: 0.5794 (mmt180) outliers start: 403 outliers final: 281 residues processed: 1447 average time/residue: 1.5041 time to fit residues: 3768.5524 Evaluate side-chains 1474 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 1155 time to evaluate : 7.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 3 TYR Chi-restraints excluded: chain 6 residue 41 LEU Chi-restraints excluded: chain 6 residue 42 VAL Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 61 LEU Chi-restraints excluded: chain 6 residue 93 ASP Chi-restraints excluded: chain 6 residue 120 ILE Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 6 residue 155 LEU Chi-restraints excluded: chain 6 residue 163 LEU Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 6 LEU Chi-restraints excluded: chain 7 residue 12 LEU Chi-restraints excluded: chain 7 residue 38 LEU Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 109 ILE Chi-restraints excluded: chain 7 residue 114 LEU Chi-restraints excluded: chain 7 residue 123 LEU Chi-restraints excluded: chain 7 residue 136 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain F residue 69 VAL Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 128 ARG Chi-restraints excluded: chain I residue 23 ILE Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 20 LYS Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 21 TYR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 40 SER Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 44 THR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 94 ASN Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 36 THR Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 81 ILE Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 155 GLU Chi-restraints excluded: chain U residue 160 ARG Chi-restraints excluded: chain U residue 188 TYR Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 212 TYR Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain U residue 260 LEU Chi-restraints excluded: chain U residue 266 ASN Chi-restraints excluded: chain U residue 292 THR Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 322 VAL Chi-restraints excluded: chain U residue 326 THR Chi-restraints excluded: chain U residue 331 TYR Chi-restraints excluded: chain U residue 359 HIS Chi-restraints excluded: chain U residue 377 VAL Chi-restraints excluded: chain U residue 378 VAL Chi-restraints excluded: chain U residue 388 THR Chi-restraints excluded: chain U residue 389 LEU Chi-restraints excluded: chain U residue 517 LEU Chi-restraints excluded: chain U residue 610 VAL Chi-restraints excluded: chain U residue 631 ILE Chi-restraints excluded: chain U residue 634 MET Chi-restraints excluded: chain U residue 668 SER Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 35 ASN Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 64 ASP Chi-restraints excluded: chain W residue 17 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 46 LEU Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 45 SER Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 65 ASN Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Y residue 18 ASP Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 19 ARG Chi-restraints excluded: chain a residue 51 TYR Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 16 CYS Chi-restraints excluded: chain b residue 20 ASN Chi-restraints excluded: chain c residue 9 ARG Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain d residue 34 TRP Chi-restraints excluded: chain d residue 39 LYS Chi-restraints excluded: chain d residue 61 LEU Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 172 ILE Chi-restraints excluded: chain f residue 223 VAL Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 64 ILE Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 201 HIS Chi-restraints excluded: chain g residue 202 LYS Chi-restraints excluded: chain g residue 204 ILE Chi-restraints excluded: chain g residue 227 ASN Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain g residue 257 LEU Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 52 LEU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 128 SER Chi-restraints excluded: chain h residue 166 THR Chi-restraints excluded: chain h residue 171 GLU Chi-restraints excluded: chain h residue 182 LEU Chi-restraints excluded: chain h residue 196 VAL Chi-restraints excluded: chain i residue 3 GLU Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 50 SER Chi-restraints excluded: chain i residue 60 SER Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 89 VAL Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 140 LEU Chi-restraints excluded: chain i residue 154 VAL Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain i residue 181 LEU Chi-restraints excluded: chain j residue 14 GLU Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 92 VAL Chi-restraints excluded: chain j residue 99 MET Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain j residue 149 VAL Chi-restraints excluded: chain k residue 11 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 60 ARG Chi-restraints excluded: chain k residue 64 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 129 THR Chi-restraints excluded: chain k residue 134 SER Chi-restraints excluded: chain k residue 143 GLN Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 30 ILE Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 43 THR Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 48 MET Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 71 ILE Chi-restraints excluded: chain o residue 88 GLU Chi-restraints excluded: chain o residue 116 LEU Chi-restraints excluded: chain o residue 127 ASP Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 29 ASN Chi-restraints excluded: chain p residue 58 VAL Chi-restraints excluded: chain p residue 68 GLU Chi-restraints excluded: chain q residue 57 THR Chi-restraints excluded: chain q residue 60 MET Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 67 MET Chi-restraints excluded: chain q residue 68 GLN Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 115 LEU Chi-restraints excluded: chain r residue 6 ARG Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain r residue 75 THR Chi-restraints excluded: chain r residue 94 VAL Chi-restraints excluded: chain r residue 120 ILE Chi-restraints excluded: chain r residue 141 GLN Chi-restraints excluded: chain s residue 3 HIS Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 38 VAL Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain s residue 73 VAL Chi-restraints excluded: chain s residue 107 ASP Chi-restraints excluded: chain s residue 117 VAL Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain t residue 36 TYR Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 88 ASP Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain t residue 95 HIS Chi-restraints excluded: chain t residue 103 GLU Chi-restraints excluded: chain u residue 6 LEU Chi-restraints excluded: chain u residue 27 THR Chi-restraints excluded: chain u residue 44 ASP Chi-restraints excluded: chain u residue 49 VAL Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain u residue 107 ASP Chi-restraints excluded: chain u residue 123 GLN Chi-restraints excluded: chain u residue 124 ASP Chi-restraints excluded: chain v residue 16 LYS Chi-restraints excluded: chain v residue 18 LEU Chi-restraints excluded: chain v residue 29 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain v residue 104 GLN Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 22 VAL Chi-restraints excluded: chain w residue 37 VAL Chi-restraints excluded: chain w residue 39 LEU Chi-restraints excluded: chain w residue 45 THR Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 88 ARG Chi-restraints excluded: chain x residue 6 ILE Chi-restraints excluded: chain x residue 13 SER Chi-restraints excluded: chain x residue 53 SER Chi-restraints excluded: chain x residue 66 GLU Chi-restraints excluded: chain x residue 76 VAL Chi-restraints excluded: chain x residue 78 GLU Chi-restraints excluded: chain x residue 100 THR Chi-restraints excluded: chain x residue 103 ILE Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 7 VAL Chi-restraints excluded: chain y residue 9 LEU Chi-restraints excluded: chain y residue 12 VAL Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain y residue 52 VAL Chi-restraints excluded: chain z residue 24 VAL Chi-restraints excluded: chain z residue 38 ILE Chi-restraints excluded: chain z residue 55 TYR Chi-restraints excluded: chain z residue 75 ILE Chi-restraints excluded: chain z residue 84 ARG Chi-restraints excluded: chain z residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 671 optimal weight: 6.9990 chunk 433 optimal weight: 10.0000 chunk 648 optimal weight: 0.9980 chunk 326 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 chunk 210 optimal weight: 8.9990 chunk 689 optimal weight: 1.9990 chunk 739 optimal weight: 6.9990 chunk 536 optimal weight: 0.0570 chunk 101 optimal weight: 20.0000 chunk 853 optimal weight: 0.2980 overall best weight: 2.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 GLN ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 HIS ** S 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 266 ASN V 12 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN ** d 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 227 ASN ** g 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 13 ASN r 141 GLN ** w 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 55 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 166981 Z= 0.200 Angle : 0.654 27.304 248612 Z= 0.325 Chirality : 0.039 1.961 31393 Planarity : 0.005 0.110 14372 Dihedral : 24.402 177.919 81164 Min Nonbonded Distance : 1.134 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.55 % Favored : 86.27 % Rotamer: Outliers : 6.07 % Allowed : 24.74 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.08 % Twisted Proline : 2.33 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.09), residues: 6592 helix: -1.43 (0.12), residues: 1571 sheet: -2.13 (0.16), residues: 985 loop : -2.94 (0.09), residues: 4036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP i 39 HIS 0.007 0.001 HIS G 82 PHE 0.036 0.002 PHE j 125 TYR 0.055 0.002 TYR F 151 ARG 0.015 0.001 ARG P 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1559 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1221 time to evaluate : 7.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 6 LEU cc_start: 0.6032 (OUTLIER) cc_final: 0.5576 (tt) REVERT: A 68 ILE cc_start: 0.7869 (mm) cc_final: 0.7506 (tt) REVERT: A 97 TRP cc_start: 0.7597 (t-100) cc_final: 0.7078 (t-100) REVERT: A 101 MET cc_start: 0.6548 (mtt) cc_final: 0.5943 (mtt) REVERT: A 226 ARG cc_start: 0.6048 (ptt-90) cc_final: 0.5725 (ptt-90) REVERT: B 3 ASN cc_start: 0.4193 (OUTLIER) cc_final: 0.3280 (p0) REVERT: C 21 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7973 (pp) REVERT: C 75 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: C 116 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6109 (tp40) REVERT: C 120 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7562 (mm) REVERT: C 126 ILE cc_start: 0.8479 (mp) cc_final: 0.7851 (tp) REVERT: C 204 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8439 (pt) REVERT: D 68 GLU cc_start: 0.8235 (mp0) cc_final: 0.7867 (mp0) REVERT: F 43 PHE cc_start: 0.4385 (OUTLIER) cc_final: 0.4093 (m-80) REVERT: F 51 GLN cc_start: 0.6195 (tp40) cc_final: 0.5345 (tp40) REVERT: G 102 ARG cc_start: 0.6960 (mpt180) cc_final: 0.6339 (mtt180) REVERT: G 138 TRP cc_start: 0.7414 (p-90) cc_final: 0.6985 (p-90) REVERT: H 128 ARG cc_start: 0.0546 (OUTLIER) cc_final: 0.0328 (pmt100) REVERT: I 24 VAL cc_start: 0.3283 (t) cc_final: 0.2823 (t) REVERT: K 19 ARG cc_start: 0.7140 (mmp80) cc_final: 0.6803 (tpp80) REVERT: K 20 LYS cc_start: 0.6888 (pmmt) cc_final: 0.6565 (pmmt) REVERT: K 111 LYS cc_start: 0.7743 (pptt) cc_final: 0.7425 (pptt) REVERT: K 114 LYS cc_start: 0.6485 (OUTLIER) cc_final: 0.6246 (ptpp) REVERT: L 21 TYR cc_start: 0.2952 (OUTLIER) cc_final: 0.0248 (m-80) REVERT: L 39 ILE cc_start: -0.1029 (OUTLIER) cc_final: -0.1515 (mp) REVERT: M 45 ARG cc_start: 0.4566 (OUTLIER) cc_final: 0.3433 (mtm180) REVERT: O 34 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7810 (tm-30) REVERT: O 50 LYS cc_start: 0.7485 (tmtt) cc_final: 0.7151 (mmtm) REVERT: O 52 ASP cc_start: 0.7396 (t0) cc_final: 0.7118 (t0) REVERT: P 14 LYS cc_start: 0.7656 (mmmm) cc_final: 0.7216 (tptp) REVERT: P 61 GLU cc_start: 0.7039 (pt0) cc_final: 0.6837 (tm-30) REVERT: S 9 ASN cc_start: 0.7802 (t0) cc_final: 0.7586 (p0) REVERT: S 72 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6438 (tp) REVERT: U 35 TYR cc_start: 0.5217 (OUTLIER) cc_final: 0.4936 (m-80) REVERT: U 73 PHE cc_start: 0.6159 (OUTLIER) cc_final: 0.5816 (t80) REVERT: U 203 GLU cc_start: 0.5966 (mp0) cc_final: 0.5725 (mp0) REVERT: U 266 ASN cc_start: 0.6947 (OUTLIER) cc_final: 0.5683 (p0) REVERT: U 507 TYR cc_start: 0.5182 (t80) cc_final: 0.4718 (t80) REVERT: U 610 VAL cc_start: 0.6841 (OUTLIER) cc_final: 0.6598 (p) REVERT: U 634 MET cc_start: 0.5743 (OUTLIER) cc_final: 0.5332 (mtp) REVERT: U 663 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7838 (m) REVERT: V 46 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8613 (mttt) REVERT: V 78 TYR cc_start: 0.8375 (m-80) cc_final: 0.8115 (m-80) REVERT: W 92 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.7894 (pptt) REVERT: W 93 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: X 12 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8231 (tm-30) REVERT: X 55 ARG cc_start: 0.8064 (mpt-90) cc_final: 0.7409 (mpt-90) REVERT: a 39 MET cc_start: 0.8059 (mmt) cc_final: 0.7789 (mmp) REVERT: a 51 TYR cc_start: 0.5865 (OUTLIER) cc_final: 0.5457 (t80) REVERT: b 37 ARG cc_start: 0.8716 (mmp80) cc_final: 0.8358 (mmp-170) REVERT: c 22 MET cc_start: 0.8156 (mmm) cc_final: 0.7643 (tmm) REVERT: c 23 ARG cc_start: 0.8420 (ptp90) cc_final: 0.7930 (ptp90) REVERT: d 39 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7542 (tttp) REVERT: d 57 ARG cc_start: 0.8687 (ptp-110) cc_final: 0.8244 (mtm110) REVERT: g 31 LYS cc_start: 0.7989 (ptmt) cc_final: 0.7297 (mmtm) REVERT: g 88 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.8372 (mtm-85) REVERT: g 151 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8489 (mtmt) REVERT: g 203 ASN cc_start: 0.7791 (t160) cc_final: 0.7554 (t0) REVERT: h 47 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8986 (p) REVERT: h 52 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.6274 (tt) REVERT: h 76 ARG cc_start: 0.7358 (mmt90) cc_final: 0.6920 (mmt180) REVERT: h 100 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7583 (mm-30) REVERT: h 164 ARG cc_start: 0.8222 (ttt90) cc_final: 0.7930 (ttt90) REVERT: h 168 MET cc_start: 0.7892 (mtm) cc_final: 0.7531 (mtp) REVERT: h 174 ASP cc_start: 0.8290 (t0) cc_final: 0.8035 (t0) REVERT: h 177 PRO cc_start: 0.8654 (Cg_exo) cc_final: 0.8353 (Cg_endo) REVERT: h 182 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8755 (tt) REVERT: h 192 ASN cc_start: 0.8511 (m-40) cc_final: 0.8160 (m110) REVERT: h 200 GLU cc_start: 0.7302 (tm-30) cc_final: 0.7084 (tm-30) REVERT: i 35 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8239 (mp0) REVERT: i 100 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8669 (p) REVERT: i 110 LEU cc_start: 0.9565 (tp) cc_final: 0.9230 (tp) REVERT: i 112 MET cc_start: 0.7515 (ttm) cc_final: 0.7124 (ttp) REVERT: i 179 GLU cc_start: 0.8394 (pp20) cc_final: 0.7767 (pp20) REVERT: j 148 MET cc_start: 0.7267 (tmm) cc_final: 0.6475 (tpt) REVERT: k 44 VAL cc_start: 0.5690 (OUTLIER) cc_final: 0.5139 (t) REVERT: k 51 ARG cc_start: 0.7088 (mmt90) cc_final: 0.6029 (mmp-170) REVERT: k 121 ILE cc_start: 0.8070 (mm) cc_final: 0.7850 (mm) REVERT: o 48 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7321 (ptp) REVERT: o 106 MET cc_start: 0.8911 (mtt) cc_final: 0.8605 (mtt) REVERT: o 109 LYS cc_start: 0.8132 (mmmm) cc_final: 0.7900 (mmmt) REVERT: p 18 LYS cc_start: 0.8888 (ttmm) cc_final: 0.8527 (ttpt) REVERT: p 107 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7527 (mtm-85) REVERT: p 120 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: q 81 GLN cc_start: 0.7247 (tp-100) cc_final: 0.6931 (tp-100) REVERT: r 6 ARG cc_start: 0.7424 (ttt90) cc_final: 0.7074 (tpt90) REVERT: r 115 MET cc_start: 0.8441 (mmm) cc_final: 0.7922 (mmm) REVERT: s 115 GLU cc_start: 0.8177 (pt0) cc_final: 0.7957 (pt0) REVERT: t 88 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7191 (p0) REVERT: t 89 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7298 (mtm110) REVERT: t 95 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.6982 (t-170) REVERT: v 84 LYS cc_start: 0.8365 (mmtm) cc_final: 0.7679 (mttt) REVERT: w 60 GLU cc_start: 0.8429 (pm20) cc_final: 0.7837 (pt0) REVERT: x 20 VAL cc_start: 0.8857 (p) cc_final: 0.8554 (t) REVERT: x 110 LYS cc_start: 0.7170 (mtmt) cc_final: 0.6817 (tttm) REVERT: y 87 GLN cc_start: 0.5940 (OUTLIER) cc_final: 0.5504 (mp10) REVERT: z 38 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6391 (mt) REVERT: z 55 TYR cc_start: 0.5011 (OUTLIER) cc_final: 0.3525 (p90) outliers start: 338 outliers final: 241 residues processed: 1426 average time/residue: 1.3901 time to fit residues: 3396.3186 Evaluate side-chains 1448 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1169 time to evaluate : 7.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 3 TYR Chi-restraints excluded: chain 6 residue 41 LEU Chi-restraints excluded: chain 6 residue 42 VAL Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 61 LEU Chi-restraints excluded: chain 6 residue 120 ILE Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 6 residue 155 LEU Chi-restraints excluded: chain 6 residue 163 LEU Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 6 LEU Chi-restraints excluded: chain 7 residue 12 LEU Chi-restraints excluded: chain 7 residue 38 LEU Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 114 LEU Chi-restraints excluded: chain 7 residue 123 LEU Chi-restraints excluded: chain 7 residue 136 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 128 PHE Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 207 TYR Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 128 ARG Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 21 TYR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 40 SER Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 73 PHE Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 160 ARG Chi-restraints excluded: chain U residue 188 TYR Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 212 TYR Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain U residue 260 LEU Chi-restraints excluded: chain U residue 266 ASN Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 322 VAL Chi-restraints excluded: chain U residue 359 HIS Chi-restraints excluded: chain U residue 377 VAL Chi-restraints excluded: chain U residue 378 VAL Chi-restraints excluded: chain U residue 388 THR Chi-restraints excluded: chain U residue 517 LEU Chi-restraints excluded: chain U residue 610 VAL Chi-restraints excluded: chain U residue 631 ILE Chi-restraints excluded: chain U residue 634 MET Chi-restraints excluded: chain U residue 652 MET Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain U residue 668 SER Chi-restraints excluded: chain V residue 12 ASN Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain V residue 64 ASP Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Y residue 18 ASP Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain a residue 19 ARG Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 51 TYR Chi-restraints excluded: chain b residue 20 ASN Chi-restraints excluded: chain c residue 9 ARG Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 34 TRP Chi-restraints excluded: chain d residue 39 LYS Chi-restraints excluded: chain d residue 61 LEU Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 12 ASP Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 26 ILE Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 117 THR Chi-restraints excluded: chain f residue 132 LEU Chi-restraints excluded: chain f residue 172 ILE Chi-restraints excluded: chain f residue 223 VAL Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 201 HIS Chi-restraints excluded: chain g residue 204 ILE Chi-restraints excluded: chain g residue 222 ARG Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain g residue 257 LEU Chi-restraints excluded: chain g residue 268 ARG Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 52 LEU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 171 GLU Chi-restraints excluded: chain h residue 182 LEU Chi-restraints excluded: chain i residue 3 GLU Chi-restraints excluded: chain i residue 19 GLU Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 50 SER Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 125 LEU Chi-restraints excluded: chain i residue 140 LEU Chi-restraints excluded: chain i residue 154 VAL Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 83 ARG Chi-restraints excluded: chain j residue 92 VAL Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 99 MET Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain j residue 149 VAL Chi-restraints excluded: chain k residue 11 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 71 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 129 THR Chi-restraints excluded: chain k residue 134 SER Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 30 ILE Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 43 THR Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 48 MET Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 88 GLU Chi-restraints excluded: chain o residue 116 LEU Chi-restraints excluded: chain o residue 127 ASP Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 58 VAL Chi-restraints excluded: chain p residue 63 VAL Chi-restraints excluded: chain p residue 120 GLU Chi-restraints excluded: chain q residue 57 THR Chi-restraints excluded: chain q residue 60 MET Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 68 GLN Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 106 LEU Chi-restraints excluded: chain q residue 115 LEU Chi-restraints excluded: chain r residue 120 ILE Chi-restraints excluded: chain r residue 141 GLN Chi-restraints excluded: chain s residue 3 HIS Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 38 VAL Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 73 VAL Chi-restraints excluded: chain s residue 107 ASP Chi-restraints excluded: chain s residue 117 VAL Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain t residue 36 TYR Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 88 ASP Chi-restraints excluded: chain t residue 89 ARG Chi-restraints excluded: chain t residue 95 HIS Chi-restraints excluded: chain u residue 6 LEU Chi-restraints excluded: chain u residue 27 THR Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain u residue 107 ASP Chi-restraints excluded: chain u residue 123 GLN Chi-restraints excluded: chain u residue 124 ASP Chi-restraints excluded: chain v residue 16 LYS Chi-restraints excluded: chain v residue 18 LEU Chi-restraints excluded: chain v residue 29 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain v residue 104 GLN Chi-restraints excluded: chain v residue 109 LEU Chi-restraints excluded: chain w residue 22 VAL Chi-restraints excluded: chain w residue 37 VAL Chi-restraints excluded: chain w residue 39 LEU Chi-restraints excluded: chain w residue 45 THR Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 88 ARG Chi-restraints excluded: chain x residue 6 ILE Chi-restraints excluded: chain x residue 13 SER Chi-restraints excluded: chain x residue 53 SER Chi-restraints excluded: chain x residue 66 GLU Chi-restraints excluded: chain x residue 76 VAL Chi-restraints excluded: chain x residue 78 GLU Chi-restraints excluded: chain x residue 103 ILE Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 7 VAL Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain y residue 52 VAL Chi-restraints excluded: chain y residue 87 GLN Chi-restraints excluded: chain z residue 24 VAL Chi-restraints excluded: chain z residue 38 ILE Chi-restraints excluded: chain z residue 55 TYR Chi-restraints excluded: chain z residue 75 ILE Chi-restraints excluded: chain z residue 85 VAL Chi-restraints excluded: chain z residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 987 optimal weight: 30.0000 chunk 1039 optimal weight: 1.9990 chunk 948 optimal weight: 9.9990 chunk 1011 optimal weight: 2.9990 chunk 608 optimal weight: 3.9990 chunk 440 optimal weight: 8.9990 chunk 794 optimal weight: 0.0040 chunk 310 optimal weight: 10.0000 chunk 913 optimal weight: 9.9990 chunk 956 optimal weight: 4.9990 chunk 1007 optimal weight: 0.7980 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN ** M 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 HIS N 62 GLN P 94 ASN R 65 ASN ** S 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 266 ASN V 12 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 65 ASN c 36 GLN ** d 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 143 GLN k 147 ASN ** r 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 166981 Z= 0.193 Angle : 0.649 27.222 248612 Z= 0.322 Chirality : 0.038 1.961 31393 Planarity : 0.006 0.175 14372 Dihedral : 24.373 177.817 81164 Min Nonbonded Distance : 1.126 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.50 % Favored : 86.30 % Rotamer: Outliers : 5.89 % Allowed : 25.22 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.08 % Twisted Proline : 2.62 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.10), residues: 6592 helix: -1.40 (0.12), residues: 1595 sheet: -2.08 (0.16), residues: 991 loop : -2.91 (0.09), residues: 4006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP i 39 HIS 0.008 0.001 HIS N 53 PHE 0.030 0.002 PHE j 125 TYR 0.048 0.002 TYR F 151 ARG 0.016 0.001 ARG M 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1519 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 1191 time to evaluate : 7.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 5 LEU cc_start: 0.6771 (mt) cc_final: 0.6534 (mp) REVERT: 7 6 LEU cc_start: 0.5978 (OUTLIER) cc_final: 0.5511 (tt) REVERT: A 68 ILE cc_start: 0.7873 (mm) cc_final: 0.7501 (tt) REVERT: A 97 TRP cc_start: 0.7576 (t-100) cc_final: 0.7133 (t-100) REVERT: A 101 MET cc_start: 0.6756 (mtt) cc_final: 0.5980 (mtt) REVERT: A 226 ARG cc_start: 0.5816 (ptt-90) cc_final: 0.5505 (ptt-90) REVERT: B 3 ASN cc_start: 0.4170 (OUTLIER) cc_final: 0.3245 (p0) REVERT: C 21 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7960 (pp) REVERT: C 75 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: C 116 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6129 (tp40) REVERT: C 120 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7656 (mm) REVERT: C 126 ILE cc_start: 0.8490 (mp) cc_final: 0.7828 (tp) REVERT: D 68 GLU cc_start: 0.8222 (mp0) cc_final: 0.7840 (mp0) REVERT: F 43 PHE cc_start: 0.4345 (OUTLIER) cc_final: 0.4064 (m-80) REVERT: F 51 GLN cc_start: 0.6241 (tp40) cc_final: 0.5379 (tp40) REVERT: G 102 ARG cc_start: 0.6946 (mpt180) cc_final: 0.6363 (mtt180) REVERT: G 138 TRP cc_start: 0.7409 (p-90) cc_final: 0.7031 (p-90) REVERT: H 128 ARG cc_start: 0.0481 (OUTLIER) cc_final: 0.0271 (pmt100) REVERT: I 24 VAL cc_start: 0.3274 (t) cc_final: 0.2816 (t) REVERT: K 19 ARG cc_start: 0.7132 (mmp80) cc_final: 0.6803 (tpp80) REVERT: K 20 LYS cc_start: 0.6847 (pmmt) cc_final: 0.6527 (pmmt) REVERT: K 47 LYS cc_start: 0.7178 (mttm) cc_final: 0.6922 (mmtt) REVERT: K 57 LYS cc_start: 0.8371 (mtmm) cc_final: 0.8014 (mtmm) REVERT: K 111 LYS cc_start: 0.7776 (pptt) cc_final: 0.7434 (pptt) REVERT: K 114 LYS cc_start: 0.6480 (OUTLIER) cc_final: 0.6253 (ptpp) REVERT: L 21 TYR cc_start: 0.3057 (OUTLIER) cc_final: 0.0132 (m-80) REVERT: L 39 ILE cc_start: -0.1004 (OUTLIER) cc_final: -0.1495 (mp) REVERT: L 58 GLU cc_start: 0.6513 (pm20) cc_final: 0.6302 (pm20) REVERT: M 45 ARG cc_start: 0.4584 (OUTLIER) cc_final: 0.3466 (mtm180) REVERT: O 50 LYS cc_start: 0.7470 (tmtt) cc_final: 0.7148 (mmtm) REVERT: O 52 ASP cc_start: 0.7344 (t0) cc_final: 0.7084 (t0) REVERT: P 61 GLU cc_start: 0.7157 (pt0) cc_final: 0.6882 (tm-30) REVERT: S 72 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6414 (tp) REVERT: U 35 TYR cc_start: 0.5149 (OUTLIER) cc_final: 0.4903 (m-80) REVERT: U 73 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.5765 (t80) REVERT: U 203 GLU cc_start: 0.5934 (mp0) cc_final: 0.5718 (mp0) REVERT: U 266 ASN cc_start: 0.7029 (OUTLIER) cc_final: 0.5928 (p0) REVERT: U 507 TYR cc_start: 0.4998 (t80) cc_final: 0.4467 (t80) REVERT: U 610 VAL cc_start: 0.6870 (OUTLIER) cc_final: 0.6617 (p) REVERT: U 634 MET cc_start: 0.5709 (OUTLIER) cc_final: 0.5319 (mtp) REVERT: U 663 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7712 (m) REVERT: V 46 LYS cc_start: 0.8913 (mmmm) cc_final: 0.8638 (mttt) REVERT: W 57 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7128 (mm-30) REVERT: W 92 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.7816 (pptt) REVERT: W 93 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7070 (mm-30) REVERT: X 12 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8221 (tm-30) REVERT: X 55 ARG cc_start: 0.8045 (mpt-90) cc_final: 0.7378 (mpt-90) REVERT: a 39 MET cc_start: 0.8057 (mmt) cc_final: 0.7789 (mmp) REVERT: a 51 TYR cc_start: 0.5851 (OUTLIER) cc_final: 0.5459 (t80) REVERT: b 37 ARG cc_start: 0.8607 (mmp80) cc_final: 0.8199 (mmp-170) REVERT: c 23 ARG cc_start: 0.8439 (ptp90) cc_final: 0.7893 (ptp90) REVERT: g 31 LYS cc_start: 0.7953 (ptmt) cc_final: 0.7249 (mmtm) REVERT: g 203 ASN cc_start: 0.7789 (t160) cc_final: 0.7536 (t0) REVERT: g 222 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.7103 (ttp80) REVERT: h 47 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.8968 (p) REVERT: h 52 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.6271 (tt) REVERT: h 76 ARG cc_start: 0.7306 (mmt90) cc_final: 0.6859 (mmt180) REVERT: h 100 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7608 (mm-30) REVERT: h 164 ARG cc_start: 0.8172 (ttt90) cc_final: 0.7865 (ttt90) REVERT: h 168 MET cc_start: 0.7931 (mtm) cc_final: 0.7545 (mtp) REVERT: h 174 ASP cc_start: 0.8281 (t0) cc_final: 0.8031 (t0) REVERT: h 177 PRO cc_start: 0.8614 (Cg_exo) cc_final: 0.8315 (Cg_endo) REVERT: h 182 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8757 (tt) REVERT: h 192 ASN cc_start: 0.8495 (m-40) cc_final: 0.8139 (m110) REVERT: h 200 GLU cc_start: 0.7293 (tm-30) cc_final: 0.7091 (tm-30) REVERT: i 35 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: i 100 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8668 (p) REVERT: i 110 LEU cc_start: 0.9556 (tp) cc_final: 0.9257 (tp) REVERT: i 112 MET cc_start: 0.7581 (ttm) cc_final: 0.7208 (ttp) REVERT: i 179 GLU cc_start: 0.8304 (pp20) cc_final: 0.7687 (pp20) REVERT: j 148 MET cc_start: 0.7358 (tmm) cc_final: 0.6712 (tpt) REVERT: k 44 VAL cc_start: 0.5748 (OUTLIER) cc_final: 0.5232 (t) REVERT: k 51 ARG cc_start: 0.7089 (mmt90) cc_final: 0.6027 (mmp-170) REVERT: k 121 ILE cc_start: 0.8076 (mm) cc_final: 0.7850 (mm) REVERT: o 48 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7183 (ptp) REVERT: p 18 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8545 (ttpt) REVERT: p 107 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7527 (mtm-85) REVERT: p 120 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7844 (tm-30) REVERT: q 81 GLN cc_start: 0.7262 (tp-100) cc_final: 0.6858 (tp-100) REVERT: r 115 MET cc_start: 0.8469 (mmm) cc_final: 0.7981 (mmm) REVERT: s 115 GLU cc_start: 0.8185 (pt0) cc_final: 0.7959 (pt0) REVERT: t 88 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7109 (p0) REVERT: t 95 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6944 (t-170) REVERT: v 16 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8784 (ttmm) REVERT: v 84 LYS cc_start: 0.8368 (mmtm) cc_final: 0.7667 (mttt) REVERT: w 60 GLU cc_start: 0.8429 (pm20) cc_final: 0.7641 (pt0) REVERT: x 20 VAL cc_start: 0.8856 (p) cc_final: 0.8556 (t) REVERT: x 110 LYS cc_start: 0.7209 (mtmt) cc_final: 0.6821 (tttm) REVERT: y 87 GLN cc_start: 0.5919 (OUTLIER) cc_final: 0.5472 (mp10) REVERT: z 38 ILE cc_start: 0.6805 (OUTLIER) cc_final: 0.6396 (mt) REVERT: z 55 TYR cc_start: 0.5005 (OUTLIER) cc_final: 0.3527 (p90) outliers start: 328 outliers final: 246 residues processed: 1389 average time/residue: 1.3911 time to fit residues: 3316.0378 Evaluate side-chains 1437 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1154 time to evaluate : 7.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 3 TYR Chi-restraints excluded: chain 6 residue 41 LEU Chi-restraints excluded: chain 6 residue 42 VAL Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 61 LEU Chi-restraints excluded: chain 6 residue 120 ILE Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 6 residue 155 LEU Chi-restraints excluded: chain 6 residue 163 LEU Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 6 LEU Chi-restraints excluded: chain 7 residue 12 LEU Chi-restraints excluded: chain 7 residue 19 VAL Chi-restraints excluded: chain 7 residue 38 LEU Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 101 LEU Chi-restraints excluded: chain 7 residue 114 LEU Chi-restraints excluded: chain 7 residue 123 LEU Chi-restraints excluded: chain 7 residue 136 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 128 ARG Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 21 TYR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 40 SER Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 77 VAL Chi-restraints excluded: chain P residue 93 GLN Chi-restraints excluded: chain P residue 94 ASN Chi-restraints excluded: chain S residue 11 SER Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 73 PHE Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 160 ARG Chi-restraints excluded: chain U residue 188 TYR Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 212 TYR Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain U residue 260 LEU Chi-restraints excluded: chain U residue 266 ASN Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 322 VAL Chi-restraints excluded: chain U residue 326 THR Chi-restraints excluded: chain U residue 359 HIS Chi-restraints excluded: chain U residue 369 LEU Chi-restraints excluded: chain U residue 377 VAL Chi-restraints excluded: chain U residue 378 VAL Chi-restraints excluded: chain U residue 388 THR Chi-restraints excluded: chain U residue 389 LEU Chi-restraints excluded: chain U residue 517 LEU Chi-restraints excluded: chain U residue 610 VAL Chi-restraints excluded: chain U residue 631 ILE Chi-restraints excluded: chain U residue 634 MET Chi-restraints excluded: chain U residue 652 MET Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 59 LEU Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain W residue 93 GLU Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 65 ASN Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Y residue 18 ASP Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain a residue 19 ARG Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 51 TYR Chi-restraints excluded: chain b residue 20 ASN Chi-restraints excluded: chain c residue 9 ARG Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 34 TRP Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 12 ASP Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 26 ILE Chi-restraints excluded: chain f residue 73 VAL Chi-restraints excluded: chain f residue 117 THR Chi-restraints excluded: chain f residue 172 ILE Chi-restraints excluded: chain f residue 190 ILE Chi-restraints excluded: chain f residue 223 VAL Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 202 LYS Chi-restraints excluded: chain g residue 204 ILE Chi-restraints excluded: chain g residue 222 ARG Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain g residue 257 LEU Chi-restraints excluded: chain g residue 268 ARG Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 47 VAL Chi-restraints excluded: chain h residue 52 LEU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 171 GLU Chi-restraints excluded: chain h residue 182 LEU Chi-restraints excluded: chain i residue 3 GLU Chi-restraints excluded: chain i residue 19 GLU Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 50 SER Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 125 LEU Chi-restraints excluded: chain i residue 154 VAL Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain j residue 14 GLU Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 83 ARG Chi-restraints excluded: chain j residue 92 VAL Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 99 MET Chi-restraints excluded: chain j residue 131 TYR Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain j residue 149 VAL Chi-restraints excluded: chain k residue 11 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 64 LEU Chi-restraints excluded: chain k residue 71 LEU Chi-restraints excluded: chain k residue 76 VAL Chi-restraints excluded: chain k residue 129 THR Chi-restraints excluded: chain k residue 134 SER Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 30 ILE Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 43 THR Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 48 MET Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain o residue 88 GLU Chi-restraints excluded: chain o residue 116 LEU Chi-restraints excluded: chain o residue 127 ASP Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 29 ASN Chi-restraints excluded: chain p residue 58 VAL Chi-restraints excluded: chain p residue 63 VAL Chi-restraints excluded: chain p residue 120 GLU Chi-restraints excluded: chain q residue 57 THR Chi-restraints excluded: chain q residue 60 MET Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 68 GLN Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 115 LEU Chi-restraints excluded: chain r residue 75 THR Chi-restraints excluded: chain r residue 120 ILE Chi-restraints excluded: chain s residue 3 HIS Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 38 VAL Chi-restraints excluded: chain s residue 44 LEU Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 73 VAL Chi-restraints excluded: chain s residue 107 ASP Chi-restraints excluded: chain s residue 117 VAL Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 35 ILE Chi-restraints excluded: chain t residue 36 TYR Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 88 ASP Chi-restraints excluded: chain t residue 95 HIS Chi-restraints excluded: chain t residue 98 VAL Chi-restraints excluded: chain u residue 6 LEU Chi-restraints excluded: chain u residue 27 THR Chi-restraints excluded: chain u residue 107 ASP Chi-restraints excluded: chain u residue 123 GLN Chi-restraints excluded: chain u residue 124 ASP Chi-restraints excluded: chain v residue 16 LYS Chi-restraints excluded: chain v residue 18 LEU Chi-restraints excluded: chain v residue 29 SER Chi-restraints excluded: chain v residue 69 CYS Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain w residue 22 VAL Chi-restraints excluded: chain w residue 37 VAL Chi-restraints excluded: chain w residue 39 LEU Chi-restraints excluded: chain w residue 45 THR Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 49 THR Chi-restraints excluded: chain w residue 88 ARG Chi-restraints excluded: chain x residue 6 ILE Chi-restraints excluded: chain x residue 13 SER Chi-restraints excluded: chain x residue 53 SER Chi-restraints excluded: chain x residue 66 GLU Chi-restraints excluded: chain x residue 76 VAL Chi-restraints excluded: chain x residue 103 ILE Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 7 VAL Chi-restraints excluded: chain y residue 9 LEU Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain y residue 52 VAL Chi-restraints excluded: chain y residue 87 GLN Chi-restraints excluded: chain z residue 24 VAL Chi-restraints excluded: chain z residue 38 ILE Chi-restraints excluded: chain z residue 55 TYR Chi-restraints excluded: chain z residue 75 ILE Chi-restraints excluded: chain z residue 85 VAL Chi-restraints excluded: chain z residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 664 optimal weight: 2.9990 chunk 1069 optimal weight: 1.9990 chunk 652 optimal weight: 20.0000 chunk 507 optimal weight: 6.9990 chunk 743 optimal weight: 2.9990 chunk 1121 optimal weight: 6.9990 chunk 1032 optimal weight: 0.7980 chunk 893 optimal weight: 0.7980 chunk 92 optimal weight: 20.0000 chunk 689 optimal weight: 0.0970 chunk 547 optimal weight: 3.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 7 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 HIS ** M 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 HIS P 26 GLN P 94 ASN ** S 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 65 ASN ** X 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN ** d 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 13 ASN ** r 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 166981 Z= 0.161 Angle : 0.627 27.112 248612 Z= 0.310 Chirality : 0.037 1.965 31393 Planarity : 0.005 0.111 14372 Dihedral : 24.329 179.447 81164 Min Nonbonded Distance : 1.160 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.74 % Favored : 87.06 % Rotamer: Outliers : 5.03 % Allowed : 26.23 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.08 % Twisted Proline : 2.33 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.10), residues: 6592 helix: -1.28 (0.12), residues: 1605 sheet: -1.99 (0.15), residues: 1010 loop : -2.85 (0.09), residues: 3977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP i 39 HIS 0.008 0.001 HIS N 53 PHE 0.028 0.002 PHE j 125 TYR 0.040 0.002 TYR j 12 ARG 0.016 0.001 ARG P 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13184 Ramachandran restraints generated. 6592 Oldfield, 0 Emsley, 6592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1208 time to evaluate : 7.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 7 6 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5295 (tt) REVERT: A 68 ILE cc_start: 0.7864 (mm) cc_final: 0.7493 (tt) REVERT: A 97 TRP cc_start: 0.7505 (t-100) cc_final: 0.7027 (t-100) REVERT: A 101 MET cc_start: 0.6524 (mtt) cc_final: 0.5938 (mtt) REVERT: A 226 ARG cc_start: 0.5615 (ptt-90) cc_final: 0.5313 (ptt-90) REVERT: B 3 ASN cc_start: 0.4071 (OUTLIER) cc_final: 0.3173 (p0) REVERT: C 21 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7850 (pp) REVERT: C 75 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7957 (m-80) REVERT: C 116 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6298 (tp40) REVERT: C 120 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7657 (mm) REVERT: C 126 ILE cc_start: 0.8461 (mp) cc_final: 0.7788 (tp) REVERT: D 68 GLU cc_start: 0.8152 (mp0) cc_final: 0.7769 (mp0) REVERT: F 43 PHE cc_start: 0.4448 (OUTLIER) cc_final: 0.4235 (m-80) REVERT: F 51 GLN cc_start: 0.6184 (tp40) cc_final: 0.5333 (tp40) REVERT: G 102 ARG cc_start: 0.6884 (mpt180) cc_final: 0.6321 (mtt180) REVERT: G 116 LYS cc_start: 0.6470 (OUTLIER) cc_final: 0.5638 (mtmt) REVERT: G 138 TRP cc_start: 0.7317 (p-90) cc_final: 0.6901 (p-90) REVERT: H 128 ARG cc_start: 0.0402 (OUTLIER) cc_final: 0.0145 (pmt100) REVERT: I 24 VAL cc_start: 0.3163 (t) cc_final: 0.2715 (t) REVERT: K 19 ARG cc_start: 0.7119 (mmp80) cc_final: 0.6818 (tpp80) REVERT: K 20 LYS cc_start: 0.6797 (pmmt) cc_final: 0.6467 (pmmt) REVERT: K 57 LYS cc_start: 0.8383 (mtmm) cc_final: 0.8037 (mtmm) REVERT: K 77 LEU cc_start: 0.6345 (OUTLIER) cc_final: 0.5785 (mt) REVERT: K 111 LYS cc_start: 0.7764 (pptt) cc_final: 0.7389 (pptt) REVERT: K 114 LYS cc_start: 0.6364 (OUTLIER) cc_final: 0.6153 (ptpp) REVERT: L 21 TYR cc_start: 0.3103 (OUTLIER) cc_final: 0.0075 (m-80) REVERT: L 39 ILE cc_start: -0.1049 (OUTLIER) cc_final: -0.1535 (mp) REVERT: M 45 ARG cc_start: 0.4537 (OUTLIER) cc_final: 0.3494 (mtm180) REVERT: O 50 LYS cc_start: 0.7373 (tmtt) cc_final: 0.7148 (mmtm) REVERT: O 52 ASP cc_start: 0.7360 (t0) cc_final: 0.7134 (t0) REVERT: P 75 ARG cc_start: 0.7194 (ttp80) cc_final: 0.6762 (ttp80) REVERT: S 72 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6385 (tp) REVERT: U 73 PHE cc_start: 0.6194 (OUTLIER) cc_final: 0.5772 (t80) REVERT: U 317 MET cc_start: 0.6352 (pmm) cc_final: 0.5190 (ptt) REVERT: U 351 ARG cc_start: 0.5932 (ttp80) cc_final: 0.5727 (ttm-80) REVERT: U 507 TYR cc_start: 0.5444 (t80) cc_final: 0.5198 (t80) REVERT: U 610 VAL cc_start: 0.6829 (OUTLIER) cc_final: 0.6569 (p) REVERT: U 634 MET cc_start: 0.5813 (OUTLIER) cc_final: 0.5387 (mtp) REVERT: U 663 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7661 (m) REVERT: V 46 LYS cc_start: 0.8866 (mmmm) cc_final: 0.8532 (mttm) REVERT: W 57 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7158 (mm-30) REVERT: W 92 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7924 (tppt) REVERT: X 12 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8150 (tm-30) REVERT: X 55 ARG cc_start: 0.8022 (mpt-90) cc_final: 0.7706 (mpt-90) REVERT: a 39 MET cc_start: 0.8064 (mmt) cc_final: 0.7772 (mmp) REVERT: a 44 THR cc_start: 0.9110 (m) cc_final: 0.8800 (m) REVERT: a 51 TYR cc_start: 0.5738 (OUTLIER) cc_final: 0.5351 (t80) REVERT: b 37 ARG cc_start: 0.8529 (mmp80) cc_final: 0.8148 (mmp-170) REVERT: c 22 MET cc_start: 0.8152 (mmm) cc_final: 0.7654 (tmm) REVERT: c 23 ARG cc_start: 0.8379 (ptp90) cc_final: 0.7861 (ptp90) REVERT: g 31 LYS cc_start: 0.7696 (ptmt) cc_final: 0.6968 (mmtm) REVERT: g 88 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8385 (mtm-85) REVERT: g 151 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8288 (mtmt) REVERT: h 52 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.6473 (tt) REVERT: h 76 ARG cc_start: 0.7255 (mmt90) cc_final: 0.6847 (mmt180) REVERT: h 100 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7703 (mm-30) REVERT: h 168 MET cc_start: 0.7953 (mtm) cc_final: 0.7555 (mtp) REVERT: h 177 PRO cc_start: 0.8609 (Cg_exo) cc_final: 0.8283 (Cg_endo) REVERT: h 182 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8743 (tt) REVERT: h 192 ASN cc_start: 0.8417 (m-40) cc_final: 0.8064 (m110) REVERT: i 100 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8646 (p) REVERT: i 110 LEU cc_start: 0.9576 (tp) cc_final: 0.9307 (tp) REVERT: i 112 MET cc_start: 0.7564 (ttm) cc_final: 0.7189 (ttp) REVERT: i 179 GLU cc_start: 0.8185 (pp20) cc_final: 0.7544 (pp20) REVERT: j 133 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.6968 (mt) REVERT: j 148 MET cc_start: 0.7375 (tmm) cc_final: 0.6738 (tpt) REVERT: k 44 VAL cc_start: 0.5683 (OUTLIER) cc_final: 0.5178 (t) REVERT: k 51 ARG cc_start: 0.7023 (mmt90) cc_final: 0.5979 (mmp-170) REVERT: k 121 ILE cc_start: 0.8077 (mm) cc_final: 0.7865 (mm) REVERT: o 48 MET cc_start: 0.7511 (ptm) cc_final: 0.7245 (ptp) REVERT: p 18 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8524 (ttpt) REVERT: p 66 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8198 (mttt) REVERT: p 105 GLU cc_start: 0.8558 (mp0) cc_final: 0.8172 (mp0) REVERT: p 107 ARG cc_start: 0.7912 (ttm110) cc_final: 0.7545 (mtm-85) REVERT: p 120 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: q 81 GLN cc_start: 0.7292 (tp-100) cc_final: 0.6885 (tp-100) REVERT: s 115 GLU cc_start: 0.8147 (pt0) cc_final: 0.7921 (pt0) REVERT: t 75 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6802 (mp0) REVERT: t 88 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.7025 (p0) REVERT: t 95 HIS cc_start: 0.7178 (OUTLIER) cc_final: 0.6877 (t-170) REVERT: u 45 PHE cc_start: 0.8991 (t80) cc_final: 0.8759 (t80) REVERT: v 84 LYS cc_start: 0.8316 (mmtm) cc_final: 0.7607 (mttt) REVERT: w 60 GLU cc_start: 0.8401 (pm20) cc_final: 0.7686 (pt0) REVERT: x 20 VAL cc_start: 0.8851 (p) cc_final: 0.8557 (t) REVERT: x 110 LYS cc_start: 0.7177 (mtmt) cc_final: 0.6822 (tttm) REVERT: y 87 GLN cc_start: 0.5856 (OUTLIER) cc_final: 0.5440 (mp10) REVERT: z 38 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.6297 (mt) REVERT: z 55 TYR cc_start: 0.4741 (OUTLIER) cc_final: 0.3260 (p90) outliers start: 280 outliers final: 206 residues processed: 1378 average time/residue: 1.3987 time to fit residues: 3297.4181 Evaluate side-chains 1396 residues out of total 5582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1158 time to evaluate : 9.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 3 TYR Chi-restraints excluded: chain 6 residue 41 LEU Chi-restraints excluded: chain 6 residue 42 VAL Chi-restraints excluded: chain 6 residue 48 PHE Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 61 LEU Chi-restraints excluded: chain 6 residue 74 VAL Chi-restraints excluded: chain 6 residue 120 ILE Chi-restraints excluded: chain 6 residue 129 SER Chi-restraints excluded: chain 6 residue 155 LEU Chi-restraints excluded: chain 6 residue 163 LEU Chi-restraints excluded: chain 7 residue 6 LEU Chi-restraints excluded: chain 7 residue 19 VAL Chi-restraints excluded: chain 7 residue 38 LEU Chi-restraints excluded: chain 7 residue 68 LEU Chi-restraints excluded: chain 7 residue 75 LEU Chi-restraints excluded: chain 7 residue 101 LEU Chi-restraints excluded: chain 7 residue 109 ILE Chi-restraints excluded: chain 7 residue 114 LEU Chi-restraints excluded: chain 7 residue 123 LEU Chi-restraints excluded: chain 7 residue 136 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain B residue 3 ASN Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 203 PHE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 43 PHE Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 128 ARG Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 77 LEU Chi-restraints excluded: chain K residue 114 LYS Chi-restraints excluded: chain K residue 116 SER Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 21 TYR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 103 THR Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 40 SER Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain P residue 51 TYR Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 94 ASN Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain U residue 21 ILE Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 28 THR Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain U residue 73 PHE Chi-restraints excluded: chain U residue 146 LEU Chi-restraints excluded: chain U residue 160 ARG Chi-restraints excluded: chain U residue 188 TYR Chi-restraints excluded: chain U residue 250 THR Chi-restraints excluded: chain U residue 260 LEU Chi-restraints excluded: chain U residue 304 ASP Chi-restraints excluded: chain U residue 326 THR Chi-restraints excluded: chain U residue 359 HIS Chi-restraints excluded: chain U residue 369 LEU Chi-restraints excluded: chain U residue 377 VAL Chi-restraints excluded: chain U residue 378 VAL Chi-restraints excluded: chain U residue 388 THR Chi-restraints excluded: chain U residue 389 LEU Chi-restraints excluded: chain U residue 481 VAL Chi-restraints excluded: chain U residue 610 VAL Chi-restraints excluded: chain U residue 631 ILE Chi-restraints excluded: chain U residue 634 MET Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain U residue 668 SER Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 92 LYS Chi-restraints excluded: chain X residue 10 LEU Chi-restraints excluded: chain X residue 37 PHE Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Y residue 18 ASP Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain a residue 19 ARG Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 51 TYR Chi-restraints excluded: chain b residue 20 ASN Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain d residue 34 TRP Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 12 ASP Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 26 ILE Chi-restraints excluded: chain f residue 117 THR Chi-restraints excluded: chain f residue 223 VAL Chi-restraints excluded: chain g residue 16 MET Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 49 ILE Chi-restraints excluded: chain g residue 94 LEU Chi-restraints excluded: chain g residue 118 VAL Chi-restraints excluded: chain g residue 145 VAL Chi-restraints excluded: chain g residue 222 ARG Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain g residue 257 LEU Chi-restraints excluded: chain g residue 268 ARG Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 52 LEU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 171 GLU Chi-restraints excluded: chain h residue 182 LEU Chi-restraints excluded: chain i residue 3 GLU Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 50 SER Chi-restraints excluded: chain i residue 78 ILE Chi-restraints excluded: chain i residue 100 THR Chi-restraints excluded: chain i residue 123 LEU Chi-restraints excluded: chain i residue 125 LEU Chi-restraints excluded: chain i residue 154 VAL Chi-restraints excluded: chain i residue 173 VAL Chi-restraints excluded: chain j residue 53 LEU Chi-restraints excluded: chain j residue 83 ARG Chi-restraints excluded: chain j residue 92 VAL Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 99 MET Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain j residue 149 VAL Chi-restraints excluded: chain k residue 11 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 71 LEU Chi-restraints excluded: chain k residue 129 THR Chi-restraints excluded: chain k residue 134 SER Chi-restraints excluded: chain o residue 15 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 30 ILE Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 43 THR Chi-restraints excluded: chain o residue 46 VAL Chi-restraints excluded: chain o residue 53 VAL Chi-restraints excluded: chain p residue 22 ILE Chi-restraints excluded: chain p residue 58 VAL Chi-restraints excluded: chain p residue 108 GLU Chi-restraints excluded: chain p residue 120 GLU Chi-restraints excluded: chain q residue 57 THR Chi-restraints excluded: chain q residue 60 MET Chi-restraints excluded: chain q residue 62 LEU Chi-restraints excluded: chain q residue 68 GLN Chi-restraints excluded: chain q residue 75 ILE Chi-restraints excluded: chain q residue 85 LEU Chi-restraints excluded: chain q residue 115 LEU Chi-restraints excluded: chain r residue 75 THR Chi-restraints excluded: chain s residue 3 HIS Chi-restraints excluded: chain s residue 20 LEU Chi-restraints excluded: chain s residue 38 VAL Chi-restraints excluded: chain s residue 54 LEU Chi-restraints excluded: chain s residue 73 VAL Chi-restraints excluded: chain s residue 107 ASP Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 36 TYR Chi-restraints excluded: chain t residue 49 VAL Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 88 ASP Chi-restraints excluded: chain t residue 95 HIS Chi-restraints excluded: chain t residue 98 VAL Chi-restraints excluded: chain u residue 6 LEU Chi-restraints excluded: chain u residue 44 ASP Chi-restraints excluded: chain u residue 123 GLN Chi-restraints excluded: chain u residue 124 ASP Chi-restraints excluded: chain v residue 29 SER Chi-restraints excluded: chain v residue 83 LEU Chi-restraints excluded: chain w residue 22 VAL Chi-restraints excluded: chain w residue 37 VAL Chi-restraints excluded: chain w residue 39 LEU Chi-restraints excluded: chain w residue 45 THR Chi-restraints excluded: chain w residue 47 VAL Chi-restraints excluded: chain w residue 88 ARG Chi-restraints excluded: chain x residue 13 SER Chi-restraints excluded: chain x residue 53 SER Chi-restraints excluded: chain x residue 66 GLU Chi-restraints excluded: chain x residue 76 VAL Chi-restraints excluded: chain x residue 78 GLU Chi-restraints excluded: chain y residue 3 THR Chi-restraints excluded: chain y residue 7 VAL Chi-restraints excluded: chain y residue 9 LEU Chi-restraints excluded: chain y residue 14 SER Chi-restraints excluded: chain y residue 35 THR Chi-restraints excluded: chain y residue 52 VAL Chi-restraints excluded: chain y residue 87 GLN Chi-restraints excluded: chain z residue 24 VAL Chi-restraints excluded: chain z residue 38 ILE Chi-restraints excluded: chain z residue 55 TYR Chi-restraints excluded: chain z residue 75 ILE Chi-restraints excluded: chain z residue 85 VAL Chi-restraints excluded: chain z residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1126 random chunks: chunk 709 optimal weight: 6.9990 chunk 951 optimal weight: 9.9990 chunk 273 optimal weight: 20.0000 chunk 823 optimal weight: 0.8980 chunk 131 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 894 optimal weight: 7.9990 chunk 374 optimal weight: 30.0000 chunk 918 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 34 ASN ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 HIS P 26 GLN ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 ASN ** S 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 ASN ** V 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 48 HIS X 65 ASN c 36 GLN ** d 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 201 HIS g 203 ASN h 48 GLN ** i 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 130 ASN ** k 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 70 GLN ** r 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.135724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.107370 restraints weight = 376187.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.107951 restraints weight = 246826.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.108307 restraints weight = 145596.266| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.136 166981 Z= 0.397 Angle : 0.807 27.937 248612 Z= 0.395 Chirality : 0.044 1.932 31393 Planarity : 0.007 0.112 14372 Dihedral : 24.440 179.549 81164 Min Nonbonded Distance : 1.070 Molprobity Statistics. All-atom Clashscore : 22.01 Ramachandran Plot: Outliers : 0.26 % Allowed : 14.90 % Favored : 84.85 % Rotamer: Outliers : 5.30 % Allowed : 26.23 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.08 % Twisted Proline : 2.33 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.09), residues: 6592 helix: -1.50 (0.12), residues: 1625 sheet: -2.27 (0.15), residues: 1009 loop : -2.97 (0.09), residues: 3958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.003 TRP i 39 HIS 0.011 0.002 HIS N 53 PHE 0.031 0.002 PHE A 105 TYR 0.053 0.003 TYR F 151 ARG 0.020 0.001 ARG i 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47225.93 seconds wall clock time: 821 minutes 37.71 seconds (49297.71 seconds total)