Starting phenix.real_space_refine on Sat Mar 16 02:08:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbx_19038/03_2024/8rbx_19038.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbx_19038/03_2024/8rbx_19038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbx_19038/03_2024/8rbx_19038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbx_19038/03_2024/8rbx_19038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbx_19038/03_2024/8rbx_19038.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbx_19038/03_2024/8rbx_19038.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 8 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 10 6.06 5 P 325 5.49 5 Mg 1 5.21 5 S 618 5.16 5 C 80362 2.51 5 N 23027 2.21 5 O 24881 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 370": "OD1" <-> "OD2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A ASP 1156": "OD1" <-> "OD2" Residue "A GLU 1324": "OE1" <-> "OE2" Residue "A ASP 1389": "OD1" <-> "OD2" Residue "A ASP 1423": "OD1" <-> "OD2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 432": "OE1" <-> "OE2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1004": "OD1" <-> "OD2" Residue "C TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 19": "OE1" <-> "OE2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "J GLU 19": "OE1" <-> "OE2" Residue "J ASP 33": "OD1" <-> "OD2" Residue "J ASP 36": "OD1" <-> "OD2" Residue "K PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 24": "OD1" <-> "OD2" Residue "K ASP 39": "OD1" <-> "OD2" Residue "K ASP 53": "OD1" <-> "OD2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "S ASP 123": "OD1" <-> "OD2" Residue "U GLU 53": "OE1" <-> "OE2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "W ASP 48": "OD1" <-> "OD2" Residue "a TYR 1285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 1842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 1861": "OD1" <-> "OD2" Residue "b ASP 1135": "OD1" <-> "OD2" Residue "d TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 533": "OD1" <-> "OD2" Residue "d ASP 567": "OD1" <-> "OD2" Residue "d ASP 628": "OD1" <-> "OD2" Residue "d TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 844": "OD1" <-> "OD2" Residue "e GLU 905": "OE1" <-> "OE2" Residue "e GLU 929": "OE1" <-> "OE2" Residue "f GLU 201": "OE1" <-> "OE2" Residue "f GLU 315": "OE1" <-> "OE2" Residue "f TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 156": "OE1" <-> "OE2" Residue "g GLU 567": "OE1" <-> "OE2" Residue "g GLU 757": "OE1" <-> "OE2" Residue "g TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 907": "OE1" <-> "OE2" Residue "h TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 433": "OE1" <-> "OE2" Residue "h GLU 719": "OE1" <-> "OE2" Residue "p TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 570": "OD1" <-> "OD2" Residue "r GLU 2039": "OE1" <-> "OE2" Residue "u GLU 109": "OE1" <-> "OE2" Residue "v GLU 68": "OE1" <-> "OE2" Residue "w PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 456": "OD1" <-> "OD2" Residue "w ASP 498": "OD1" <-> "OD2" Time to flip residues: 0.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 129226 Number of models: 1 Model: "" Number of chains: 56 Chain: "1" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 11008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1391, 11008 Classifications: {'peptide': 1391} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1322} Chain breaks: 7 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 8901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8901 Classifications: {'peptide': 1112} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 1058} Chain breaks: 7 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2096 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 15, 'TRANS': 245} Chain breaks: 1 Chain: "D" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 977 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 627 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1316 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 944 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 106} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 383 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 729 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "N" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3050 Classifications: {'DNA': 148} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 147} Chain: "O" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 647 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 370 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 3} Link IDs: {'rna2p': 5, 'rna3p': 11} Chain: "Q" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "R" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 82} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "S" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 732 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 88} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "T" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 3277 Classifications: {'DNA': 161} Link IDs: {'rna3p': 160} Chain: "U" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 634 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "W" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Y" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 95 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 4, 'TRANS': 8} Chain: "Z" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2167 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 266} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "a" Number of atoms: 11692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1718, 11692 Classifications: {'peptide': 1718} Incomplete info: {'truncation_to_alanine': 560} Link IDs: {'PCIS': 1, 'PTRANS': 74, 'TRANS': 1642} Chain breaks: 20 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 2039 Unresolved non-hydrogen angles: 2606 Unresolved non-hydrogen dihedrals: 1675 Unresolved non-hydrogen chiralities: 203 Planarities with less than four sites: {'GLN:plan1': 28, 'HIS:plan': 16, 'TYR:plan': 15, 'ASN:plan1': 32, 'TRP:plan': 11, 'ASP:plan': 32, 'PHE:plan': 19, 'GLU:plan': 53, 'ARG:plan': 38} Unresolved non-hydrogen planarities: 1104 Chain: "b" Number of atoms: 7991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 7991 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 52, 'TRANS': 998} Chain breaks: 8 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 338 Unresolved non-hydrogen dihedrals: 239 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 16, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 184 Chain: "d" Number of atoms: 6407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6407 Classifications: {'peptide': 820} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 41, 'TRANS': 778} Chain breaks: 4 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "e" Number of atoms: 6260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 856, 6260 Classifications: {'peptide': 856} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 801} Chain breaks: 10 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 368 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 171 Chain: "f" Number of atoms: 4137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4137 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 45, 'TRANS': 498} Chain breaks: 6 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 95 Chain: "g" Number of atoms: 6722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 886, 6722 Classifications: {'peptide': 886} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 29, 'TRANS': 856} Chain breaks: 4 Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 167 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 123 Chain: "h" Number of atoms: 6751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 887, 6751 Classifications: {'peptide': 887} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 32, 'TRANS': 854} Chain breaks: 10 Unresolved non-hydrogen bonds: 390 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 316 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 23, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 231 Chain: "i" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4870 Classifications: {'peptide': 626} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 47, 'TRANS': 578} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 52 Chain: "j" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 3313 Classifications: {'peptide': 668} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 599} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 648} Chain breaks: 3 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 2247 Unresolved non-hydrogen angles: 2873 Unresolved non-hydrogen dihedrals: 1878 Unresolved non-hydrogen chiralities: 198 Planarities with less than four sites: {'GLN:plan1': 37, 'HIS:plan': 17, 'TYR:plan': 24, 'ASN:plan1': 33, 'TRP:plan': 10, 'ASP:plan': 29, 'PHE:plan': 31, 'GLU:plan': 51, 'ARG:plan': 41} Unresolved non-hydrogen planarities: 1272 Chain: "k" Number of atoms: 4090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4090 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 26, 'TRANS': 525} Chain breaks: 5 Unresolved non-hydrogen bonds: 299 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 249 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 191 Chain: "m" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 2864 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 475} Link IDs: {'PTRANS': 26, 'TRANS': 525} Chain breaks: 6 Unresolved chain link angles: 26 Unresolved non-hydrogen bonds: 1637 Unresolved non-hydrogen angles: 2094 Unresolved non-hydrogen dihedrals: 1356 Unresolved non-hydrogen chiralities: 155 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 24, 'TYR:plan': 13, 'ASN:plan1': 24, 'TRP:plan': 5, 'ASP:plan': 26, 'PHE:plan': 14, 'GLU:plan': 40, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 863 Chain: "n" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 2484 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 438} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 469} Chain breaks: 1 Unresolved chain link angles: 33 Unresolved non-hydrogen bonds: 1520 Unresolved non-hydrogen angles: 1950 Unresolved non-hydrogen dihedrals: 1261 Unresolved non-hydrogen chiralities: 146 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 27, 'TYR:plan': 12, 'ASN:plan1': 23, 'TRP:plan': 5, 'HIS:plan': 12, 'PHE:plan': 21, 'GLU:plan': 33, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 773 Chain: "o" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 1824 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 331} Link IDs: {'PTRANS': 18, 'TRANS': 348} Chain breaks: 2 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1130 Unresolved non-hydrogen angles: 1446 Unresolved non-hydrogen dihedrals: 920 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 21, 'TYR:plan': 9, 'ASN:plan1': 11, 'TRP:plan': 3, 'HIS:plan': 7, 'PHE:plan': 13, 'GLU:plan': 18, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 556 Chain: "p" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4431 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 26, 'TRANS': 553} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "q" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2322 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 278} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "r" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 250 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "u" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1395 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 171} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "v" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 2070 Classifications: {'peptide': 451} Incomplete info: {'backbone_only': 337, 'truncation_to_alanine': 33} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 9 Unresolved non-hydrogen bonds: 1588 Unresolved non-hydrogen angles: 2272 Unresolved non-hydrogen dihedrals: 1011 Unresolved non-hydrogen chiralities: 452 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 8, 'ASN:plan1': 8, 'TYR:plan': 8, 'UNK:plan-1': 33, 'TRP:plan': 3, 'ASP:plan': 21, 'PHE:plan': 23, 'GLU:plan': 28, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 748 Chain: "w" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3825 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 487} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 136 Chain: "x" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 808 SG CYS A 111 160.437 218.364 127.519 1.00403.76 S ATOM 836 SG CYS A 114 163.393 219.820 129.486 1.00443.30 S ATOM 1145 SG CYS A 154 159.792 221.050 128.959 1.00443.74 S ATOM 504 SG CYS A 71 157.813 170.928 132.764 1.00327.88 S ATOM 526 SG CYS A 74 156.123 170.700 136.283 1.00336.08 S ATOM 573 SG CYS A 81 154.082 171.773 133.172 1.00225.60 S ATOM 19518 SG CYS B1119 155.400 184.786 145.537 1.00310.87 S ATOM 19540 SG CYS B1122 155.795 186.734 142.104 1.00328.48 S ATOM 19655 SG CYS B1137 156.971 183.219 142.505 1.00301.35 S ATOM 19676 SG CYS B1140 158.794 185.862 144.348 1.00265.99 S ATOM 20643 SG CYS C 88 107.948 123.049 125.524 1.00155.07 S ATOM 20656 SG CYS C 90 111.162 123.301 123.819 1.00172.63 S ATOM 20691 SG CYS C 94 108.587 121.079 122.391 1.00153.04 S ATOM 20713 SG CYS C 97 108.334 124.930 122.097 1.00143.35 S ATOM 27941 SG CYS I 17 125.559 233.310 72.400 1.00290.19 S ATOM 27965 SG CYS I 20 128.473 230.906 72.844 1.00313.65 S ATOM 28126 SG CYS I 39 127.946 233.146 75.680 1.00230.09 S ATOM 28151 SG CYS I 42 129.036 234.396 72.163 1.00375.93 S ATOM 28503 SG CYS I 86 86.285 213.168 73.353 1.00245.38 S ATOM 28527 SG CYS I 89 85.520 211.416 70.007 1.00345.41 S ATOM 28725 SG CYS I 114 87.613 209.602 72.453 1.00201.69 S ATOM 28760 SG CYS I 119 88.872 212.711 70.603 1.00339.03 S ATOM 28871 SG CYS J 7 93.254 147.810 107.805 1.00156.12 S ATOM 28895 SG CYS J 10 90.610 145.566 109.380 1.00133.85 S ATOM 29159 SG CYS J 44 89.659 149.143 108.196 1.00152.66 S ATOM 29165 SG CYS J 45 90.176 146.204 105.968 1.00193.03 S ATOM 30324 SG CYS L 19 131.854 142.893 87.783 1.00265.39 S ATOM 30343 SG CYS L 22 131.468 140.765 84.468 1.00320.77 S ATOM 30460 SG CYS L 36 134.548 140.763 86.911 1.00354.49 S ATOM 30486 SG CYS L 39 133.308 143.696 84.397 1.00433.70 S Time building chain proxies: 51.42, per 1000 atoms: 0.40 Number of scatterers: 129226 At special positions: 0 Unit cell: (255.15, 331.8, 289.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 10 29.99 Mn 2 24.99 S 618 16.00 P 325 15.00 Mg 1 11.99 O 24881 8.00 N 23027 7.00 C 80362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 38.35 Conformation dependent library (CDL) restraints added in 17.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 74 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1137 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1140 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1119 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1122 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 97 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 39 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb=" ZN k1001 " pdb="ZN ZN k1001 " - pdb=" NE2 HIS k 73 " pdb="ZN ZN k1001 " - pdb=" NE2 HIS k 414 " pdb=" ZN k1002 " pdb="ZN ZN k1002 " - pdb=" NE2 HIS k 68 " pdb="ZN ZN k1002 " - pdb=" ND1 HIS k 70 " pdb="ZN ZN k1002 " - pdb=" NE2 HIS k 157 " Number of angles added : 39 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31640 Finding SS restraints... Secondary structure from input PDB file: 834 helices and 89 sheets defined 60.3% alpha, 7.3% beta 150 base pairs and 253 stacking pairs defined. Time for finding SS restraints: 35.57 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 134 removed outlier: 3.600A pdb=" N SER A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.982A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.825A pdb=" N MET A 248 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 338 through 345 removed outlier: 4.115A pdb=" N GLY A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 381 through 388 Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.591A pdb=" N GLY A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.508A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 549 removed outlier: 3.524A pdb=" N LEU A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 removed outlier: 3.656A pdb=" N MET A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.527A pdb=" N ASP A 614 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 662 through 684 removed outlier: 4.078A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.624A pdb=" N ILE A 693 " --> pdb=" O GLY A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 817 through 820 Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.115A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.582A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1079 Processing helix chain 'A' and resid 1086 through 1102 Proline residue: A1098 - end of helix Processing helix chain 'A' and resid 1119 through 1129 Processing helix chain 'A' and resid 1144 through 1149 Processing helix chain 'A' and resid 1150 through 1160 Processing helix chain 'A' and resid 1165 through 1170 Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1240 removed outlier: 3.504A pdb=" N ILE A1231 " --> pdb=" O THR A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1243 No H-bonds generated for 'chain 'A' and resid 1241 through 1243' Processing helix chain 'A' and resid 1281 through 1295 Processing helix chain 'A' and resid 1342 through 1349 Processing helix chain 'A' and resid 1362 through 1370 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 3.688A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.859A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 removed outlier: 3.600A pdb=" N ASN A1420 " --> pdb=" O ARG A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1433 Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.712A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1478 through 1483 Processing helix chain 'B' and resid 18 through 37 removed outlier: 4.482A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 281 through 289 Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.503A pdb=" N LEU B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 313 through 324 removed outlier: 4.036A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 removed outlier: 3.504A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.660A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.941A pdb=" N SER B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 552 through 556 Processing helix chain 'B' and resid 557 through 563 removed outlier: 3.815A pdb=" N ILE B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 563 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.986A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.689A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 650 Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 678 through 683 removed outlier: 3.504A pdb=" N GLN B 683 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 705 through 711 removed outlier: 3.622A pdb=" N ILE B 710 " --> pdb=" O VAL B 706 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE B 711 " --> pdb=" O CYS B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 3.960A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 844 through 848 removed outlier: 3.895A pdb=" N LYS B 847 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.797A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 116 through 120 Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 Processing helix chain 'D' and resid 23 through 29 removed outlier: 4.117A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 72 removed outlier: 3.796A pdb=" N MET D 62 " --> pdb=" O SER D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 88 removed outlier: 3.559A pdb=" N LEU D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 54 through 59 removed outlier: 3.633A pdb=" N THR E 59 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 removed outlier: 3.564A pdb=" N GLU E 97 " --> pdb=" O ARG E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.825A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 removed outlier: 3.580A pdb=" N ILE F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.741A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.550A pdb=" N GLN H 87 " --> pdb=" O ARG H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.894A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 Processing helix chain 'J' and resid 55 through 61 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.777A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.892A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 115 Processing helix chain 'M' and resid 46 through 57 Processing helix chain 'M' and resid 63 through 79 removed outlier: 3.548A pdb=" N PHE M 67 " --> pdb=" O ARG M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 Processing helix chain 'M' and resid 120 through 132 removed outlier: 4.072A pdb=" N ILE M 124 " --> pdb=" O MET M 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 29 removed outlier: 3.868A pdb=" N ILE O 29 " --> pdb=" O ILE O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 41 removed outlier: 4.250A pdb=" N ILE O 34 " --> pdb=" O THR O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 74 removed outlier: 4.548A pdb=" N TYR O 51 " --> pdb=" O SER O 47 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLU O 52 " --> pdb=" O GLY O 48 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU O 53 " --> pdb=" O LEU O 49 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY O 56 " --> pdb=" O GLU O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 through 77' Processing helix chain 'O' and resid 82 through 94 Processing helix chain 'Q' and resid 16 through 21 removed outlier: 3.580A pdb=" N ARG Q 20 " --> pdb=" O SER Q 16 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA Q 21 " --> pdb=" O ARG Q 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 16 through 21' Processing helix chain 'Q' and resid 27 through 37 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 3.635A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 removed outlier: 3.849A pdb=" N ASP Q 90 " --> pdb=" O ALA Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'Q' and resid 98 through 100 No H-bonds generated for 'chain 'Q' and resid 98 through 100' Processing helix chain 'R' and resid 39 through 46 Processing helix chain 'R' and resid 52 through 81 Processing helix chain 'R' and resid 87 through 99 removed outlier: 3.638A pdb=" N ILE R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 121 Processing helix chain 'S' and resid 45 through 57 removed outlier: 3.987A pdb=" N ARG S 49 " --> pdb=" O THR S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 79 removed outlier: 3.707A pdb=" N GLN S 68 " --> pdb=" O LYS S 64 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG S 69 " --> pdb=" O LEU S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 113 removed outlier: 3.846A pdb=" N HIS S 113 " --> pdb=" O LEU S 109 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 132 removed outlier: 3.750A pdb=" N ILE S 124 " --> pdb=" O MET S 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 39 Processing helix chain 'U' and resid 47 through 76 removed outlier: 3.536A pdb=" N TYR U 51 " --> pdb=" O SER U 47 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU U 52 " --> pdb=" O GLY U 48 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA U 76 " --> pdb=" O TYR U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 92 Processing helix chain 'V' and resid 16 through 22 removed outlier: 3.931A pdb=" N ARG V 20 " --> pdb=" O SER V 16 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 37 removed outlier: 3.775A pdb=" N LEU V 33 " --> pdb=" O ARG V 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 71 removed outlier: 3.782A pdb=" N TYR V 50 " --> pdb=" O GLY V 46 " (cutoff:3.500A) Processing helix chain 'V' and resid 72 through 74 No H-bonds generated for 'chain 'V' and resid 72 through 74' Processing helix chain 'V' and resid 79 through 89 Processing helix chain 'V' and resid 90 through 97 Processing helix chain 'W' and resid 34 through 46 removed outlier: 4.012A pdb=" N VAL W 38 " --> pdb=" O TYR W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 81 Processing helix chain 'W' and resid 88 through 99 Processing helix chain 'W' and resid 100 through 122 Processing helix chain 'Z' and resid 514 through 518 Processing helix chain 'a' and resid 118 through 120 No H-bonds generated for 'chain 'a' and resid 118 through 120' Processing helix chain 'a' and resid 121 through 133 Processing helix chain 'a' and resid 134 through 152 Processing helix chain 'a' and resid 157 through 171 Processing helix chain 'a' and resid 172 through 176 removed outlier: 3.733A pdb=" N PHE a 175 " --> pdb=" O PRO a 172 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA a 176 " --> pdb=" O ASN a 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 172 through 176' Processing helix chain 'a' and resid 177 through 189 removed outlier: 3.821A pdb=" N LEU a 188 " --> pdb=" O LEU a 184 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG a 189 " --> pdb=" O CYS a 185 " (cutoff:3.500A) Processing helix chain 'a' and resid 202 through 216 Processing helix chain 'a' and resid 224 through 236 removed outlier: 4.750A pdb=" N LYS a 228 " --> pdb=" O GLU a 224 " (cutoff:3.500A) Processing helix chain 'a' and resid 243 through 245 No H-bonds generated for 'chain 'a' and resid 243 through 245' Processing helix chain 'a' and resid 246 through 258 removed outlier: 3.594A pdb=" N ILE a 253 " --> pdb=" O PHE a 249 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ALA a 256 " --> pdb=" O ASN a 252 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE a 257 " --> pdb=" O ILE a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 321 through 339 Processing helix chain 'a' and resid 342 through 346 Processing helix chain 'a' and resid 351 through 356 removed outlier: 3.646A pdb=" N THR a 355 " --> pdb=" O ARG a 352 " (cutoff:3.500A) Processing helix chain 'a' and resid 366 through 375 Processing helix chain 'a' and resid 381 through 398 Processing helix chain 'a' and resid 403 through 410 Processing helix chain 'a' and resid 416 through 433 Processing helix chain 'a' and resid 433 through 452 Processing helix chain 'a' and resid 455 through 469 Processing helix chain 'a' and resid 472 through 488 Processing helix chain 'a' and resid 491 through 506 Processing helix chain 'a' and resid 511 through 520 Processing helix chain 'a' and resid 526 through 530 removed outlier: 3.807A pdb=" N GLU a 530 " --> pdb=" O GLN a 527 " (cutoff:3.500A) Processing helix chain 'a' and resid 531 through 548 Processing helix chain 'a' and resid 554 through 567 Processing helix chain 'a' and resid 571 through 600 removed outlier: 3.731A pdb=" N VAL a 597 " --> pdb=" O LEU a 593 " (cutoff:3.500A) Proline residue: a 598 - end of helix Processing helix chain 'a' and resid 604 through 616 removed outlier: 3.648A pdb=" N LEU a 616 " --> pdb=" O LEU a 612 " (cutoff:3.500A) Processing helix chain 'a' and resid 635 through 643 removed outlier: 4.320A pdb=" N PHE a 639 " --> pdb=" O ASP a 635 " (cutoff:3.500A) Processing helix chain 'a' and resid 650 through 662 removed outlier: 4.165A pdb=" N SER a 662 " --> pdb=" O VAL a 658 " (cutoff:3.500A) Processing helix chain 'a' and resid 668 through 685 Processing helix chain 'a' and resid 699 through 712 Processing helix chain 'a' and resid 730 through 738 Processing helix chain 'a' and resid 739 through 741 No H-bonds generated for 'chain 'a' and resid 739 through 741' Processing helix chain 'a' and resid 754 through 760 Processing helix chain 'a' and resid 760 through 774 Processing helix chain 'a' and resid 782 through 815 Processing helix chain 'a' and resid 849 through 860 Processing helix chain 'a' and resid 947 through 956 removed outlier: 4.189A pdb=" N ASP a 956 " --> pdb=" O GLY a 952 " (cutoff:3.500A) Processing helix chain 'a' and resid 964 through 976 removed outlier: 3.501A pdb=" N THR a 968 " --> pdb=" O ASP a 964 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL a 971 " --> pdb=" O THR a 967 " (cutoff:3.500A) Processing helix chain 'a' and resid 977 through 981 Processing helix chain 'a' and resid 983 through 999 Processing helix chain 'a' and resid 1026 through 1032 removed outlier: 3.712A pdb=" N LEU a1030 " --> pdb=" O TYR a1026 " (cutoff:3.500A) Processing helix chain 'a' and resid 1036 through 1040 Processing helix chain 'a' and resid 1042 through 1057 removed outlier: 3.824A pdb=" N THR a1046 " --> pdb=" O VAL a1042 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N HIS a1055 " --> pdb=" O GLN a1051 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET a1056 " --> pdb=" O GLN a1052 " (cutoff:3.500A) Processing helix chain 'a' and resid 1059 through 1073 Processing helix chain 'a' and resid 1078 through 1096 removed outlier: 3.537A pdb=" N ARG a1096 " --> pdb=" O LEU a1092 " (cutoff:3.500A) Processing helix chain 'a' and resid 1097 through 1104 Processing helix chain 'a' and resid 1110 through 1134 Processing helix chain 'a' and resid 1164 through 1174 removed outlier: 3.666A pdb=" N LEU a1174 " --> pdb=" O MET a1170 " (cutoff:3.500A) Processing helix chain 'a' and resid 1183 through 1194 Processing helix chain 'a' and resid 1216 through 1226 removed outlier: 3.857A pdb=" N ARG a1222 " --> pdb=" O TRP a1218 " (cutoff:3.500A) Processing helix chain 'a' and resid 1228 through 1237 removed outlier: 3.516A pdb=" N GLN a1237 " --> pdb=" O ASP a1233 " (cutoff:3.500A) Processing helix chain 'a' and resid 1240 through 1249 Processing helix chain 'a' and resid 1254 through 1272 Processing helix chain 'a' and resid 1272 through 1280 removed outlier: 4.210A pdb=" N LEU a1276 " --> pdb=" O ASP a1272 " (cutoff:3.500A) Processing helix chain 'a' and resid 1283 through 1296 Processing helix chain 'a' and resid 1301 through 1312 removed outlier: 3.834A pdb=" N SER a1311 " --> pdb=" O LEU a1307 " (cutoff:3.500A) Processing helix chain 'a' and resid 1361 through 1369 Processing helix chain 'a' and resid 1374 through 1393 Processing helix chain 'a' and resid 1402 through 1415 Processing helix chain 'a' and resid 1421 through 1427 removed outlier: 3.698A pdb=" N ARG a1427 " --> pdb=" O MET a1423 " (cutoff:3.500A) Processing helix chain 'a' and resid 1428 through 1446 Proline residue: a1434 - end of helix Processing helix chain 'a' and resid 1451 through 1468 Processing helix chain 'a' and resid 1469 through 1473 Processing helix chain 'a' and resid 1475 through 1492 removed outlier: 3.543A pdb=" N ARG a1492 " --> pdb=" O ALA a1488 " (cutoff:3.500A) Processing helix chain 'a' and resid 1496 through 1510 removed outlier: 3.595A pdb=" N GLY a1500 " --> pdb=" O ASP a1496 " (cutoff:3.500A) Processing helix chain 'a' and resid 1513 through 1530 Processing helix chain 'a' and resid 1537 through 1552 Processing helix chain 'a' and resid 1555 through 1565 Processing helix chain 'a' and resid 1579 through 1589 Processing helix chain 'a' and resid 1614 through 1626 Processing helix chain 'a' and resid 1633 through 1642 removed outlier: 3.549A pdb=" N GLN a1637 " --> pdb=" O CYS a1633 " (cutoff:3.500A) Processing helix chain 'a' and resid 1656 through 1668 removed outlier: 3.808A pdb=" N SER a1668 " --> pdb=" O PHE a1664 " (cutoff:3.500A) Processing helix chain 'a' and resid 1669 through 1683 Processing helix chain 'a' and resid 1690 through 1703 Processing helix chain 'a' and resid 1704 through 1709 removed outlier: 3.746A pdb=" N TRP a1708 " --> pdb=" O VAL a1704 " (cutoff:3.500A) Processing helix chain 'a' and resid 1728 through 1748 removed outlier: 3.734A pdb=" N GLN a1748 " --> pdb=" O GLU a1744 " (cutoff:3.500A) Processing helix chain 'a' and resid 1755 through 1761 Processing helix chain 'a' and resid 1761 through 1770 Processing helix chain 'a' and resid 1772 through 1791 Processing helix chain 'a' and resid 1793 through 1810 Processing helix chain 'a' and resid 1818 through 1824 Processing helix chain 'a' and resid 1825 through 1829 removed outlier: 3.631A pdb=" N ALA a1828 " --> pdb=" O GLU a1825 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER a1829 " --> pdb=" O GLY a1826 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1825 through 1829' Processing helix chain 'a' and resid 1835 through 1848 removed outlier: 3.501A pdb=" N ASP a1848 " --> pdb=" O THR a1844 " (cutoff:3.500A) Processing helix chain 'a' and resid 1852 through 1873 Processing helix chain 'a' and resid 1873 through 1879 removed outlier: 4.146A pdb=" N LEU a1877 " --> pdb=" O HIS a1873 " (cutoff:3.500A) Processing helix chain 'a' and resid 1880 through 1891 removed outlier: 3.607A pdb=" N ILE a1884 " --> pdb=" O HIS a1880 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY a1890 " --> pdb=" O ALA a1886 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG a1891 " --> pdb=" O LEU a1887 " (cutoff:3.500A) Processing helix chain 'a' and resid 1895 through 1902 Processing helix chain 'a' and resid 1904 through 1919 removed outlier: 3.522A pdb=" N GLN a1919 " --> pdb=" O LEU a1915 " (cutoff:3.500A) Processing helix chain 'a' and resid 1924 through 1945 Processing helix chain 'a' and resid 1948 through 1951 removed outlier: 4.385A pdb=" N HIS a1951 " --> pdb=" O SER a1948 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1948 through 1951' Processing helix chain 'a' and resid 1952 through 1970 Processing helix chain 'a' and resid 1970 through 1981 Processing helix chain 'a' and resid 1981 through 1992 removed outlier: 3.562A pdb=" N LEU a1985 " --> pdb=" O HIS a1981 " (cutoff:3.500A) Processing helix chain 'a' and resid 1995 through 2005 removed outlier: 3.655A pdb=" N LYS a1999 " --> pdb=" O LEU a1995 " (cutoff:3.500A) Processing helix chain 'a' and resid 2043 through 2056 removed outlier: 3.618A pdb=" N MET a2047 " --> pdb=" O THR a2043 " (cutoff:3.500A) Proline residue: a2049 - end of helix Processing helix chain 'a' and resid 2059 through 2077 Processing helix chain 'a' and resid 2078 through 2083 removed outlier: 3.611A pdb=" N LEU a2081 " --> pdb=" O PRO a2078 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER a2082 " --> pdb=" O GLU a2079 " (cutoff:3.500A) Processing helix chain 'a' and resid 2084 through 2092 removed outlier: 3.500A pdb=" N ARG a2090 " --> pdb=" O THR a2086 " (cutoff:3.500A) Processing helix chain 'a' and resid 2096 through 2114 Processing helix chain 'a' and resid 2116 through 2120 removed outlier: 3.821A pdb=" N ALA a2119 " --> pdb=" O SER a2116 " (cutoff:3.500A) Processing helix chain 'a' and resid 2121 through 2131 Processing helix chain 'a' and resid 2133 through 2143 Processing helix chain 'a' and resid 2143 through 2150 Processing helix chain 'a' and resid 2154 through 2169 Processing helix chain 'a' and resid 2173 through 2189 Processing helix chain 'b' and resid 19 through 29 Processing helix chain 'b' and resid 30 through 35 Processing helix chain 'b' and resid 38 through 55 removed outlier: 4.278A pdb=" N LEU b 44 " --> pdb=" O PRO b 40 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU b 45 " --> pdb=" O GLU b 41 " (cutoff:3.500A) Proline residue: b 47 - end of helix removed outlier: 3.553A pdb=" N CYS b 55 " --> pdb=" O ARG b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 61 through 75 Processing helix chain 'b' and resid 76 through 79 removed outlier: 5.583A pdb=" N GLU b 79 " --> pdb=" O SER b 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 76 through 79' Processing helix chain 'b' and resid 80 through 89 removed outlier: 3.703A pdb=" N ILE b 84 " --> pdb=" O ALA b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 107 removed outlier: 3.908A pdb=" N LEU b 95 " --> pdb=" O ASP b 91 " (cutoff:3.500A) Processing helix chain 'b' and resid 126 through 132 Processing helix chain 'b' and resid 134 through 156 Processing helix chain 'b' and resid 174 through 188 Processing helix chain 'b' and resid 193 through 204 Processing helix chain 'b' and resid 206 through 218 removed outlier: 4.102A pdb=" N PHE b 210 " --> pdb=" O ASN b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 231 removed outlier: 3.626A pdb=" N LYS b 231 " --> pdb=" O ARG b 227 " (cutoff:3.500A) Processing helix chain 'b' and resid 240 through 257 Processing helix chain 'b' and resid 260 through 272 Processing helix chain 'b' and resid 274 through 286 removed outlier: 3.553A pdb=" N GLY b 278 " --> pdb=" O LEU b 274 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR b 286 " --> pdb=" O THR b 282 " (cutoff:3.500A) Processing helix chain 'b' and resid 296 through 308 Processing helix chain 'b' and resid 310 through 327 Processing helix chain 'b' and resid 334 through 351 removed outlier: 3.842A pdb=" N GLN b 338 " --> pdb=" O SER b 334 " (cutoff:3.500A) Processing helix chain 'b' and resid 380 through 398 removed outlier: 4.510A pdb=" N LYS b 384 " --> pdb=" O GLU b 380 " (cutoff:3.500A) Processing helix chain 'b' and resid 404 through 416 Processing helix chain 'b' and resid 422 through 439 Processing helix chain 'b' and resid 440 through 443 Processing helix chain 'b' and resid 445 through 462 Processing helix chain 'b' and resid 476 through 489 Processing helix chain 'b' and resid 491 through 504 Processing helix chain 'b' and resid 511 through 524 Processing helix chain 'b' and resid 527 through 538 removed outlier: 3.815A pdb=" N ARG b 537 " --> pdb=" O ALA b 533 " (cutoff:3.500A) Processing helix chain 'b' and resid 552 through 563 Processing helix chain 'b' and resid 564 through 569 Processing helix chain 'b' and resid 573 through 583 Processing helix chain 'b' and resid 591 through 604 Processing helix chain 'b' and resid 615 through 623 Processing helix chain 'b' and resid 644 through 665 Processing helix chain 'b' and resid 666 through 669 removed outlier: 3.541A pdb=" N LEU b 669 " --> pdb=" O THR b 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 666 through 669' Processing helix chain 'b' and resid 680 through 687 Processing helix chain 'b' and resid 688 through 699 Processing helix chain 'b' and resid 699 through 704 removed outlier: 3.738A pdb=" N LEU b 703 " --> pdb=" O LEU b 699 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY b 704 " --> pdb=" O GLN b 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 699 through 704' Processing helix chain 'b' and resid 704 through 718 removed outlier: 4.081A pdb=" N SER b 708 " --> pdb=" O GLY b 704 " (cutoff:3.500A) Processing helix chain 'b' and resid 719 through 722 Processing helix chain 'b' and resid 723 through 729 removed outlier: 3.540A pdb=" N CYS b 729 " --> pdb=" O ASP b 725 " (cutoff:3.500A) Processing helix chain 'b' and resid 735 through 745 removed outlier: 3.653A pdb=" N LEU b 745 " --> pdb=" O ARG b 741 " (cutoff:3.500A) Processing helix chain 'b' and resid 748 through 752 Processing helix chain 'b' and resid 753 through 763 Processing helix chain 'b' and resid 767 through 779 Processing helix chain 'b' and resid 786 through 788 No H-bonds generated for 'chain 'b' and resid 786 through 788' Processing helix chain 'b' and resid 789 through 796 Processing helix chain 'b' and resid 796 through 801 removed outlier: 3.753A pdb=" N LEU b 800 " --> pdb=" O ASN b 796 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU b 801 " --> pdb=" O MET b 797 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 796 through 801' Processing helix chain 'b' and resid 806 through 821 Processing helix chain 'b' and resid 824 through 834 removed outlier: 3.537A pdb=" N ASN b 834 " --> pdb=" O VAL b 830 " (cutoff:3.500A) Processing helix chain 'b' and resid 835 through 837 No H-bonds generated for 'chain 'b' and resid 835 through 837' Processing helix chain 'b' and resid 849 through 856 Processing helix chain 'b' and resid 857 through 863 removed outlier: 3.612A pdb=" N CYS b 863 " --> pdb=" O VAL b 860 " (cutoff:3.500A) Processing helix chain 'b' and resid 864 through 869 removed outlier: 3.599A pdb=" N VAL b 867 " --> pdb=" O ASP b 864 " (cutoff:3.500A) Processing helix chain 'b' and resid 870 through 901 removed outlier: 3.641A pdb=" N SER b 893 " --> pdb=" O LYS b 889 " (cutoff:3.500A) Processing helix chain 'b' and resid 923 through 946 Processing helix chain 'b' and resid 949 through 954 Processing helix chain 'b' and resid 988 through 1008 Processing helix chain 'b' and resid 1008 through 1019 removed outlier: 3.822A pdb=" N ALA b1012 " --> pdb=" O ASP b1008 " (cutoff:3.500A) Processing helix chain 'b' and resid 1021 through 1023 No H-bonds generated for 'chain 'b' and resid 1021 through 1023' Processing helix chain 'b' and resid 1024 through 1032 removed outlier: 3.633A pdb=" N ILE b1032 " --> pdb=" O THR b1028 " (cutoff:3.500A) Processing helix chain 'b' and resid 1033 through 1040 removed outlier: 4.094A pdb=" N HIS b1036 " --> pdb=" O PRO b1033 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE b1037 " --> pdb=" O SER b1034 " (cutoff:3.500A) Processing helix chain 'b' and resid 1041 through 1047 Processing helix chain 'b' and resid 1050 through 1068 Processing helix chain 'b' and resid 1070 through 1087 Processing helix chain 'b' and resid 1088 through 1090 No H-bonds generated for 'chain 'b' and resid 1088 through 1090' Processing helix chain 'b' and resid 1092 through 1104 Proline residue: b1102 - end of helix Processing helix chain 'b' and resid 1104 through 1114 removed outlier: 4.276A pdb=" N VAL b1108 " --> pdb=" O LEU b1104 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER b1109 " --> pdb=" O PRO b1105 " (cutoff:3.500A) Processing helix chain 'b' and resid 1117 through 1139 removed outlier: 4.114A pdb=" N GLN b1139 " --> pdb=" O ASP b1135 " (cutoff:3.500A) Processing helix chain 'b' and resid 1144 through 1149 Processing helix chain 'b' and resid 1180 through 1201 Processing helix chain 'd' and resid 36 through 43 Processing helix chain 'd' and resid 50 through 60 Processing helix chain 'd' and resid 65 through 83 Processing helix chain 'd' and resid 85 through 101 removed outlier: 3.515A pdb=" N ARG d 89 " --> pdb=" O ASP d 85 " (cutoff:3.500A) Processing helix chain 'd' and resid 107 through 119 removed outlier: 4.024A pdb=" N ASP d 113 " --> pdb=" O CYS d 109 " (cutoff:3.500A) Processing helix chain 'd' and resid 123 through 141 Processing helix chain 'd' and resid 144 through 158 removed outlier: 3.664A pdb=" N GLN d 148 " --> pdb=" O ASN d 144 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 177 Processing helix chain 'd' and resid 196 through 203 removed outlier: 3.677A pdb=" N TYR d 203 " --> pdb=" O ILE d 199 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 208 through 225 Processing helix chain 'd' and resid 232 through 242 removed outlier: 4.066A pdb=" N GLN d 236 " --> pdb=" O THR d 232 " (cutoff:3.500A) Processing helix chain 'd' and resid 246 through 263 Processing helix chain 'd' and resid 278 through 290 removed outlier: 3.614A pdb=" N ASP d 282 " --> pdb=" O ARG d 278 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET d 290 " --> pdb=" O LYS d 286 " (cutoff:3.500A) Processing helix chain 'd' and resid 291 through 293 No H-bonds generated for 'chain 'd' and resid 291 through 293' Processing helix chain 'd' and resid 295 through 309 Processing helix chain 'd' and resid 313 through 322 Processing helix chain 'd' and resid 377 through 384 removed outlier: 3.702A pdb=" N HIS d 381 " --> pdb=" O GLY d 377 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 405 Processing helix chain 'd' and resid 406 through 411 removed outlier: 3.736A pdb=" N GLU d 410 " --> pdb=" O SER d 407 " (cutoff:3.500A) Processing helix chain 'd' and resid 412 through 419 Processing helix chain 'd' and resid 420 through 422 No H-bonds generated for 'chain 'd' and resid 420 through 422' Processing helix chain 'd' and resid 424 through 439 Processing helix chain 'd' and resid 445 through 455 removed outlier: 3.923A pdb=" N VAL d 455 " --> pdb=" O THR d 451 " (cutoff:3.500A) Processing helix chain 'd' and resid 456 through 458 No H-bonds generated for 'chain 'd' and resid 456 through 458' Processing helix chain 'd' and resid 460 through 474 removed outlier: 3.654A pdb=" N CYS d 473 " --> pdb=" O GLU d 469 " (cutoff:3.500A) Processing helix chain 'd' and resid 478 through 496 Processing helix chain 'd' and resid 499 through 514 Processing helix chain 'd' and resid 514 through 519 Processing helix chain 'd' and resid 521 through 526 Processing helix chain 'd' and resid 541 through 555 Processing helix chain 'd' and resid 556 through 558 No H-bonds generated for 'chain 'd' and resid 556 through 558' Processing helix chain 'd' and resid 561 through 565 Processing helix chain 'd' and resid 566 through 580 Processing helix chain 'd' and resid 609 through 624 Processing helix chain 'd' and resid 628 through 650 Processing helix chain 'd' and resid 653 through 675 Processing helix chain 'd' and resid 692 through 710 Processing helix chain 'd' and resid 715 through 741 Processing helix chain 'd' and resid 743 through 765 removed outlier: 4.000A pdb=" N LEU d 747 " --> pdb=" O GLY d 743 " (cutoff:3.500A) Processing helix chain 'd' and resid 768 through 772 Processing helix chain 'd' and resid 775 through 782 Processing helix chain 'd' and resid 783 through 788 removed outlier: 4.173A pdb=" N MET d 788 " --> pdb=" O MET d 784 " (cutoff:3.500A) Processing helix chain 'd' and resid 791 through 805 Processing helix chain 'd' and resid 856 through 860 Processing helix chain 'd' and resid 878 through 880 No H-bonds generated for 'chain 'd' and resid 878 through 880' Processing helix chain 'e' and resid 27 through 41 Processing helix chain 'e' and resid 51 through 64 Processing helix chain 'e' and resid 66 through 68 No H-bonds generated for 'chain 'e' and resid 66 through 68' Processing helix chain 'e' and resid 69 through 95 removed outlier: 3.826A pdb=" N VAL e 73 " --> pdb=" O ALA e 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR e 95 " --> pdb=" O ALA e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 118 through 136 Processing helix chain 'e' and resid 136 through 160 removed outlier: 3.709A pdb=" N TRP e 140 " --> pdb=" O ASN e 136 " (cutoff:3.500A) Proline residue: e 142 - end of helix Processing helix chain 'e' and resid 172 through 183 removed outlier: 3.748A pdb=" N CYS e 183 " --> pdb=" O LEU e 179 " (cutoff:3.500A) Processing helix chain 'e' and resid 184 through 200 Processing helix chain 'e' and resid 204 through 219 removed outlier: 3.737A pdb=" N CYS e 208 " --> pdb=" O CYS e 204 " (cutoff:3.500A) Processing helix chain 'e' and resid 223 through 234 removed outlier: 4.065A pdb=" N VAL e 227 " --> pdb=" O PHE e 223 " (cutoff:3.500A) Processing helix chain 'e' and resid 235 through 254 Processing helix chain 'e' and resid 291 through 303 Processing helix chain 'e' and resid 306 through 320 removed outlier: 3.717A pdb=" N ARG e 310 " --> pdb=" O GLY e 306 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER e 320 " --> pdb=" O MET e 316 " (cutoff:3.500A) Processing helix chain 'e' and resid 339 through 348 Processing helix chain 'e' and resid 351 through 362 removed outlier: 4.081A pdb=" N GLY e 357 " --> pdb=" O GLY e 353 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL e 360 " --> pdb=" O SER e 356 " (cutoff:3.500A) Processing helix chain 'e' and resid 367 through 377 Processing helix chain 'e' and resid 380 through 398 Processing helix chain 'e' and resid 402 through 415 removed outlier: 4.057A pdb=" N LEU e 406 " --> pdb=" O GLY e 402 " (cutoff:3.500A) Processing helix chain 'e' and resid 429 through 451 Processing helix chain 'e' and resid 471 through 478 Processing helix chain 'e' and resid 480 through 489 Processing helix chain 'e' and resid 494 through 510 Processing helix chain 'e' and resid 514 through 526 Processing helix chain 'e' and resid 528 through 544 removed outlier: 4.206A pdb=" N VAL e 544 " --> pdb=" O ALA e 540 " (cutoff:3.500A) Processing helix chain 'e' and resid 548 through 563 Processing helix chain 'e' and resid 567 through 587 Processing helix chain 'e' and resid 589 through 596 Processing helix chain 'e' and resid 598 through 604 Processing helix chain 'e' and resid 606 through 611 Processing helix chain 'e' and resid 612 through 616 Processing helix chain 'e' and resid 618 through 632 Processing helix chain 'e' and resid 640 through 663 Processing helix chain 'e' and resid 664 through 666 No H-bonds generated for 'chain 'e' and resid 664 through 666' Processing helix chain 'e' and resid 667 through 680 Processing helix chain 'e' and resid 681 through 697 Processing helix chain 'e' and resid 702 through 706 Processing helix chain 'e' and resid 727 through 735 Processing helix chain 'e' and resid 768 through 788 Processing helix chain 'e' and resid 805 through 821 Processing helix chain 'e' and resid 833 through 839 Processing helix chain 'e' and resid 840 through 854 Processing helix chain 'e' and resid 855 through 867 removed outlier: 3.993A pdb=" N GLU e 859 " --> pdb=" O PRO e 855 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA e 867 " --> pdb=" O LEU e 863 " (cutoff:3.500A) Processing helix chain 'e' and resid 868 through 873 Processing helix chain 'e' and resid 874 through 891 Processing helix chain 'e' and resid 896 through 899 removed outlier: 3.631A pdb=" N HIS e 899 " --> pdb=" O ASP e 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 896 through 899' Processing helix chain 'e' and resid 900 through 917 Processing helix chain 'e' and resid 923 through 927 removed outlier: 3.550A pdb=" N ASN e 926 " --> pdb=" O ALA e 923 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET e 927 " --> pdb=" O LEU e 924 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 923 through 927' Processing helix chain 'e' and resid 935 through 953 Processing helix chain 'e' and resid 972 through 977 removed outlier: 3.574A pdb=" N ARG e 975 " --> pdb=" O ASP e 972 " (cutoff:3.500A) Processing helix chain 'e' and resid 981 through 995 Processing helix chain 'e' and resid 1000 through 1007 removed outlier: 4.205A pdb=" N GLY e1004 " --> pdb=" O LEU e1001 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE e1006 " --> pdb=" O SER e1003 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN e1007 " --> pdb=" O GLY e1004 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 16 Processing helix chain 'f' and resid 23 through 40 Processing helix chain 'f' and resid 57 through 61 Processing helix chain 'f' and resid 69 through 79 Processing helix chain 'f' and resid 87 through 100 Processing helix chain 'f' and resid 154 through 158 removed outlier: 3.714A pdb=" N THR f 158 " --> pdb=" O SER f 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 182 through 187 removed outlier: 3.593A pdb=" N GLN f 185 " --> pdb=" O GLU f 182 " (cutoff:3.500A) Processing helix chain 'f' and resid 195 through 203 removed outlier: 4.474A pdb=" N MET f 199 " --> pdb=" O ALA f 195 " (cutoff:3.500A) Processing helix chain 'f' and resid 212 through 226 Processing helix chain 'f' and resid 332 through 341 Processing helix chain 'f' and resid 385 through 388 Processing helix chain 'f' and resid 389 through 400 removed outlier: 3.769A pdb=" N HIS f 400 " --> pdb=" O LEU f 396 " (cutoff:3.500A) Processing helix chain 'f' and resid 405 through 418 removed outlier: 3.512A pdb=" N THR f 418 " --> pdb=" O SER f 414 " (cutoff:3.500A) Processing helix chain 'f' and resid 419 through 422 removed outlier: 6.345A pdb=" N TYR f 422 " --> pdb=" O MET f 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 419 through 422' Processing helix chain 'f' and resid 423 through 435 removed outlier: 3.539A pdb=" N GLY f 435 " --> pdb=" O VAL f 431 " (cutoff:3.500A) Processing helix chain 'f' and resid 439 through 444 removed outlier: 3.928A pdb=" N SER f 443 " --> pdb=" O ILE f 440 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET f 444 " --> pdb=" O ALA f 441 " (cutoff:3.500A) Processing helix chain 'f' and resid 449 through 475 removed outlier: 4.126A pdb=" N GLY f 475 " --> pdb=" O ILE f 471 " (cutoff:3.500A) Processing helix chain 'f' and resid 543 through 547 Processing helix chain 'f' and resid 551 through 564 removed outlier: 3.716A pdb=" N HIS f 555 " --> pdb=" O ASN f 551 " (cutoff:3.500A) Processing helix chain 'f' and resid 589 through 596 Processing helix chain 'g' and resid 22 through 35 Processing helix chain 'g' and resid 37 through 55 Proline residue: g 49 - end of helix Processing helix chain 'g' and resid 57 through 74 Processing helix chain 'g' and resid 76 through 90 Processing helix chain 'g' and resid 91 through 97 Processing helix chain 'g' and resid 99 through 109 Processing helix chain 'g' and resid 110 through 113 Processing helix chain 'g' and resid 115 through 129 Processing helix chain 'g' and resid 136 through 148 removed outlier: 4.002A pdb=" N ASP g 148 " --> pdb=" O ARG g 144 " (cutoff:3.500A) Processing helix chain 'g' and resid 151 through 169 Processing helix chain 'g' and resid 169 through 186 removed outlier: 4.298A pdb=" N ASN g 178 " --> pdb=" O VAL g 174 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS g 179 " --> pdb=" O GLY g 175 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 198 Processing helix chain 'g' and resid 199 through 204 removed outlier: 3.576A pdb=" N GLN g 202 " --> pdb=" O PRO g 199 " (cutoff:3.500A) Processing helix chain 'g' and resid 207 through 225 Processing helix chain 'g' and resid 227 through 245 Processing helix chain 'g' and resid 248 through 263 Processing helix chain 'g' and resid 265 through 283 Processing helix chain 'g' and resid 284 through 287 Processing helix chain 'g' and resid 288 through 302 Processing helix chain 'g' and resid 304 through 321 removed outlier: 3.728A pdb=" N THR g 321 " --> pdb=" O THR g 317 " (cutoff:3.500A) Processing helix chain 'g' and resid 322 through 328 Processing helix chain 'g' and resid 342 through 353 removed outlier: 4.058A pdb=" N TYR g 353 " --> pdb=" O GLN g 349 " (cutoff:3.500A) Processing helix chain 'g' and resid 356 through 374 Processing helix chain 'g' and resid 378 through 398 removed outlier: 3.656A pdb=" N LEU g 382 " --> pdb=" O ASP g 378 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN g 384 " --> pdb=" O LEU g 380 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP g 385 " --> pdb=" O ALA g 381 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER g 398 " --> pdb=" O LEU g 394 " (cutoff:3.500A) Processing helix chain 'g' and resid 402 through 423 Processing helix chain 'g' and resid 426 through 439 removed outlier: 3.750A pdb=" N VAL g 430 " --> pdb=" O LEU g 426 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N HIS g 439 " --> pdb=" O LEU g 435 " (cutoff:3.500A) Processing helix chain 'g' and resid 442 through 460 Processing helix chain 'g' and resid 463 through 476 removed outlier: 4.049A pdb=" N MET g 467 " --> pdb=" O LEU g 463 " (cutoff:3.500A) Processing helix chain 'g' and resid 477 through 481 removed outlier: 3.926A pdb=" N ARG g 480 " --> pdb=" O VAL g 477 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER g 481 " --> pdb=" O ILE g 478 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 477 through 481' Processing helix chain 'g' and resid 485 through 501 Processing helix chain 'g' and resid 506 through 520 Processing helix chain 'g' and resid 523 through 536 Processing helix chain 'g' and resid 538 through 549 removed outlier: 3.642A pdb=" N ALA g 542 " --> pdb=" O ASN g 538 " (cutoff:3.500A) Processing helix chain 'g' and resid 555 through 575 removed outlier: 3.772A pdb=" N LEU g 575 " --> pdb=" O ALA g 571 " (cutoff:3.500A) Processing helix chain 'g' and resid 576 through 578 No H-bonds generated for 'chain 'g' and resid 576 through 578' Processing helix chain 'g' and resid 582 through 607 removed outlier: 3.624A pdb=" N PHE g 596 " --> pdb=" O GLU g 592 " (cutoff:3.500A) Processing helix chain 'g' and resid 614 through 644 removed outlier: 4.452A pdb=" N LYS g 642 " --> pdb=" O CYS g 638 " (cutoff:3.500A) Processing helix chain 'g' and resid 664 through 692 Processing helix chain 'g' and resid 696 through 721 Processing helix chain 'g' and resid 734 through 738 Processing helix chain 'g' and resid 742 through 761 Processing helix chain 'g' and resid 770 through 787 removed outlier: 3.531A pdb=" N THR g 774 " --> pdb=" O SER g 770 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL g 787 " --> pdb=" O ALA g 783 " (cutoff:3.500A) Processing helix chain 'g' and resid 792 through 797 removed outlier: 3.555A pdb=" N PHE g 796 " --> pdb=" O GLN g 792 " (cutoff:3.500A) Processing helix chain 'g' and resid 933 through 944 Processing helix chain 'h' and resid 23 through 30 Processing helix chain 'h' and resid 48 through 58 Processing helix chain 'h' and resid 76 through 91 Processing helix chain 'h' and resid 95 through 103 removed outlier: 4.996A pdb=" N LYS h 101 " --> pdb=" O ASP h 97 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER h 102 " --> pdb=" O ILE h 98 " (cutoff:3.500A) Processing helix chain 'h' and resid 104 through 120 Processing helix chain 'h' and resid 127 through 131 Processing helix chain 'h' and resid 136 through 159 removed outlier: 3.817A pdb=" N VAL h 143 " --> pdb=" O THR h 139 " (cutoff:3.500A) Processing helix chain 'h' and resid 177 through 194 Processing helix chain 'h' and resid 194 through 207 Processing helix chain 'h' and resid 244 through 265 removed outlier: 3.789A pdb=" N VAL h 252 " --> pdb=" O MET h 248 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER h 265 " --> pdb=" O PHE h 261 " (cutoff:3.500A) Processing helix chain 'h' and resid 266 through 269 removed outlier: 6.614A pdb=" N ALA h 269 " --> pdb=" O THR h 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 266 through 269' Processing helix chain 'h' and resid 270 through 288 Processing helix chain 'h' and resid 298 through 313 Processing helix chain 'h' and resid 324 through 336 Processing helix chain 'h' and resid 338 through 352 removed outlier: 3.639A pdb=" N LEU h 350 " --> pdb=" O ILE h 346 " (cutoff:3.500A) Processing helix chain 'h' and resid 355 through 373 Processing helix chain 'h' and resid 374 through 376 No H-bonds generated for 'chain 'h' and resid 374 through 376' Processing helix chain 'h' and resid 377 through 395 Processing helix chain 'h' and resid 400 through 407 Processing helix chain 'h' and resid 411 through 427 removed outlier: 4.611A pdb=" N ASN h 427 " --> pdb=" O SER h 423 " (cutoff:3.500A) Processing helix chain 'h' and resid 432 through 449 Processing helix chain 'h' and resid 452 through 461 removed outlier: 3.762A pdb=" N VAL h 456 " --> pdb=" O ASP h 452 " (cutoff:3.500A) Processing helix chain 'h' and resid 462 through 469 Processing helix chain 'h' and resid 471 through 485 removed outlier: 4.014A pdb=" N SER h 485 " --> pdb=" O MET h 481 " (cutoff:3.500A) Processing helix chain 'h' and resid 504 through 519 Processing helix chain 'h' and resid 521 through 535 Processing helix chain 'h' and resid 540 through 544 Processing helix chain 'h' and resid 551 through 553 No H-bonds generated for 'chain 'h' and resid 551 through 553' Processing helix chain 'h' and resid 554 through 560 Processing helix chain 'h' and resid 563 through 583 Processing helix chain 'h' and resid 585 through 604 removed outlier: 4.757A pdb=" N GLU h 602 " --> pdb=" O GLU h 598 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE h 603 " --> pdb=" O LEU h 599 " (cutoff:3.500A) Processing helix chain 'h' and resid 604 through 625 Processing helix chain 'h' and resid 636 through 647 removed outlier: 3.543A pdb=" N SER h 640 " --> pdb=" O SER h 636 " (cutoff:3.500A) Processing helix chain 'h' and resid 656 through 670 removed outlier: 3.908A pdb=" N ALA h 660 " --> pdb=" O ARG h 656 " (cutoff:3.500A) Processing helix chain 'h' and resid 672 through 678 Processing helix chain 'h' and resid 681 through 688 removed outlier: 3.601A pdb=" N LEU h 685 " --> pdb=" O PRO h 681 " (cutoff:3.500A) Processing helix chain 'h' and resid 688 through 703 Processing helix chain 'h' and resid 706 through 725 removed outlier: 3.760A pdb=" N ARG h 712 " --> pdb=" O LYS h 708 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR h 713 " --> pdb=" O GLU h 709 " (cutoff:3.500A) Processing helix chain 'h' and resid 740 through 745 Processing helix chain 'h' and resid 753 through 762 Processing helix chain 'h' and resid 766 through 784 removed outlier: 3.943A pdb=" N ARG h 784 " --> pdb=" O LEU h 780 " (cutoff:3.500A) Processing helix chain 'h' and resid 810 through 829 Processing helix chain 'h' and resid 832 through 846 Processing helix chain 'h' and resid 848 through 864 Processing helix chain 'h' and resid 865 through 868 Processing helix chain 'h' and resid 877 through 891 Processing helix chain 'h' and resid 893 through 901 Processing helix chain 'h' and resid 908 through 917 Processing helix chain 'h' and resid 924 through 929 removed outlier: 3.567A pdb=" N TYR h 929 " --> pdb=" O ASP h 926 " (cutoff:3.500A) Processing helix chain 'h' and resid 934 through 948 Processing helix chain 'h' and resid 950 through 962 Processing helix chain 'h' and resid 971 through 995 Processing helix chain 'i' and resid 31 through 38 removed outlier: 4.131A pdb=" N SER i 34 " --> pdb=" O ASP i 31 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 51 Processing helix chain 'i' and resid 87 through 91 removed outlier: 3.572A pdb=" N LEU i 90 " --> pdb=" O GLU i 87 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE i 91 " --> pdb=" O THR i 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 87 through 91' Processing helix chain 'i' and resid 109 through 117 removed outlier: 3.825A pdb=" N THR i 117 " --> pdb=" O ILE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 127 through 145 Processing helix chain 'i' and resid 154 through 157 Processing helix chain 'i' and resid 158 through 164 removed outlier: 3.523A pdb=" N LEU i 164 " --> pdb=" O ASP i 160 " (cutoff:3.500A) Processing helix chain 'i' and resid 166 through 171 removed outlier: 3.625A pdb=" N ASP i 171 " --> pdb=" O SER i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 174 through 178 Processing helix chain 'i' and resid 183 through 192 Processing helix chain 'i' and resid 252 through 256 Processing helix chain 'i' and resid 273 through 292 Processing helix chain 'i' and resid 304 through 320 removed outlier: 3.657A pdb=" N ASP i 317 " --> pdb=" O TYR i 313 " (cutoff:3.500A) Processing helix chain 'i' and resid 332 through 343 Processing helix chain 'i' and resid 344 through 347 Processing helix chain 'i' and resid 348 through 357 removed outlier: 3.628A pdb=" N LEU i 357 " --> pdb=" O SER i 353 " (cutoff:3.500A) Processing helix chain 'i' and resid 363 through 370 Processing helix chain 'i' and resid 382 through 387 removed outlier: 3.664A pdb=" N PHE i 387 " --> pdb=" O PHE i 383 " (cutoff:3.500A) Processing helix chain 'i' and resid 403 through 413 removed outlier: 4.069A pdb=" N HIS i 407 " --> pdb=" O GLY i 403 " (cutoff:3.500A) Processing helix chain 'i' and resid 428 through 433 Processing helix chain 'i' and resid 434 through 437 Processing helix chain 'i' and resid 453 through 465 Processing helix chain 'i' and resid 474 through 476 No H-bonds generated for 'chain 'i' and resid 474 through 476' Processing helix chain 'i' and resid 485 through 489 removed outlier: 3.554A pdb=" N MET i 489 " --> pdb=" O MET i 486 " (cutoff:3.500A) Processing helix chain 'i' and resid 519 through 524 Processing helix chain 'i' and resid 590 through 602 Processing helix chain 'i' and resid 640 through 655 Processing helix chain 'j' and resid 3 through 18 Processing helix chain 'j' and resid 21 through 31 Processing helix chain 'j' and resid 39 through 50 removed outlier: 3.541A pdb=" N GLU j 50 " --> pdb=" O MET j 46 " (cutoff:3.500A) Processing helix chain 'j' and resid 52 through 70 removed outlier: 3.988A pdb=" N TYR j 64 " --> pdb=" O GLY j 60 " (cutoff:3.500A) Processing helix chain 'j' and resid 73 through 89 removed outlier: 3.724A pdb=" N TRP j 77 " --> pdb=" O GLN j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 93 through 106 removed outlier: 3.539A pdb=" N LEU j 106 " --> pdb=" O LEU j 102 " (cutoff:3.500A) Processing helix chain 'j' and resid 107 through 122 Processing helix chain 'j' and resid 124 through 139 Processing helix chain 'j' and resid 140 through 147 removed outlier: 3.689A pdb=" N VAL j 143 " --> pdb=" O PRO j 140 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL j 144 " --> pdb=" O GLU j 141 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY j 147 " --> pdb=" O VAL j 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 148 through 160 Processing helix chain 'j' and resid 168 through 177 Processing helix chain 'j' and resid 177 through 185 Processing helix chain 'j' and resid 191 through 212 Processing helix chain 'j' and resid 254 through 270 Processing helix chain 'j' and resid 284 through 294 removed outlier: 3.771A pdb=" N TYR j 294 " --> pdb=" O ASP j 290 " (cutoff:3.500A) Processing helix chain 'j' and resid 300 through 328 removed outlier: 5.515A pdb=" N TYR j 306 " --> pdb=" O ALA j 302 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS j 307 " --> pdb=" O HIS j 303 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN j 309 " --> pdb=" O LYS j 305 " (cutoff:3.500A) Processing helix chain 'j' and resid 367 through 373 Processing helix chain 'j' and resid 406 through 424 Processing helix chain 'j' and resid 427 through 440 Processing helix chain 'j' and resid 441 through 444 Processing helix chain 'j' and resid 445 through 460 Processing helix chain 'j' and resid 461 through 479 Processing helix chain 'j' and resid 491 through 507 removed outlier: 4.289A pdb=" N ALA j 495 " --> pdb=" O GLU j 491 " (cutoff:3.500A) Processing helix chain 'j' and resid 508 through 520 Processing helix chain 'j' and resid 560 through 578 removed outlier: 3.555A pdb=" N THR j 578 " --> pdb=" O LEU j 574 " (cutoff:3.500A) Processing helix chain 'j' and resid 582 through 593 Processing helix chain 'j' and resid 600 through 611 removed outlier: 4.388A pdb=" N PHE j 604 " --> pdb=" O GLY j 600 " (cutoff:3.500A) Processing helix chain 'j' and resid 628 through 639 removed outlier: 3.974A pdb=" N LEU j 632 " --> pdb=" O ASN j 628 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE j 635 " --> pdb=" O MET j 631 " (cutoff:3.500A) Processing helix chain 'j' and resid 640 through 644 removed outlier: 3.573A pdb=" N GLY j 643 " --> pdb=" O THR j 640 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY j 644 " --> pdb=" O GLN j 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 640 through 644' Processing helix chain 'j' and resid 653 through 658 Processing helix chain 'j' and resid 669 through 685 Processing helix chain 'j' and resid 689 through 705 Processing helix chain 'k' and resid 47 through 51 removed outlier: 3.624A pdb=" N TYR k 50 " --> pdb=" O ASP k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 70 through 75 Processing helix chain 'k' and resid 76 through 82 Processing helix chain 'k' and resid 94 through 114 Proline residue: k 101 - end of helix Processing helix chain 'k' and resid 122 through 130 Processing helix chain 'k' and resid 131 through 133 No H-bonds generated for 'chain 'k' and resid 131 through 133' Processing helix chain 'k' and resid 214 through 232 Processing helix chain 'k' and resid 241 through 260 Processing helix chain 'k' and resid 270 through 282 removed outlier: 3.627A pdb=" N LYS k 274 " --> pdb=" O GLY k 270 " (cutoff:3.500A) Processing helix chain 'k' and resid 287 through 293 Processing helix chain 'k' and resid 394 through 406 Processing helix chain 'k' and resid 416 through 430 Processing helix chain 'k' and resid 458 through 469 Processing helix chain 'k' and resid 495 through 500 removed outlier: 4.150A pdb=" N LYS k 500 " --> pdb=" O GLN k 497 " (cutoff:3.500A) Processing helix chain 'k' and resid 522 through 538 Processing helix chain 'k' and resid 580 through 591 removed outlier: 3.929A pdb=" N PHE k 586 " --> pdb=" O GLU k 582 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 70 removed outlier: 3.765A pdb=" N CYS m 54 " --> pdb=" O SER m 50 " (cutoff:3.500A) Processing helix chain 'm' and resid 93 through 96 Processing helix chain 'm' and resid 97 through 109 removed outlier: 3.906A pdb=" N LEU m 101 " --> pdb=" O ASN m 97 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY m 109 " --> pdb=" O LEU m 105 " (cutoff:3.500A) Processing helix chain 'm' and resid 122 through 133 Processing helix chain 'm' and resid 141 through 148 Processing helix chain 'm' and resid 151 through 156 Processing helix chain 'm' and resid 168 through 192 Processing helix chain 'm' and resid 240 through 256 removed outlier: 3.971A pdb=" N PHE m 255 " --> pdb=" O VAL m 251 " (cutoff:3.500A) Processing helix chain 'm' and resid 286 through 291 removed outlier: 4.118A pdb=" N ALA m 289 " --> pdb=" O HIS m 286 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS m 290 " --> pdb=" O LYS m 287 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL m 291 " --> pdb=" O ASP m 288 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 286 through 291' Processing helix chain 'm' and resid 344 through 357 removed outlier: 3.659A pdb=" N ASN m 356 " --> pdb=" O ASN m 352 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY m 357 " --> pdb=" O PHE m 353 " (cutoff:3.500A) Processing helix chain 'm' and resid 414 through 425 removed outlier: 3.542A pdb=" N PHE m 418 " --> pdb=" O ARG m 414 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU m 424 " --> pdb=" O GLU m 420 " (cutoff:3.500A) Processing helix chain 'm' and resid 443 through 455 Processing helix chain 'm' and resid 467 through 471 removed outlier: 3.624A pdb=" N ASN m 470 " --> pdb=" O THR m 467 " (cutoff:3.500A) Processing helix chain 'm' and resid 474 through 483 removed outlier: 4.258A pdb=" N ALA m 478 " --> pdb=" O VAL m 474 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE m 481 " --> pdb=" O LEU m 477 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL m 482 " --> pdb=" O ALA m 478 " (cutoff:3.500A) Processing helix chain 'm' and resid 487 through 508 Processing helix chain 'm' and resid 524 through 545 removed outlier: 3.622A pdb=" N GLN m 528 " --> pdb=" O LYS m 524 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA m 542 " --> pdb=" O THR m 538 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS m 543 " --> pdb=" O LEU m 539 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN m 545 " --> pdb=" O ARG m 541 " (cutoff:3.500A) Processing helix chain 'm' and resid 547 through 560 removed outlier: 3.620A pdb=" N GLN m 551 " --> pdb=" O SER m 547 " (cutoff:3.500A) Processing helix chain 'm' and resid 656 through 667 Processing helix chain 'm' and resid 672 through 677 removed outlier: 3.883A pdb=" N LEU m 676 " --> pdb=" O PHE m 672 " (cutoff:3.500A) Processing helix chain 'n' and resid 26 through 34 Processing helix chain 'n' and resid 36 through 45 removed outlier: 4.413A pdb=" N GLU n 40 " --> pdb=" O THR n 36 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS n 41 " --> pdb=" O MET n 37 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N MET n 42 " --> pdb=" O LEU n 38 " (cutoff:3.500A) Processing helix chain 'n' and resid 69 through 79 removed outlier: 3.593A pdb=" N LEU n 73 " --> pdb=" O ASP n 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 87 through 104 Processing helix chain 'n' and resid 136 through 140 Processing helix chain 'n' and resid 159 through 166 Processing helix chain 'n' and resid 167 through 179 Processing helix chain 'n' and resid 195 through 202 Processing helix chain 'n' and resid 299 through 306 removed outlier: 3.813A pdb=" N ALA n 303 " --> pdb=" O ALA n 299 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE n 306 " --> pdb=" O ILE n 302 " (cutoff:3.500A) Processing helix chain 'n' and resid 314 through 318 removed outlier: 4.591A pdb=" N LYS n 318 " --> pdb=" O GLY n 315 " (cutoff:3.500A) Processing helix chain 'n' and resid 360 through 364 removed outlier: 3.823A pdb=" N GLY n 364 " --> pdb=" O PRO n 361 " (cutoff:3.500A) Processing helix chain 'n' and resid 371 through 375 removed outlier: 4.155A pdb=" N ASP n 374 " --> pdb=" O PRO n 371 " (cutoff:3.500A) Processing helix chain 'n' and resid 397 through 401 removed outlier: 3.674A pdb=" N ALA n 400 " --> pdb=" O ARG n 397 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN n 401 " --> pdb=" O SER n 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 397 through 401' Processing helix chain 'n' and resid 411 through 421 removed outlier: 3.631A pdb=" N GLN n 417 " --> pdb=" O GLN n 413 " (cutoff:3.500A) Processing helix chain 'n' and resid 435 through 448 Processing helix chain 'n' and resid 450 through 455 removed outlier: 4.363A pdb=" N LYS n 454 " --> pdb=" O ASP n 451 " (cutoff:3.500A) Processing helix chain 'n' and resid 459 through 464 removed outlier: 3.670A pdb=" N CYS n 464 " --> pdb=" O LEU n 460 " (cutoff:3.500A) Processing helix chain 'n' and resid 472 through 487 removed outlier: 4.541A pdb=" N ALA n 476 " --> pdb=" O HIS n 472 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N HIS n 481 " --> pdb=" O PHE n 477 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA n 482 " --> pdb=" O GLN n 478 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA n 483 " --> pdb=" O LEU n 479 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS n 487 " --> pdb=" O ALA n 483 " (cutoff:3.500A) Processing helix chain 'n' and resid 488 through 492 Processing helix chain 'o' and resid 2 through 8 Processing helix chain 'o' and resid 15 through 33 removed outlier: 4.518A pdb=" N GLN o 33 " --> pdb=" O SER o 29 " (cutoff:3.500A) Processing helix chain 'o' and resid 42 through 53 Processing helix chain 'o' and resid 67 through 84 removed outlier: 3.837A pdb=" N LEU o 72 " --> pdb=" O SER o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 99 Processing helix chain 'o' and resid 106 through 124 Processing helix chain 'o' and resid 126 through 139 Processing helix chain 'o' and resid 141 through 158 removed outlier: 3.620A pdb=" N CYS o 158 " --> pdb=" O ASP o 154 " (cutoff:3.500A) Processing helix chain 'o' and resid 162 through 174 Processing helix chain 'o' and resid 174 through 189 Processing helix chain 'o' and resid 199 through 209 Processing helix chain 'o' and resid 212 through 224 removed outlier: 4.238A pdb=" N THR o 224 " --> pdb=" O THR o 220 " (cutoff:3.500A) Processing helix chain 'o' and resid 239 through 249 Processing helix chain 'o' and resid 251 through 257 removed outlier: 3.574A pdb=" N LYS o 257 " --> pdb=" O ALA o 253 " (cutoff:3.500A) Processing helix chain 'o' and resid 276 through 280 removed outlier: 3.760A pdb=" N MET o 279 " --> pdb=" O GLY o 276 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASP o 280 " --> pdb=" O VAL o 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 276 through 280' Processing helix chain 'o' and resid 283 through 292 Processing helix chain 'o' and resid 292 through 306 removed outlier: 4.342A pdb=" N GLN o 296 " --> pdb=" O LEU o 292 " (cutoff:3.500A) Processing helix chain 'o' and resid 321 through 333 Processing helix chain 'o' and resid 341 through 362 Processing helix chain 'o' and resid 374 through 379 Processing helix chain 'o' and resid 382 through 390 removed outlier: 3.590A pdb=" N GLN o 386 " --> pdb=" O ASN o 382 " (cutoff:3.500A) Processing helix chain 'p' and resid 12 through 22 removed outlier: 3.774A pdb=" N GLU p 19 " --> pdb=" O VAL p 15 " (cutoff:3.500A) Processing helix chain 'p' and resid 24 through 34 Processing helix chain 'p' and resid 34 through 42 removed outlier: 3.584A pdb=" N LEU p 42 " --> pdb=" O ILE p 38 " (cutoff:3.500A) Processing helix chain 'p' and resid 43 through 57 removed outlier: 5.621A pdb=" N LEU p 52 " --> pdb=" O ARG p 48 " (cutoff:3.500A) Proline residue: p 53 - end of helix Processing helix chain 'p' and resid 65 through 76 Processing helix chain 'p' and resid 85 through 88 Processing helix chain 'p' and resid 89 through 97 removed outlier: 3.784A pdb=" N LEU p 93 " --> pdb=" O LEU p 89 " (cutoff:3.500A) Processing helix chain 'p' and resid 102 through 115 removed outlier: 3.690A pdb=" N ASP p 106 " --> pdb=" O THR p 102 " (cutoff:3.500A) Processing helix chain 'p' and resid 116 through 119 Processing helix chain 'p' and resid 120 through 127 Processing helix chain 'p' and resid 127 through 137 Processing helix chain 'p' and resid 140 through 152 removed outlier: 3.573A pdb=" N ARG p 144 " --> pdb=" O TRP p 140 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER p 152 " --> pdb=" O CYS p 148 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 175 removed outlier: 4.002A pdb=" N GLU p 165 " --> pdb=" O ALA p 161 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER p 175 " --> pdb=" O ARG p 171 " (cutoff:3.500A) Processing helix chain 'p' and resid 178 through 193 removed outlier: 3.575A pdb=" N ARG p 182 " --> pdb=" O THR p 178 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY p 190 " --> pdb=" O ALA p 186 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU p 191 " --> pdb=" O SER p 187 " (cutoff:3.500A) Processing helix chain 'p' and resid 197 through 214 removed outlier: 4.446A pdb=" N ILE p 206 " --> pdb=" O LYS p 202 " (cutoff:3.500A) Proline residue: p 207 - end of helix Processing helix chain 'p' and resid 217 through 233 removed outlier: 4.215A pdb=" N VAL p 229 " --> pdb=" O VAL p 225 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ASN p 230 " --> pdb=" O GLU p 226 " (cutoff:3.500A) Processing helix chain 'p' and resid 237 through 242 removed outlier: 3.834A pdb=" N GLU p 241 " --> pdb=" O GLN p 237 " (cutoff:3.500A) Processing helix chain 'p' and resid 244 through 253 removed outlier: 4.308A pdb=" N GLU p 253 " --> pdb=" O ARG p 249 " (cutoff:3.500A) Processing helix chain 'p' and resid 256 through 265 Processing helix chain 'p' and resid 266 through 274 removed outlier: 3.668A pdb=" N LEU p 270 " --> pdb=" O LYS p 266 " (cutoff:3.500A) Processing helix chain 'p' and resid 275 through 283 removed outlier: 3.872A pdb=" N THR p 279 " --> pdb=" O GLY p 275 " (cutoff:3.500A) Processing helix chain 'p' and resid 283 through 291 Processing helix chain 'p' and resid 295 through 304 removed outlier: 3.621A pdb=" N ARG p 299 " --> pdb=" O GLU p 295 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS p 304 " --> pdb=" O ALA p 300 " (cutoff:3.500A) Processing helix chain 'p' and resid 305 through 312 removed outlier: 3.703A pdb=" N PHE p 309 " --> pdb=" O LYS p 305 " (cutoff:3.500A) Processing helix chain 'p' and resid 317 through 326 Processing helix chain 'p' and resid 326 through 335 removed outlier: 4.201A pdb=" N GLU p 332 " --> pdb=" O PRO p 328 " (cutoff:3.500A) Processing helix chain 'p' and resid 338 through 347 Processing helix chain 'p' and resid 348 through 350 No H-bonds generated for 'chain 'p' and resid 348 through 350' Processing helix chain 'p' and resid 351 through 357 removed outlier: 4.601A pdb=" N ILE p 355 " --> pdb=" O GLY p 351 " (cutoff:3.500A) Processing helix chain 'p' and resid 358 through 374 removed outlier: 4.543A pdb=" N LEU p 366 " --> pdb=" O ILE p 362 " (cutoff:3.500A) Proline residue: p 367 - end of helix Processing helix chain 'p' and resid 377 through 386 removed outlier: 3.587A pdb=" N ARG p 381 " --> pdb=" O CYS p 377 " (cutoff:3.500A) Processing helix chain 'p' and resid 387 through 396 removed outlier: 4.019A pdb=" N VAL p 391 " --> pdb=" O ASN p 387 " (cutoff:3.500A) Processing helix chain 'p' and resid 396 through 404 removed outlier: 3.541A pdb=" N LEU p 400 " --> pdb=" O GLY p 396 " (cutoff:3.500A) Processing helix chain 'p' and resid 404 through 412 Processing helix chain 'p' and resid 416 through 432 removed outlier: 3.648A pdb=" N ARG p 420 " --> pdb=" O LYS p 416 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR p 426 " --> pdb=" O ALA p 422 " (cutoff:3.500A) Proline residue: p 428 - end of helix Processing helix chain 'p' and resid 435 through 443 Processing helix chain 'p' and resid 443 through 450 removed outlier: 3.530A pdb=" N TRP p 450 " --> pdb=" O LEU p 446 " (cutoff:3.500A) Processing helix chain 'p' and resid 451 through 453 No H-bonds generated for 'chain 'p' and resid 451 through 453' Processing helix chain 'p' and resid 455 through 473 removed outlier: 3.572A pdb=" N SER p 464 " --> pdb=" O GLU p 460 " (cutoff:3.500A) Processing helix chain 'p' and resid 474 through 479 Processing helix chain 'p' and resid 481 through 491 removed outlier: 4.146A pdb=" N LYS p 485 " --> pdb=" O THR p 481 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY p 491 " --> pdb=" O LEU p 487 " (cutoff:3.500A) Processing helix chain 'p' and resid 494 through 510 removed outlier: 4.092A pdb=" N GLU p 510 " --> pdb=" O ASN p 506 " (cutoff:3.500A) Processing helix chain 'p' and resid 513 through 529 removed outlier: 4.458A pdb=" N LEU p 522 " --> pdb=" O THR p 518 " (cutoff:3.500A) Proline residue: p 523 - end of helix removed outlier: 3.638A pdb=" N ALA p 529 " --> pdb=" O VAL p 525 " (cutoff:3.500A) Processing helix chain 'p' and resid 533 through 548 Processing helix chain 'p' and resid 552 through 568 removed outlier: 3.732A pdb=" N LEU p 556 " --> pdb=" O ASP p 552 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN p 557 " --> pdb=" O ASN p 553 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER p 558 " --> pdb=" O SER p 554 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS p 561 " --> pdb=" O GLN p 557 " (cutoff:3.500A) Proline residue: p 562 - end of helix Processing helix chain 'p' and resid 572 through 587 Processing helix chain 'q' and resid 7 through 19 removed outlier: 3.564A pdb=" N GLU q 19 " --> pdb=" O GLU q 15 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 42 removed outlier: 4.251A pdb=" N LYS q 41 " --> pdb=" O GLU q 37 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU q 42 " --> pdb=" O ILE q 38 " (cutoff:3.500A) Processing helix chain 'q' and resid 61 through 73 Processing helix chain 'q' and resid 92 through 107 Processing helix chain 'q' and resid 120 through 127 Processing helix chain 'q' and resid 128 through 138 Processing helix chain 'q' and resid 140 through 151 removed outlier: 3.612A pdb=" N ASP q 151 " --> pdb=" O THR q 147 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 182 removed outlier: 3.679A pdb=" N ILE q 180 " --> pdb=" O THR q 176 " (cutoff:3.500A) Processing helix chain 'q' and resid 193 through 201 Processing helix chain 'q' and resid 221 through 233 Processing helix chain 'r' and resid 2048 through 2057 Processing helix chain 'u' and resid 8 through 17 Processing helix chain 'u' and resid 28 through 33 Processing helix chain 'u' and resid 34 through 39 Processing helix chain 'u' and resid 40 through 43 Processing helix chain 'u' and resid 49 through 59 Processing helix chain 'u' and resid 65 through 70 removed outlier: 4.222A pdb=" N GLU u 70 " --> pdb=" O ARG u 66 " (cutoff:3.500A) Processing helix chain 'u' and resid 71 through 84 removed outlier: 4.022A pdb=" N LEU u 75 " --> pdb=" O MET u 71 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU u 84 " --> pdb=" O GLN u 80 " (cutoff:3.500A) Processing helix chain 'u' and resid 87 through 97 Processing helix chain 'u' and resid 99 through 104 removed outlier: 4.038A pdb=" N THR u 103 " --> pdb=" O SER u 99 " (cutoff:3.500A) Processing helix chain 'u' and resid 116 through 131 removed outlier: 3.829A pdb=" N ILE u 120 " --> pdb=" O ASN u 116 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU u 124 " --> pdb=" O ILE u 120 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU u 126 " --> pdb=" O GLY u 122 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS u 127 " --> pdb=" O GLU u 123 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY u 129 " --> pdb=" O ARG u 125 " (cutoff:3.500A) Processing helix chain 'u' and resid 139 through 144 removed outlier: 4.224A pdb=" N TYR u 143 " --> pdb=" O LEU u 139 " (cutoff:3.500A) Processing helix chain 'u' and resid 145 through 154 Processing helix chain 'u' and resid 170 through 188 Processing helix chain 'v' and resid 41 through 46 Processing helix chain 'v' and resid 46 through 53 removed outlier: 4.041A pdb=" N PHE v 50 " --> pdb=" O SER v 46 " (cutoff:3.500A) Processing helix chain 'v' and resid 57 through 76 removed outlier: 3.712A pdb=" N PHE v 61 " --> pdb=" O PRO v 57 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG v 76 " --> pdb=" O LYS v 72 " (cutoff:3.500A) Processing helix chain 'v' and resid 76 through 82 removed outlier: 3.724A pdb=" N ILE v 80 " --> pdb=" O ARG v 76 " (cutoff:3.500A) Processing helix chain 'v' and resid 87 through 100 removed outlier: 3.505A pdb=" N LYS v 91 " --> pdb=" O GLU v 87 " (cutoff:3.500A) Processing helix chain 'v' and resid 109 through 118 Processing helix chain 'v' and resid 127 through 138 Processing helix chain 'v' and resid 141 through 152 Processing helix chain 'v' and resid 160 through 175 removed outlier: 3.535A pdb=" N ILE v 169 " --> pdb=" O LEU v 165 " (cutoff:3.500A) Processing helix chain 'v' and resid 199 through 206 Processing helix chain 'v' and resid 210 through 228 removed outlier: 3.589A pdb=" N GLN v 220 " --> pdb=" O ASP v 216 " (cutoff:3.500A) Processing helix chain 'v' and resid 230 through 246 removed outlier: 4.132A pdb=" N TYR v 234 " --> pdb=" O ARG v 230 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS v 235 " --> pdb=" O ASN v 231 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU v 237 " --> pdb=" O HIS v 233 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG v 238 " --> pdb=" O TYR v 234 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU v 240 " --> pdb=" O THR v 236 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU v 241 " --> pdb=" O LEU v 237 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N MET v 243 " --> pdb=" O ALA v 239 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER v 244 " --> pdb=" O GLU v 240 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N HIS v 246 " --> pdb=" O LEU v 242 " (cutoff:3.500A) Processing helix chain 'v' and resid 247 through 249 No H-bonds generated for 'chain 'v' and resid 247 through 249' Processing helix chain 'v' and resid 250 through 257 removed outlier: 3.529A pdb=" N CYS v 254 " --> pdb=" O VAL v 250 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP v 257 " --> pdb=" O ILE v 253 " (cutoff:3.500A) Processing helix chain 'v' and resid 259 through 273 removed outlier: 3.765A pdb=" N CYS v 265 " --> pdb=" O LYS v 261 " (cutoff:3.500A) Processing helix chain 'v' and resid 276 through 288 removed outlier: 3.698A pdb=" N ARG v 281 " --> pdb=" O SER v 277 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU v 282 " --> pdb=" O LYS v 278 " (cutoff:3.500A) Processing helix chain 'v' and resid 292 through 306 removed outlier: 3.726A pdb=" N LEU v 298 " --> pdb=" O GLN v 294 " (cutoff:3.500A) Processing helix chain 'v' and resid 307 through 329 removed outlier: 3.760A pdb=" N ILE v 311 " --> pdb=" O ASP v 307 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA v 315 " --> pdb=" O ILE v 311 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU v 316 " --> pdb=" O ASN v 312 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY v 327 " --> pdb=" O GLN v 323 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN v 328 " --> pdb=" O GLU v 324 " (cutoff:3.500A) Processing helix chain 'v' and resid 339 through 356 removed outlier: 3.693A pdb=" N MET v 354 " --> pdb=" O GLY v 350 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE v 355 " --> pdb=" O ALA v 351 " (cutoff:3.500A) Processing helix chain 'v' and resid 366 through 387 removed outlier: 3.753A pdb=" N LEU v 374 " --> pdb=" O ILE v 370 " (cutoff:3.500A) Proline residue: v 375 - end of helix removed outlier: 4.186A pdb=" N PHE v 380 " --> pdb=" O MET v 376 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU v 381 " --> pdb=" O LEU v 377 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR v 385 " --> pdb=" O LEU v 381 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR v 386 " --> pdb=" O VAL v 382 " (cutoff:3.500A) Processing helix chain 'v' and resid 409 through 418 Processing helix chain 'v' and resid 419 through 432 removed outlier: 3.654A pdb=" N GLU v 423 " --> pdb=" O ARG v 419 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE v 432 " --> pdb=" O TYR v 428 " (cutoff:3.500A) Processing helix chain 'v' and resid 439 through 444 removed outlier: 3.772A pdb=" N LEU v 444 " --> pdb=" O ALA v 440 " (cutoff:3.500A) Processing helix chain 'v' and resid 444 through 455 Processing helix chain 'v' and resid 464 through 469 Processing helix chain 'v' and resid 479 through 490 removed outlier: 4.976A pdb=" N LEU v 485 " --> pdb=" O PHE v 481 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE v 486 " --> pdb=" O CYS v 482 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLY v 488 " --> pdb=" O SER v 484 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE v 489 " --> pdb=" O LEU v 485 " (cutoff:3.500A) Processing helix chain 'v' and resid 500 through 506 removed outlier: 3.679A pdb=" N ALA v 504 " --> pdb=" O VAL v 500 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 85 removed outlier: 3.587A pdb=" N ILE w 80 " --> pdb=" O PRO w 76 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER w 84 " --> pdb=" O ILE w 80 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU w 85 " --> pdb=" O GLN w 81 " (cutoff:3.500A) Processing helix chain 'w' and resid 88 through 105 removed outlier: 4.371A pdb=" N VAL w 94 " --> pdb=" O VAL w 90 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN w 95 " --> pdb=" O ALA w 91 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE w 102 " --> pdb=" O ALA w 98 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY w 105 " --> pdb=" O LEU w 101 " (cutoff:3.500A) Processing helix chain 'w' and resid 109 through 124 removed outlier: 3.825A pdb=" N GLU w 113 " --> pdb=" O VAL w 109 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU w 122 " --> pdb=" O HIS w 118 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE w 124 " --> pdb=" O LYS w 120 " (cutoff:3.500A) Processing helix chain 'w' and resid 127 through 136 removed outlier: 3.763A pdb=" N LYS w 131 " --> pdb=" O PHE w 127 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP w 133 " --> pdb=" O PRO w 129 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER w 134 " --> pdb=" O ARG w 130 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE w 135 " --> pdb=" O LYS w 131 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE w 136 " --> pdb=" O ALA w 132 " (cutoff:3.500A) Processing helix chain 'w' and resid 137 through 142 removed outlier: 4.336A pdb=" N GLU w 141 " --> pdb=" O THR w 137 " (cutoff:3.500A) Processing helix chain 'w' and resid 145 through 150 Processing helix chain 'w' and resid 152 through 166 removed outlier: 3.740A pdb=" N TYR w 160 " --> pdb=" O ARG w 156 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS w 161 " --> pdb=" O ASP w 157 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA w 165 " --> pdb=" O LYS w 161 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS w 166 " --> pdb=" O LEU w 162 " (cutoff:3.500A) Processing helix chain 'w' and resid 169 through 180 removed outlier: 3.949A pdb=" N LYS w 177 " --> pdb=" O ASN w 173 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU w 178 " --> pdb=" O PHE w 174 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE w 179 " --> pdb=" O THR w 175 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER w 180 " --> pdb=" O VAL w 176 " (cutoff:3.500A) Processing helix chain 'w' and resid 192 through 197 removed outlier: 3.711A pdb=" N GLN w 196 " --> pdb=" O SER w 192 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN w 197 " --> pdb=" O THR w 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 192 through 197' Processing helix chain 'w' and resid 197 through 216 removed outlier: 3.870A pdb=" N GLY w 216 " --> pdb=" O ILE w 212 " (cutoff:3.500A) Processing helix chain 'w' and resid 218 through 229 removed outlier: 4.082A pdb=" N LYS w 222 " --> pdb=" O GLU w 218 " (cutoff:3.500A) Proline residue: w 225 - end of helix Processing helix chain 'w' and resid 230 through 232 No H-bonds generated for 'chain 'w' and resid 230 through 232' Processing helix chain 'w' and resid 235 through 240 removed outlier: 3.904A pdb=" N PHE w 240 " --> pdb=" O HIS w 236 " (cutoff:3.500A) Processing helix chain 'w' and resid 243 through 251 removed outlier: 3.641A pdb=" N GLU w 251 " --> pdb=" O VAL w 247 " (cutoff:3.500A) Processing helix chain 'w' and resid 254 through 272 removed outlier: 4.483A pdb=" N VAL w 258 " --> pdb=" O GLY w 254 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG w 259 " --> pdb=" O GLY w 255 " (cutoff:3.500A) Processing helix chain 'w' and resid 279 through 284 Processing helix chain 'w' and resid 285 through 288 removed outlier: 3.715A pdb=" N SER w 288 " --> pdb=" O THR w 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 285 through 288' Processing helix chain 'w' and resid 289 through 303 removed outlier: 3.656A pdb=" N ALA w 298 " --> pdb=" O GLN w 294 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET w 299 " --> pdb=" O ALA w 295 " (cutoff:3.500A) Processing helix chain 'w' and resid 306 through 318 removed outlier: 3.667A pdb=" N ILE w 310 " --> pdb=" O ASN w 306 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR w 318 " --> pdb=" O PHE w 314 " (cutoff:3.500A) Processing helix chain 'w' and resid 324 through 329 removed outlier: 4.178A pdb=" N ILE w 328 " --> pdb=" O PRO w 324 " (cutoff:3.500A) Processing helix chain 'w' and resid 330 through 342 Processing helix chain 'w' and resid 349 through 363 Processing helix chain 'w' and resid 380 through 400 Processing helix chain 'w' and resid 407 through 409 No H-bonds generated for 'chain 'w' and resid 407 through 409' Processing helix chain 'w' and resid 410 through 420 removed outlier: 3.614A pdb=" N TYR w 415 " --> pdb=" O LEU w 411 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN w 416 " --> pdb=" O SER w 412 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE w 420 " --> pdb=" O GLN w 416 " (cutoff:3.500A) Processing helix chain 'w' and resid 420 through 436 removed outlier: 3.785A pdb=" N ALA w 424 " --> pdb=" O PHE w 420 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET w 425 " --> pdb=" O PRO w 421 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY w 426 " --> pdb=" O VAL w 422 " (cutoff:3.500A) Processing helix chain 'w' and resid 439 through 444 Processing helix chain 'w' and resid 449 through 462 Processing helix chain 'w' and resid 465 through 479 Processing helix chain 'w' and resid 485 through 506 Processing helix chain 'w' and resid 509 through 522 Processing helix chain 'w' and resid 526 through 540 removed outlier: 3.749A pdb=" N ILE w 530 " --> pdb=" O ASP w 526 " (cutoff:3.500A) Processing helix chain 'w' and resid 546 through 558 Proline residue: w 555 - end of helix Processing helix chain 'w' and resid 562 through 566 removed outlier: 3.555A pdb=" N ILE w 566 " --> pdb=" O ALA w 563 " (cutoff:3.500A) Processing helix chain 'w' and resid 575 through 586 removed outlier: 3.670A pdb=" N LYS w 583 " --> pdb=" O ILE w 579 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER w 584 " --> pdb=" O ALA w 580 " (cutoff:3.500A) Processing helix chain 'x' and resid 4 through 20 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain 'A' and resid 86 through 94 removed outlier: 6.765A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 194 removed outlier: 3.859A pdb=" N GLU A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.772A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.555A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.037A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.334A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N MET H 37 " --> pdb=" O SER H 32 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.803A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 3.758A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A1358 " --> pdb=" O THR A1140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1244 through 1247 removed outlier: 3.624A pdb=" N THR A1173 " --> pdb=" O ASN I 56 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1319 through 1322 removed outlier: 3.565A pdb=" N LYS A1319 " --> pdb=" O LEU A1331 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AB9, first strand: chain 'B' and resid 66 through 67 removed outlier: 5.777A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AC2, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC3, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.032A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 205 through 208 removed outlier: 4.092A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 223 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP B 236 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC6, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC7, first strand: chain 'B' and resid 572 through 577 removed outlier: 4.500A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.822A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 858 " --> pdb=" O VAL B 904 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 747 through 751 removed outlier: 6.822A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD2, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 6.728A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD4, first strand: chain 'B' and resid 865 through 867 removed outlier: 7.043A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1113 through 1119 Processing sheet with id=AD6, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD7, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.363A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.363A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.599A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 113 through 115 removed outlier: 3.789A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.279A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 30 through 31 removed outlier: 4.279A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 60 through 63 removed outlier: 5.947A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 147 through 151 removed outlier: 3.598A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N VAL E 190 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 104 through 108 removed outlier: 3.973A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 128 through 129 Processing sheet with id=AE8, first strand: chain 'G' and resid 151 through 152 Processing sheet with id=AE9, first strand: chain 'I' and resid 26 through 29 removed outlier: 4.321A pdb=" N ASP I 29 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE I 34 " --> pdb=" O ASP I 29 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS I 39 " --> pdb=" O TYR I 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR I 44 " --> pdb=" O CYS I 39 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF2, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF3, first strand: chain 'M' and resid 83 through 84 removed outlier: 7.897A pdb=" N ARG M 83 " --> pdb=" O VAL O 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'Z' and resid 437 through 439 removed outlier: 3.989A pdb=" N GLY Z 438 " --> pdb=" O VAL Z 426 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL Z 426 " --> pdb=" O GLY Z 438 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG Z 469 " --> pdb=" O GLU Z 427 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 477 through 479 Processing sheet with id=AF6, first strand: chain 'Z' and resid 539 through 541 removed outlier: 3.827A pdb=" N VAL Z 540 " --> pdb=" O GLY Z 548 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 558 through 562 removed outlier: 3.616A pdb=" N PHE Z 558 " --> pdb=" O VAL Z 570 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS Z 566 " --> pdb=" O ASN Z 562 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 600 through 602 Processing sheet with id=AF9, first strand: chain 'Z' and resid 621 through 625 removed outlier: 4.799A pdb=" N ALA Z 622 " --> pdb=" O CYS Z 638 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N CYS Z 638 " --> pdb=" O ALA Z 622 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N PHE Z 636 " --> pdb=" O LEU Z 624 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.591A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 1159 through 1163 Processing sheet with id=AG3, first strand: chain 'd' and resid 821 through 824 removed outlier: 3.539A pdb=" N LEU d 851 " --> pdb=" O HIS d 890 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ARG d 889 " --> pdb=" O PRO d 885 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'd' and resid 835 through 838 removed outlier: 5.941A pdb=" N LEU d 835 " --> pdb=" O MET d 957 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS d 959 " --> pdb=" O LEU d 835 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE d 837 " --> pdb=" O LYS d 959 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'd' and resid 835 through 838 removed outlier: 5.941A pdb=" N LEU d 835 " --> pdb=" O MET d 957 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS d 959 " --> pdb=" O LEU d 835 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE d 837 " --> pdb=" O LYS d 959 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'e' and resid 752 through 753 Processing sheet with id=AG7, first strand: chain 'e' and resid 961 through 963 removed outlier: 3.646A pdb=" N GLN e 963 " --> pdb=" O ARG e 968 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG e 968 " --> pdb=" O GLN e 963 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'f' and resid 62 through 64 removed outlier: 5.940A pdb=" N LEU f 52 " --> pdb=" O LYS f 63 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU f 4 " --> pdb=" O MET f 51 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL f 53 " --> pdb=" O LEU f 4 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N PHE f 6 " --> pdb=" O VAL f 53 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG f 167 " --> pdb=" O ALA f 123 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N TYR f 208 " --> pdb=" O LEU f 168 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA f 170 " --> pdb=" O TYR f 208 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL f 210 " --> pdb=" O ALA f 170 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL f 172 " --> pdb=" O VAL f 210 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'f' and resid 263 through 269 removed outlier: 4.201A pdb=" N GLN f 349 " --> pdb=" O SER f 310 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY f 366 " --> pdb=" O VAL f 350 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN f 378 " --> pdb=" O LYS f 369 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP f 325 " --> pdb=" O VAL f 381 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'g' and resid 802 through 804 removed outlier: 3.753A pdb=" N SER g 803 " --> pdb=" O GLN g 836 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'g' and resid 802 through 804 removed outlier: 3.753A pdb=" N SER g 803 " --> pdb=" O GLN g 836 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'g' and resid 819 through 822 removed outlier: 5.741A pdb=" N ILE g 819 " --> pdb=" O LYS g 929 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU g 931 " --> pdb=" O ILE g 819 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL g 821 " --> pdb=" O LEU g 931 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'g' and resid 909 through 911 Processing sheet with id=AH5, first strand: chain 'i' and resid 194 through 197 removed outlier: 6.432A pdb=" N VAL i 123 " --> pdb=" O GLN i 195 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL i 197 " --> pdb=" O VAL i 123 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA i 125 " --> pdb=" O VAL i 197 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE i 99 " --> pdb=" O TYR i 124 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR i 126 " --> pdb=" O ILE i 99 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS i 2 " --> pdb=" O LYS i 18 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU i 503 " --> pdb=" O CYS i 5 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'i' and resid 68 through 71 Processing sheet with id=AH7, first strand: chain 'i' and resid 203 through 205 removed outlier: 6.872A pdb=" N SER i 235 " --> pdb=" O VAL i 262 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'i' and resid 373 through 376 removed outlier: 6.233A pdb=" N LEU i 326 " --> pdb=" O LYS i 374 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR i 376 " --> pdb=" O LEU i 326 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE i 328 " --> pdb=" O TYR i 376 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL i 295 " --> pdb=" O VAL i 393 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR i 395 " --> pdb=" O VAL i 295 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL i 297 " --> pdb=" O THR i 395 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU i 296 " --> pdb=" O ILE i 421 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'i' and resid 471 through 472 removed outlier: 6.950A pdb=" N CYS i 471 " --> pdb=" O TYR i 499 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'i' and resid 513 through 516 removed outlier: 3.706A pdb=" N GLU i 514 " --> pdb=" O ILE k 456 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'i' and resid 529 through 530 Processing sheet with id=AI3, first strand: chain 'i' and resid 529 through 530 removed outlier: 3.593A pdb=" N ALA i 538 " --> pdb=" O LEU k 483 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'i' and resid 609 through 611 removed outlier: 3.962A pdb=" N GLU i 609 " --> pdb=" O ILE i 616 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR i 611 " --> pdb=" O GLY i 614 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY i 614 " --> pdb=" O THR i 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER i 632 " --> pdb=" O GLU i 629 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'i' and resid 609 through 611 removed outlier: 3.962A pdb=" N GLU i 609 " --> pdb=" O ILE i 616 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR i 611 " --> pdb=" O GLY i 614 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY i 614 " --> pdb=" O THR i 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER i 632 " --> pdb=" O GLU i 629 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ARG k 514 " --> pdb=" O ILE i 635 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N CYS i 637 " --> pdb=" O ARG k 514 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N HIS k 516 " --> pdb=" O CYS i 637 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'k' and resid 61 through 64 removed outlier: 7.175A pdb=" N ASN k 28 " --> pdb=" O ASP k 62 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL k 64 " --> pdb=" O ASN k 28 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET k 30 " --> pdb=" O VAL k 64 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N CYS k 19 " --> pdb=" O LEU k 9 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'k' and resid 91 through 93 removed outlier: 6.130A pdb=" N MET k 92 " --> pdb=" O VAL k 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'k' and resid 141 through 143 removed outlier: 7.005A pdb=" N SER k 172 " --> pdb=" O LEU k 199 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ILE k 201 " --> pdb=" O SER k 172 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL k 174 " --> pdb=" O ILE k 201 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N GLN k 203 " --> pdb=" O VAL k 174 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU k 200 " --> pdb=" O LEU k 411 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL k 413 " --> pdb=" O LEU k 200 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N THR k 202 " --> pdb=" O VAL k 413 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'k' and resid 234 through 236 removed outlier: 6.332A pdb=" N LYS k 234 " --> pdb=" O MET k 347 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ILE k 349 " --> pdb=" O LYS k 234 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU k 236 " --> pdb=" O ILE k 349 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'm' and resid 160 through 161 removed outlier: 7.173A pdb=" N ILE m 160 " --> pdb=" O ILE m 207 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'm' and resid 335 through 336 removed outlier: 3.587A pdb=" N TYR m 335 " --> pdb=" O LEU m 386 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'n' and resid 256 through 257 Processing sheet with id=AJ4, first strand: chain 'n' and resid 271 through 272 Processing sheet with id=AJ5, first strand: chain 'q' and resid 45 through 48 Processing sheet with id=AJ6, first strand: chain 'q' and resid 202 through 203 Processing sheet with id=AJ7, first strand: chain 'q' and resid 237 through 239 removed outlier: 6.374A pdb=" N VAL q 237 " --> pdb=" O VAL q 257 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE q 259 " --> pdb=" O VAL q 237 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ARG q 239 " --> pdb=" O ILE q 259 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'u' and resid 163 through 165 7191 hydrogen bonds defined for protein. 20787 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 387 hydrogen bonds 774 hydrogen bond angles 0 basepair planarities 150 basepair parallelities 253 stacking parallelities Total time for adding SS restraints: 77.69 Time building geometry restraints manager: 42.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 21429 1.31 - 1.44: 34059 1.44 - 1.57: 74965 1.57 - 1.70: 656 1.70 - 1.83: 941 Bond restraints: 132050 Sorted by residual: bond pdb=" CA VAL d 522 " pdb=" CB VAL d 522 " ideal model delta sigma weight residual 1.537 1.571 -0.034 5.00e-03 4.00e+04 4.67e+01 bond pdb=" CG1 ILE U 46 " pdb=" CD1 ILE U 46 " ideal model delta sigma weight residual 1.513 1.327 0.186 3.90e-02 6.57e+02 2.27e+01 bond pdb=" CD LYS S 56 " pdb=" CE LYS S 56 " ideal model delta sigma weight residual 1.520 1.390 0.130 3.00e-02 1.11e+03 1.87e+01 bond pdb=" C PHE B 713 " pdb=" O PHE B 713 " ideal model delta sigma weight residual 1.233 1.253 -0.020 4.80e-03 4.34e+04 1.73e+01 bond pdb=" N THR g 609 " pdb=" CA THR g 609 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.45e+01 ... (remaining 132045 not shown) Histogram of bond angle deviations from ideal: 92.56 - 101.16: 374 101.16 - 109.76: 21066 109.76 - 118.36: 84121 118.36 - 126.96: 73143 126.96 - 135.56: 2138 Bond angle restraints: 180842 Sorted by residual: angle pdb=" N LYS S 56 " pdb=" CA LYS S 56 " pdb=" CB LYS S 56 " ideal model delta sigma weight residual 110.16 120.00 -9.84 1.48e+00 4.57e-01 4.42e+01 angle pdb=" N PRO p 91 " pdb=" CA PRO p 91 " pdb=" C PRO p 91 " ideal model delta sigma weight residual 110.70 118.31 -7.61 1.22e+00 6.72e-01 3.89e+01 angle pdb=" CD1 LEU e 538 " pdb=" CG LEU e 538 " pdb=" CD2 LEU e 538 " ideal model delta sigma weight residual 110.80 98.27 12.53 2.20e+00 2.07e-01 3.24e+01 angle pdb=" CA PRO p 91 " pdb=" C PRO p 91 " pdb=" N PRO p 92 " ideal model delta sigma weight residual 117.93 124.50 -6.57 1.20e+00 6.94e-01 2.99e+01 angle pdb=" C ARG S 63 " pdb=" CA ARG S 63 " pdb=" CB ARG S 63 " ideal model delta sigma weight residual 112.00 102.78 9.22 1.79e+00 3.12e-01 2.65e+01 ... (remaining 180837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 74946 35.44 - 70.88: 3594 70.88 - 106.32: 254 106.32 - 141.77: 0 141.77 - 177.21: 3 Dihedral angle restraints: 78797 sinusoidal: 29974 harmonic: 48823 Sorted by residual: dihedral pdb=" O4' U P -10 " pdb=" C1' U P -10 " pdb=" N1 U P -10 " pdb=" C2 U P -10 " ideal model delta sinusoidal sigma weight residual -160.00 0.46 -160.46 1 1.50e+01 4.44e-03 8.29e+01 dihedral pdb=" CA PHE e 223 " pdb=" C PHE e 223 " pdb=" N ASP e 224 " pdb=" CA ASP e 224 " ideal model delta harmonic sigma weight residual -180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA ARG a1685 " pdb=" C ARG a1685 " pdb=" N GLU a1686 " pdb=" CA GLU a1686 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 78794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.059: 21247 1.059 - 2.117: 0 2.117 - 3.176: 0 3.176 - 4.235: 0 4.235 - 5.293: 2 Chirality restraints: 21249 Sorted by residual: chirality pdb=" CB ILE W 66 " pdb=" CA ILE W 66 " pdb=" CG1 ILE W 66 " pdb=" CG2 ILE W 66 " both_signs ideal model delta sigma weight residual False 2.64 -2.65 5.29 2.00e-01 2.50e+01 7.00e+02 chirality pdb=" CB ILE R 66 " pdb=" CA ILE R 66 " pdb=" CG1 ILE R 66 " pdb=" CG2 ILE R 66 " both_signs ideal model delta sigma weight residual False 2.64 -2.64 5.28 2.00e-01 2.50e+01 6.98e+02 chirality pdb=" CB ILE S 62 " pdb=" CA ILE S 62 " pdb=" CG1 ILE S 62 " pdb=" CG2 ILE S 62 " both_signs ideal model delta sigma weight residual False 2.64 1.95 0.69 2.00e-01 2.50e+01 1.19e+01 ... (remaining 21246 not shown) Planarity restraints: 22474 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C P -11 " -0.043 2.00e-02 2.50e+03 3.09e-02 2.15e+01 pdb=" N1 C P -11 " 0.077 2.00e-02 2.50e+03 pdb=" C2 C P -11 " -0.027 2.00e-02 2.50e+03 pdb=" O2 C P -11 " 0.009 2.00e-02 2.50e+03 pdb=" N3 C P -11 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C P -11 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C P -11 " -0.007 2.00e-02 2.50e+03 pdb=" C5 C P -11 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C P -11 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL d 268 " -0.065 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO d 269 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO d 269 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO d 269 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP k 47 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C ASP k 47 " -0.063 2.00e-02 2.50e+03 pdb=" O ASP k 47 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE k 48 " 0.021 2.00e-02 2.50e+03 ... (remaining 22471 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 3285 2.69 - 3.24: 126628 3.24 - 3.80: 217822 3.80 - 4.35: 267054 4.35 - 4.90: 436699 Nonbonded interactions: 1051488 Sorted by model distance: nonbonded pdb=" OD1 ASN q 117 " pdb="MN MN q1001 " model vdw 2.138 2.320 nonbonded pdb=" O MET A 535 " pdb=" OH TYR A 669 " model vdw 2.196 2.440 nonbonded pdb=" ND1 HIS q 241 " pdb="MN MN q1001 " model vdw 2.196 2.400 nonbonded pdb=" O2' C P -11 " pdb=" O2 U P -10 " model vdw 2.200 2.440 nonbonded pdb=" OG SER k 23 " pdb=" OD1 ASN k 28 " model vdw 2.209 2.440 ... (remaining 1051483 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 'M' and (resid 45 through 86 or (resid 87 through 88 and (name N or name \ CA or name C or name O or name CB )) or resid 89 through 134)) selection = (chain 'S' and resid 45 through 134) } ncs_group { reference = (chain 'O' and (resid 23 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 102)) selection = (chain 'U' and (resid 23 through 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 68 through 102)) } ncs_group { reference = (chain 'Q' and resid 13 through 118) selection = chain 'V' } ncs_group { reference = chain 'R' selection = (chain 'W' and resid 38 through 122) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.980 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: 0.130 Extract box with map and model: 27.530 Check model and map are aligned: 1.420 Set scattering table: 0.870 Process input model: 331.630 Find NCS groups from input model: 4.730 Set up NCS constraints: 0.440 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 375.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3054 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 : 0.007 0.186 132050 Z= 0.425 Angle : 0.907 16.585 180842 Z= 0.478 Chirality : 0.074 5.293 21249 Planarity : 0.006 0.095 22474 Dihedral : 18.741 177.208 47157 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 0.56 % Allowed : 21.50 % Favored : 77.94 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.07), residues: 16602 helix: 0.98 (0.05), residues: 9140 sheet: -0.85 (0.16), residues: 1103 loop : -1.29 (0.08), residues: 6359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 236 HIS 0.020 0.002 HIS A 620 PHE 0.040 0.003 PHE h 407 TYR 0.043 0.003 TYR E 8 ARG 0.040 0.001 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1535 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1470 time to evaluate : 10.474 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.6972 (mtm) cc_final: 0.5858 (mmt) REVERT: A 1262 MET cc_start: 0.4950 (mmm) cc_final: 0.4686 (mpp) REVERT: E 151 MET cc_start: -0.4471 (ptm) cc_final: -0.4942 (mtm) REVERT: H 37 MET cc_start: 0.0140 (ttm) cc_final: -0.0069 (ttm) REVERT: I 108 MET cc_start: -0.3156 (ttt) cc_final: -0.3466 (ttt) REVERT: K 114 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7906 (tt0) REVERT: M 119 ILE cc_start: -0.0709 (OUTLIER) cc_final: -0.1174 (mp) REVERT: O 40 ARG cc_start: -0.1013 (ttt-90) cc_final: -0.1676 (mtt90) REVERT: U 84 MET cc_start: -0.2326 (tmm) cc_final: -0.4580 (tpt) REVERT: Z 460 MET cc_start: 0.2094 (mmt) cc_final: 0.1072 (tpt) REVERT: Z 635 MET cc_start: 0.0886 (tpt) cc_final: -0.0811 (tpt) REVERT: a 973 ASP cc_start: 0.9347 (t70) cc_final: 0.9125 (m-30) REVERT: a 1423 MET cc_start: 0.8340 (mpp) cc_final: 0.7825 (mmp) REVERT: a 1463 MET cc_start: 0.6691 (mmt) cc_final: 0.5590 (mmt) REVERT: a 1466 TRP cc_start: 0.6475 (t60) cc_final: 0.6112 (m-10) REVERT: a 1663 LEU cc_start: 0.8652 (mt) cc_final: 0.7995 (mt) REVERT: a 1664 PHE cc_start: 0.8634 (t80) cc_final: 0.7582 (t80) REVERT: a 1702 ILE cc_start: 0.8484 (mm) cc_final: 0.8192 (mm) REVERT: a 1712 ASP cc_start: 0.7222 (t70) cc_final: 0.6962 (p0) REVERT: a 1846 LEU cc_start: 0.7071 (pp) cc_final: 0.6766 (pp) REVERT: a 1950 ARG cc_start: 0.7438 (mmp-170) cc_final: 0.6996 (mmp-170) REVERT: a 1959 PHE cc_start: 0.6904 (t80) cc_final: 0.6593 (t80) REVERT: a 2069 ASP cc_start: 0.7829 (m-30) cc_final: 0.6904 (m-30) REVERT: a 2183 ILE cc_start: 0.7544 (mt) cc_final: 0.7333 (mt) REVERT: b 26 MET cc_start: -0.1894 (ttt) cc_final: -0.2536 (ttt) REVERT: b 502 THR cc_start: 0.5011 (m) cc_final: 0.4476 (m) REVERT: b 517 MET cc_start: 0.8648 (tpt) cc_final: 0.8384 (mmt) REVERT: b 579 ARG cc_start: 0.7217 (mtm110) cc_final: 0.6894 (ptm160) REVERT: b 699 LEU cc_start: 0.8313 (mp) cc_final: 0.7918 (mp) REVERT: b 746 THR cc_start: 0.7267 (m) cc_final: 0.7052 (p) REVERT: b 755 LYS cc_start: 0.8309 (pttt) cc_final: 0.7912 (pptt) REVERT: b 769 THR cc_start: 0.8354 (m) cc_final: 0.7950 (p) REVERT: b 773 GLN cc_start: 0.8633 (mt0) cc_final: 0.8131 (tp40) REVERT: b 792 VAL cc_start: 0.7660 (m) cc_final: 0.7455 (p) REVERT: b 809 ILE cc_start: 0.8590 (mt) cc_final: 0.8383 (mt) REVERT: b 812 THR cc_start: 0.7239 (m) cc_final: 0.6738 (m) REVERT: b 820 LEU cc_start: 0.8597 (mt) cc_final: 0.8354 (mt) REVERT: b 824 MET cc_start: 0.8173 (ptm) cc_final: 0.7789 (ppp) REVERT: b 830 VAL cc_start: 0.8290 (t) cc_final: 0.8049 (m) REVERT: b 859 ILE cc_start: 0.7672 (mt) cc_final: 0.6778 (mt) REVERT: b 941 ILE cc_start: 0.8160 (mt) cc_final: 0.7580 (mt) REVERT: b 994 GLN cc_start: 0.8244 (mt0) cc_final: 0.7365 (mt0) REVERT: b 997 ILE cc_start: 0.8689 (mt) cc_final: 0.8416 (mt) REVERT: b 998 CYS cc_start: 0.8515 (m) cc_final: 0.8166 (m) REVERT: b 1008 ASP cc_start: 0.7966 (t0) cc_final: 0.7707 (t0) REVERT: b 1083 VAL cc_start: 0.5118 (p) cc_final: 0.4524 (t) REVERT: d 244 ASP cc_start: 0.0356 (OUTLIER) cc_final: -0.0105 (t70) REVERT: d 289 HIS cc_start: 0.5765 (t70) cc_final: 0.5417 (t-170) REVERT: d 309 MET cc_start: -0.2835 (mtm) cc_final: -0.3069 (ttp) REVERT: d 315 HIS cc_start: 0.8785 (m90) cc_final: 0.8408 (t70) REVERT: d 316 PHE cc_start: 0.7329 (m-80) cc_final: 0.6964 (m-80) REVERT: d 441 ASN cc_start: 0.7923 (m-40) cc_final: 0.7237 (p0) REVERT: d 492 ASN cc_start: 0.6334 (t0) cc_final: 0.5984 (m110) REVERT: d 503 ILE cc_start: 0.5690 (mp) cc_final: 0.5212 (mt) REVERT: d 507 LEU cc_start: 0.6259 (mt) cc_final: 0.5983 (mt) REVERT: d 510 LEU cc_start: 0.6935 (tp) cc_final: 0.6716 (tp) REVERT: d 619 GLU cc_start: 0.8705 (pt0) cc_final: 0.8253 (pp20) REVERT: d 638 PHE cc_start: 0.6543 (m-80) cc_final: 0.5949 (m-80) REVERT: d 701 MET cc_start: 0.3518 (mmm) cc_final: 0.2749 (mmt) REVERT: d 805 GLN cc_start: 0.7829 (mp10) cc_final: 0.7608 (mp10) REVERT: d 908 GLN cc_start: 0.4228 (pp30) cc_final: 0.3997 (pp30) REVERT: e 575 LEU cc_start: 0.7701 (mt) cc_final: 0.7407 (mt) REVERT: e 609 ASP cc_start: 0.5251 (m-30) cc_final: 0.4307 (m-30) REVERT: e 774 TYR cc_start: 0.4117 (m-80) cc_final: 0.2965 (m-80) REVERT: e 777 GLN cc_start: 0.2927 (tp40) cc_final: 0.2677 (mm110) REVERT: e 900 SER cc_start: 0.5363 (m) cc_final: 0.4861 (t) REVERT: f 38 LEU cc_start: 0.6679 (mt) cc_final: 0.6088 (tp) REVERT: f 51 MET cc_start: 0.6748 (mtt) cc_final: 0.6484 (mmp) REVERT: f 434 MET cc_start: 0.5279 (mtp) cc_final: 0.4694 (ptt) REVERT: g 30 ASP cc_start: 0.8885 (t70) cc_final: 0.8600 (m-30) REVERT: g 48 PHE cc_start: 0.7570 (m-80) cc_final: 0.7343 (m-80) REVERT: g 57 PHE cc_start: 0.8131 (m-10) cc_final: 0.7854 (m-10) REVERT: g 92 LYS cc_start: 0.7695 (ptmm) cc_final: 0.6621 (tptp) REVERT: g 102 GLU cc_start: 0.8256 (tp30) cc_final: 0.7724 (tp30) REVERT: g 105 LYS cc_start: 0.7826 (tmtt) cc_final: 0.7415 (tmmt) REVERT: g 170 LYS cc_start: 0.8608 (tttp) cc_final: 0.8310 (tptm) REVERT: g 177 CYS cc_start: 0.7851 (t) cc_final: 0.7082 (p) REVERT: g 184 ILE cc_start: 0.8848 (mm) cc_final: 0.8593 (mm) REVERT: g 222 VAL cc_start: 0.8801 (m) cc_final: 0.8580 (p) REVERT: g 249 THR cc_start: 0.6920 (m) cc_final: 0.6526 (p) REVERT: g 428 GLN cc_start: 0.8027 (tp-100) cc_final: 0.7553 (tm-30) REVERT: g 536 MET cc_start: 0.7007 (mmt) cc_final: 0.4830 (tpt) REVERT: g 622 LYS cc_start: 0.7042 (mttp) cc_final: 0.6774 (ptpt) REVERT: g 634 LEU cc_start: 0.8783 (tp) cc_final: 0.8538 (tt) REVERT: g 637 THR cc_start: 0.6779 (OUTLIER) cc_final: 0.6561 (t) REVERT: g 667 ILE cc_start: 0.5114 (tp) cc_final: 0.4732 (mp) REVERT: h 260 TYR cc_start: 0.6958 (m-80) cc_final: 0.6743 (m-10) REVERT: h 535 MET cc_start: 0.1430 (ptt) cc_final: 0.1193 (ppp) REVERT: h 569 LEU cc_start: 0.6759 (tp) cc_final: 0.6427 (tp) REVERT: h 597 LEU cc_start: 0.6639 (tp) cc_final: 0.5900 (tp) REVERT: h 648 MET cc_start: 0.0029 (ptt) cc_final: -0.1302 (ptt) REVERT: h 723 GLN cc_start: 0.8510 (mp10) cc_final: 0.8252 (pt0) REVERT: h 875 VAL cc_start: 0.5859 (t) cc_final: 0.5640 (p) REVERT: h 910 LYS cc_start: 0.6418 (tttt) cc_final: 0.6212 (tptp) REVERT: h 950 GLU cc_start: 0.3408 (pm20) cc_final: 0.1942 (mm-30) REVERT: h 976 GLN cc_start: 0.7596 (mp10) cc_final: 0.7070 (mp10) REVERT: i 24 ILE cc_start: 0.5837 (mp) cc_final: 0.5606 (mp) REVERT: i 382 ASP cc_start: 0.6704 (t0) cc_final: 0.6033 (t0) REVERT: i 383 PHE cc_start: 0.6773 (t80) cc_final: 0.6143 (t80) REVERT: i 386 ASP cc_start: 0.6322 (m-30) cc_final: 0.5584 (m-30) REVERT: k 37 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8464 (mpp) REVERT: k 59 ASP cc_start: 0.8242 (t70) cc_final: 0.7430 (p0) REVERT: k 420 MET cc_start: 0.1468 (mtt) cc_final: 0.0397 (tpp) REVERT: p 255 LYS cc_start: 0.9676 (tptp) cc_final: 0.9401 (pptt) REVERT: p 427 MET cc_start: 0.8407 (tpp) cc_final: 0.8184 (mmp) REVERT: p 499 MET cc_start: 0.6731 (mmp) cc_final: 0.6293 (mtp) REVERT: p 521 MET cc_start: 0.6982 (mmt) cc_final: 0.6158 (mtp) REVERT: q 66 MET cc_start: 0.6738 (mmm) cc_final: 0.6221 (mtp) REVERT: q 82 PHE cc_start: 0.6561 (m-80) cc_final: 0.5916 (m-80) REVERT: q 130 TYR cc_start: 0.6148 (t80) cc_final: 0.5943 (t80) REVERT: q 195 MET cc_start: 0.1463 (ttm) cc_final: 0.0608 (tmm) REVERT: w 245 MET cc_start: -0.4486 (pmm) cc_final: -0.5050 (ptp) REVERT: w 425 MET cc_start: -0.0922 (pmm) cc_final: -0.1296 (mmt) outliers start: 65 outliers final: 11 residues processed: 1522 average time/residue: 1.0614 time to fit residues: 2828.9571 Evaluate side-chains 1028 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1013 time to evaluate : 10.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1711 random chunks: chunk 1444 optimal weight: 9.9990 chunk 1296 optimal weight: 50.0000 chunk 719 optimal weight: 0.8980 chunk 443 optimal weight: 120.0000 chunk 874 optimal weight: 10.0000 chunk 692 optimal weight: 0.3980 chunk 1341 optimal weight: 20.0000 chunk 518 optimal weight: 20.0000 chunk 815 optimal weight: 9.9990 chunk 998 optimal weight: 0.9990 chunk 1553 optimal weight: 6.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 312 GLN B 344 GLN B 481 HIS ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS D 48 ASN I 41 ASN I 67 GLN I 98 GLN I 100 HIS L 26 ASN ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 94 ASN ** Z 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1889 HIS ** a1928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2087 ASN ** a2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2132 GLN a2170 GLN b 62 GLN b 326 GLN b 450 GLN b 488 HIS b 491 GLN ** b 707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 850 GLN b 934 GLN ** b1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b1152 GLN ** d 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 197 GLN d 403 GLN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 630 GLN ** d 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 667 GLN ** d 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 452 HIS e 537 GLN ** e 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 785 HIS e 953 HIS e1007 GLN ** f 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 145 GLN g 185 GLN g 219 GLN ** g 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 293 GLN g 355 ASN ** g 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 399 GLN ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 598 HIS ** g 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 792 GLN g 800 GLN ** g 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 875 ASN ** h 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 781 HIS ** h 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 892 ASN ** h 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 917 GLN i 188 ASN k 304 HIS k 429 GLN p 72 GLN p 230 ASN p 383 ASN ** p 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 44 ASN q 63 HIS ** q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 152 HIS ** w 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 394 HIS ** w 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 489 GLN w 502 HIS Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3556 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.166 132050 Z= 0.380 Angle : 0.812 17.000 180842 Z= 0.419 Chirality : 0.047 0.335 21249 Planarity : 0.006 0.132 22474 Dihedral : 14.807 178.617 21584 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.53 % Favored : 95.45 % Rotamer: Outliers : 0.45 % Allowed : 5.41 % Favored : 94.14 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.06), residues: 16602 helix: 0.70 (0.05), residues: 9204 sheet: -0.71 (0.15), residues: 1079 loop : -1.25 (0.08), residues: 6319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP r2041 HIS 0.020 0.002 HIS a1889 PHE 0.057 0.003 PHE a1842 TYR 0.109 0.003 TYR w 362 ARG 0.124 0.001 ARG a1841 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1202 time to evaluate : 9.715 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 MET cc_start: 0.7280 (mpp) cc_final: 0.6246 (mmt) REVERT: A 868 MET cc_start: 0.1833 (mmt) cc_final: 0.1570 (mpp) REVERT: A 1207 ILE cc_start: 0.8505 (mt) cc_final: 0.8243 (mm) REVERT: A 1262 MET cc_start: 0.4885 (mmm) cc_final: 0.4093 (mpp) REVERT: A 1292 MET cc_start: -0.5009 (ptt) cc_final: -0.6372 (ttt) REVERT: B 407 MET cc_start: -0.4169 (mtp) cc_final: -0.4720 (mmm) REVERT: B 594 MET cc_start: -0.2353 (mmp) cc_final: -0.2669 (mmt) REVERT: B 764 MET cc_start: -0.5102 (ptt) cc_final: -0.5391 (ptt) REVERT: B 796 MET cc_start: 0.0929 (mtt) cc_final: 0.0594 (mtt) REVERT: B 1163 MET cc_start: 0.4249 (mtm) cc_final: 0.3718 (ttt) REVERT: E 94 MET cc_start: -0.6354 (ttt) cc_final: -0.6846 (ttt) REVERT: E 151 MET cc_start: -0.4681 (ptm) cc_final: -0.5065 (mtm) REVERT: I 108 MET cc_start: -0.3315 (ttt) cc_final: -0.3782 (ttt) REVERT: J 48 MET cc_start: 0.1014 (mmm) cc_final: 0.0673 (tpt) REVERT: M 120 MET cc_start: -0.0146 (pmm) cc_final: -0.0736 (mmp) REVERT: O 40 ARG cc_start: -0.1013 (ttt-90) cc_final: -0.1861 (mpt180) REVERT: U 84 MET cc_start: -0.2279 (tmm) cc_final: -0.4298 (tpt) REVERT: Z 460 MET cc_start: 0.2110 (mmt) cc_final: 0.1370 (tpt) REVERT: Z 508 MET cc_start: -0.1500 (tpt) cc_final: -0.2043 (tpt) REVERT: Z 635 MET cc_start: 0.1373 (tpt) cc_final: 0.0376 (mmt) REVERT: a 1131 MET cc_start: -0.2684 (mmt) cc_final: -0.3227 (ppp) REVERT: a 1502 LEU cc_start: 0.8280 (mt) cc_final: 0.7991 (mp) REVERT: a 1506 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8803 (mm-30) REVERT: a 1663 LEU cc_start: 0.8897 (mt) cc_final: 0.8659 (mt) REVERT: a 1664 PHE cc_start: 0.8997 (t80) cc_final: 0.8317 (t80) REVERT: a 1766 LEU cc_start: 0.8993 (pp) cc_final: 0.8759 (tt) REVERT: a 1842 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6637 (m-10) REVERT: a 1950 ARG cc_start: 0.7241 (mmp-170) cc_final: 0.6816 (mmp-170) REVERT: a 2053 ARG cc_start: 0.7781 (ttp-110) cc_final: 0.7502 (ttp-170) REVERT: a 2069 ASP cc_start: 0.7989 (m-30) cc_final: 0.6962 (m-30) REVERT: a 2121 PHE cc_start: 0.0956 (m-80) cc_final: 0.0650 (m-80) REVERT: a 2147 TYR cc_start: 0.5561 (t80) cc_final: 0.5139 (t80) REVERT: a 2187 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7586 (tt0) REVERT: b 589 HIS cc_start: 0.8244 (t70) cc_final: 0.7988 (t70) REVERT: b 684 MET cc_start: 0.8997 (tpp) cc_final: 0.8715 (mmt) REVERT: b 713 LEU cc_start: 0.8887 (mm) cc_final: 0.8196 (mm) REVERT: b 716 THR cc_start: 0.8752 (m) cc_final: 0.8288 (p) REVERT: b 717 ASN cc_start: 0.8568 (m110) cc_final: 0.7985 (m110) REVERT: b 773 GLN cc_start: 0.9139 (mt0) cc_final: 0.8488 (tm-30) REVERT: b 781 LEU cc_start: 0.8633 (mp) cc_final: 0.8306 (mp) REVERT: b 792 VAL cc_start: 0.8628 (m) cc_final: 0.8425 (p) REVERT: b 803 SER cc_start: 0.8624 (t) cc_final: 0.8373 (t) REVERT: b 854 MET cc_start: 0.7490 (ttm) cc_final: 0.7046 (mtp) REVERT: b 891 TYR cc_start: 0.8667 (t80) cc_final: 0.8330 (t80) REVERT: b 944 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7868 (mt-10) REVERT: b 987 LEU cc_start: 0.8262 (mp) cc_final: 0.7925 (mt) REVERT: b 1035 MET cc_start: 0.8226 (mmm) cc_final: 0.7445 (mmt) REVERT: b 1040 ASP cc_start: 0.8897 (m-30) cc_final: 0.8572 (m-30) REVERT: b 1079 LEU cc_start: 0.8164 (tt) cc_final: 0.7923 (tt) REVERT: b 1101 MET cc_start: 0.8206 (ttm) cc_final: 0.7888 (ttp) REVERT: d 441 ASN cc_start: 0.8448 (m-40) cc_final: 0.7550 (p0) REVERT: d 445 ARG cc_start: 0.7933 (mtm110) cc_final: 0.7691 (ptt180) REVERT: d 492 ASN cc_start: 0.7888 (t0) cc_final: 0.7111 (m110) REVERT: d 503 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.6954 (mp) REVERT: d 662 THR cc_start: 0.6081 (m) cc_final: 0.5821 (p) REVERT: d 680 ASN cc_start: 0.2285 (OUTLIER) cc_final: 0.2021 (p0) REVERT: d 701 MET cc_start: 0.4074 (tpt) cc_final: 0.3216 (mmt) REVERT: d 717 LYS cc_start: 0.6572 (ptpp) cc_final: 0.5701 (tptt) REVERT: d 735 ILE cc_start: 0.2298 (mm) cc_final: 0.2095 (tp) REVERT: d 750 MET cc_start: 0.2850 (tpt) cc_final: 0.2566 (ptt) REVERT: d 759 ASP cc_start: 0.8385 (t70) cc_final: 0.8177 (m-30) REVERT: d 776 PHE cc_start: 0.8617 (t80) cc_final: 0.8100 (t80) REVERT: d 915 LEU cc_start: 0.7595 (tp) cc_final: 0.7386 (tp) REVERT: e 152 MET cc_start: -0.8144 (ttm) cc_final: -0.8347 (ttm) REVERT: e 234 PHE cc_start: 0.7788 (t80) cc_final: 0.7564 (t80) REVERT: e 415 MET cc_start: 0.2904 (ptm) cc_final: 0.2678 (ptt) REVERT: e 777 GLN cc_start: 0.3350 (tp40) cc_final: 0.2207 (mm-40) REVERT: e 862 LYS cc_start: 0.6975 (mttt) cc_final: 0.6009 (mmmt) REVERT: f 51 MET cc_start: 0.7472 (mtt) cc_final: 0.7221 (mpp) REVERT: f 152 LEU cc_start: 0.8859 (tt) cc_final: 0.8416 (mm) REVERT: f 434 MET cc_start: 0.5924 (mtt) cc_final: 0.5592 (mtm) REVERT: f 554 ASP cc_start: 0.8390 (m-30) cc_final: 0.7777 (p0) REVERT: f 587 MET cc_start: 0.2136 (tpt) cc_final: 0.1562 (mmm) REVERT: g 135 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8318 (mm-30) REVERT: g 177 CYS cc_start: 0.8238 (t) cc_final: 0.7579 (p) REVERT: g 178 ASN cc_start: 0.8778 (p0) cc_final: 0.8472 (p0) REVERT: g 187 LEU cc_start: 0.7714 (tp) cc_final: 0.7345 (tp) REVERT: g 204 MET cc_start: 0.8319 (mmp) cc_final: 0.8015 (mmp) REVERT: g 428 GLN cc_start: 0.8227 (tp-100) cc_final: 0.7709 (tm-30) REVERT: g 467 MET cc_start: 0.2865 (tmm) cc_final: 0.2653 (tmm) REVERT: g 536 MET cc_start: 0.7176 (mmt) cc_final: 0.5176 (tpt) REVERT: g 622 LYS cc_start: 0.7309 (mttp) cc_final: 0.6869 (mttt) REVERT: g 628 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6780 (mt) REVERT: h 648 MET cc_start: -0.0605 (ptt) cc_final: -0.1525 (ptt) REVERT: h 723 GLN cc_start: 0.8859 (mp10) cc_final: 0.8430 (pm20) REVERT: h 882 LYS cc_start: 0.8746 (tttm) cc_final: 0.8355 (tptt) REVERT: h 884 MET cc_start: 0.7044 (mtp) cc_final: 0.6644 (tpt) REVERT: h 900 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6904 (mp) REVERT: h 910 LYS cc_start: 0.6521 (tttt) cc_final: 0.6214 (tptt) REVERT: h 990 MET cc_start: 0.2743 (mmm) cc_final: 0.2260 (mmm) REVERT: i 15 ASN cc_start: 0.8209 (t0) cc_final: 0.7716 (m-40) REVERT: i 43 LEU cc_start: 0.7126 (tt) cc_final: 0.6513 (pp) REVERT: i 250 MET cc_start: 0.6373 (tpp) cc_final: 0.5489 (ttt) REVERT: i 383 PHE cc_start: 0.7043 (t80) cc_final: 0.6397 (t80) REVERT: i 386 ASP cc_start: 0.6514 (m-30) cc_final: 0.6237 (p0) REVERT: i 429 TYR cc_start: 0.5145 (p90) cc_final: 0.4944 (p90) REVERT: i 441 MET cc_start: 0.5159 (tmm) cc_final: 0.4917 (tmm) REVERT: i 445 TYR cc_start: 0.4421 (t80) cc_final: 0.4215 (t80) REVERT: k 59 ASP cc_start: 0.8971 (t70) cc_final: 0.7901 (p0) REVERT: k 92 MET cc_start: 0.6574 (pmm) cc_final: 0.6322 (pmm) REVERT: p 427 MET cc_start: 0.8742 (tpp) cc_final: 0.8489 (mmm) REVERT: p 499 MET cc_start: 0.7154 (mmp) cc_final: 0.6835 (mtp) REVERT: p 521 MET cc_start: 0.7007 (mmt) cc_final: 0.6586 (mtt) REVERT: q 80 TYR cc_start: 0.3651 (m-80) cc_final: 0.3329 (m-80) REVERT: q 130 TYR cc_start: 0.6702 (t80) cc_final: 0.6448 (t80) REVERT: q 144 LYS cc_start: 0.8573 (tmmt) cc_final: 0.8372 (tppt) REVERT: q 275 ILE cc_start: 0.5315 (pt) cc_final: 0.5041 (mt) REVERT: u 76 MET cc_start: 0.7039 (mmt) cc_final: 0.6652 (mmt) REVERT: w 245 MET cc_start: -0.4052 (pmm) cc_final: -0.5053 (ptp) outliers start: 52 outliers final: 16 residues processed: 1241 average time/residue: 1.0581 time to fit residues: 2313.6158 Evaluate side-chains 972 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 951 time to evaluate : 10.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1711 random chunks: chunk 863 optimal weight: 2.9990 chunk 482 optimal weight: 40.0000 chunk 1293 optimal weight: 50.0000 chunk 1058 optimal weight: 0.7980 chunk 428 optimal weight: 10.0000 chunk 1556 optimal weight: 10.0000 chunk 1681 optimal weight: 50.0000 chunk 1386 optimal weight: 40.0000 chunk 1543 optimal weight: 9.9990 chunk 530 optimal weight: 10.0000 chunk 1248 optimal weight: 30.0000 overall best weight: 6.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 ASN A 507 GLN A 576 GLN ** A 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 GLN B 145 GLN B 390 ASN B 906 GLN B1101 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 ASN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 82 HIS ** Z 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1055 HIS ** a1082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1385 GLN a1429 HIS a1443 GLN a1465 GLN a1713 GLN a1840 HIS a1889 HIS ** a1904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 HIS ** b 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 717 ASN b 747 ASN ** b 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b1063 HIS b1082 ASN ** b1184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1187 HIS d 172 GLN ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 908 GLN e 537 GLN ** e 562 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 145 HIS f 217 ASN f 234 ASN ** f 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 486 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 532 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 570 HIS ** g 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 511 GLN ** h 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 879 GLN ** h 892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 105 HIS i 341 GLN ** i 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 549 ASN ** k 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 117 HIS p 399 GLN p 444 ASN ** p 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 545 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 12 GLN ** q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 230 HIS ** q 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 145 ASN w 197 GLN w 401 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4087 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.136 132050 Z= 0.563 Angle : 1.031 21.749 180842 Z= 0.530 Chirality : 0.055 0.810 21249 Planarity : 0.008 0.154 22474 Dihedral : 15.017 179.949 21584 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 28.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.07 % Favored : 93.81 % Rotamer: Outliers : 1.26 % Allowed : 7.17 % Favored : 91.57 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.25 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.07), residues: 16602 helix: 0.11 (0.05), residues: 9180 sheet: -1.14 (0.15), residues: 1091 loop : -1.37 (0.08), residues: 6331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP d 679 HIS 0.034 0.003 HIS g 140 PHE 0.058 0.004 PHE q 69 TYR 0.071 0.003 TYR g 259 ARG 0.032 0.001 ARG e 893 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1142 time to evaluate : 10.499 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 868 MET cc_start: 0.3307 (mmt) cc_final: 0.2926 (mmp) REVERT: A 1054 MET cc_start: -0.3362 (tpp) cc_final: -0.3756 (ttm) REVERT: A 1262 MET cc_start: 0.4601 (mmm) cc_final: 0.4399 (mpp) REVERT: A 1296 MET cc_start: -0.2991 (tpp) cc_final: -0.3517 (ttt) REVERT: B 298 MET cc_start: 0.5365 (tpt) cc_final: 0.4923 (tpp) REVERT: B 594 MET cc_start: -0.2054 (mmp) cc_final: -0.2414 (mmt) REVERT: B 796 MET cc_start: 0.2655 (mtt) cc_final: 0.2259 (mtt) REVERT: B 976 MET cc_start: 0.6345 (tpp) cc_final: 0.6131 (mmt) REVERT: B 1163 MET cc_start: 0.4275 (mtm) cc_final: 0.3644 (ttt) REVERT: E 94 MET cc_start: -0.6585 (ttt) cc_final: -0.6835 (ttt) REVERT: I 108 MET cc_start: -0.2868 (ttt) cc_final: -0.3548 (ttt) REVERT: J 48 MET cc_start: 0.1165 (mmm) cc_final: 0.0806 (tpt) REVERT: M 120 MET cc_start: -0.0541 (pmm) cc_final: -0.0763 (mmp) REVERT: O 40 ARG cc_start: -0.0950 (ttt-90) cc_final: -0.1625 (mtt90) REVERT: O 55 ARG cc_start: -0.2571 (mmt180) cc_final: -0.3558 (mmt180) REVERT: U 84 MET cc_start: -0.2276 (tmm) cc_final: -0.4207 (tpt) REVERT: Z 460 MET cc_start: 0.2521 (mmt) cc_final: 0.2243 (tpt) REVERT: Z 508 MET cc_start: -0.1858 (tpt) cc_final: -0.2454 (tpt) REVERT: Z 635 MET cc_start: 0.1536 (tpt) cc_final: 0.0652 (mmt) REVERT: a 1463 MET cc_start: 0.7163 (tpt) cc_final: 0.6844 (tmm) REVERT: a 1502 LEU cc_start: 0.8880 (mt) cc_final: 0.8641 (mt) REVERT: a 1661 LEU cc_start: 0.9055 (tp) cc_final: 0.8772 (tp) REVERT: a 1740 LEU cc_start: 0.8462 (mt) cc_final: 0.7971 (tp) REVERT: a 1950 ARG cc_start: 0.7575 (mmp-170) cc_final: 0.7143 (mmp-170) REVERT: a 1997 MET cc_start: 0.1925 (ptt) cc_final: 0.1355 (tmm) REVERT: a 2069 ASP cc_start: 0.8652 (m-30) cc_final: 0.8160 (m-30) REVERT: a 2111 MET cc_start: 0.7353 (ptt) cc_final: 0.6930 (ptt) REVERT: a 2114 SER cc_start: 0.8207 (t) cc_final: 0.7798 (p) REVERT: a 2117 ILE cc_start: 0.8567 (pt) cc_final: 0.8162 (pt) REVERT: a 2171 MET cc_start: 0.6774 (ppp) cc_final: 0.6506 (ppp) REVERT: b 314 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.5581 (ttm110) REVERT: b 505 MET cc_start: 0.4600 (ptt) cc_final: 0.4123 (ttt) REVERT: b 575 ASP cc_start: 0.9315 (m-30) cc_final: 0.8674 (p0) REVERT: b 616 ASN cc_start: 0.9525 (t0) cc_final: 0.9212 (p0) REVERT: b 755 LYS cc_start: 0.9381 (ptmt) cc_final: 0.8522 (tmmt) REVERT: b 776 GLU cc_start: 0.9063 (tp30) cc_final: 0.8697 (tp30) REVERT: b 793 LEU cc_start: 0.9096 (pp) cc_final: 0.8355 (pp) REVERT: b 797 MET cc_start: 0.9031 (ttm) cc_final: 0.8651 (ttm) REVERT: b 831 MET cc_start: 0.8074 (ppp) cc_final: 0.7785 (ppp) REVERT: b 925 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7603 (mp0) REVERT: b 1035 MET cc_start: 0.8621 (mmm) cc_final: 0.7061 (mmm) REVERT: b 1101 MET cc_start: 0.7462 (ttm) cc_final: 0.6813 (ttm) REVERT: d 309 MET cc_start: 0.1546 (ttp) cc_final: 0.0110 (tmm) REVERT: d 400 MET cc_start: 0.5860 (ptm) cc_final: 0.5549 (ptm) REVERT: d 441 ASN cc_start: 0.9210 (m-40) cc_final: 0.8648 (p0) REVERT: d 448 GLN cc_start: 0.7632 (mt0) cc_final: 0.7155 (tt0) REVERT: d 473 CYS cc_start: 0.8372 (m) cc_final: 0.6864 (t) REVERT: d 488 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8481 (tp30) REVERT: d 625 GLN cc_start: 0.8377 (tt0) cc_final: 0.7992 (tt0) REVERT: d 701 MET cc_start: 0.7135 (tpt) cc_final: 0.6577 (mmt) REVERT: d 705 TYR cc_start: 0.7952 (m-10) cc_final: 0.7647 (m-10) REVERT: d 707 MET cc_start: 0.7229 (ttp) cc_final: 0.6838 (ttp) REVERT: d 803 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6772 (mt) REVERT: d 846 ASP cc_start: 0.8319 (p0) cc_final: 0.7867 (m-30) REVERT: d 856 ASP cc_start: 0.8623 (p0) cc_final: 0.8412 (p0) REVERT: d 859 ASN cc_start: 0.8858 (m110) cc_final: 0.8648 (m110) REVERT: d 866 LEU cc_start: 0.8556 (tp) cc_final: 0.8079 (tp) REVERT: d 878 LYS cc_start: 0.8611 (pttt) cc_final: 0.8270 (ptpt) REVERT: d 911 VAL cc_start: 0.9195 (m) cc_final: 0.8841 (m) REVERT: e 655 PHE cc_start: 0.5461 (t80) cc_final: 0.4861 (t80) REVERT: e 862 LYS cc_start: 0.7621 (mttt) cc_final: 0.6513 (mmmt) REVERT: f 434 MET cc_start: 0.6463 (mtt) cc_final: 0.6167 (mtm) REVERT: f 626 MET cc_start: 0.1783 (mmm) cc_final: 0.1545 (tpt) REVERT: g 34 ARG cc_start: 0.9072 (mmm160) cc_final: 0.8603 (mmp80) REVERT: g 95 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8893 (mp0) REVERT: g 178 ASN cc_start: 0.8965 (p0) cc_final: 0.8630 (p0) REVERT: g 204 MET cc_start: 0.8911 (mmp) cc_final: 0.8286 (mmp) REVERT: g 230 MET cc_start: 0.8802 (mmm) cc_final: 0.8552 (tpp) REVERT: g 255 LEU cc_start: 0.9040 (tp) cc_final: 0.8815 (tp) REVERT: g 300 LEU cc_start: 0.9576 (mt) cc_final: 0.9334 (mt) REVERT: g 349 GLN cc_start: 0.8097 (mt0) cc_final: 0.7697 (mm-40) REVERT: g 393 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8367 (mm) REVERT: g 416 MET cc_start: 0.5713 (tpp) cc_final: 0.5483 (tpp) REVERT: g 428 GLN cc_start: 0.8840 (tp-100) cc_final: 0.8558 (tm-30) REVERT: g 458 MET cc_start: 0.5793 (ptt) cc_final: 0.5467 (ptm) REVERT: g 541 MET cc_start: 0.4021 (ttm) cc_final: 0.3316 (tmm) REVERT: g 598 HIS cc_start: 0.5287 (OUTLIER) cc_final: 0.4586 (t-90) REVERT: g 616 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6441 (p90) REVERT: g 631 PHE cc_start: 0.7181 (m-80) cc_final: 0.6707 (m-80) REVERT: g 800 GLN cc_start: 0.6618 (pt0) cc_final: 0.6259 (pt0) REVERT: g 843 LEU cc_start: 0.7895 (tt) cc_final: 0.7457 (mm) REVERT: g 917 VAL cc_start: 0.8272 (t) cc_final: 0.8004 (p) REVERT: h 343 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8782 (mm-40) REVERT: h 383 LYS cc_start: 0.8345 (mttp) cc_final: 0.8084 (mmtt) REVERT: h 535 MET cc_start: 0.2748 (ppp) cc_final: 0.2455 (ppp) REVERT: h 588 HIS cc_start: 0.8822 (m170) cc_final: 0.8506 (m-70) REVERT: h 590 LYS cc_start: 0.8928 (mttt) cc_final: 0.8663 (mmtp) REVERT: h 591 GLN cc_start: 0.8511 (pt0) cc_final: 0.8115 (pm20) REVERT: h 648 MET cc_start: -0.0557 (ptt) cc_final: -0.0943 (ptt) REVERT: h 728 SER cc_start: 0.6440 (p) cc_final: 0.6194 (m) REVERT: h 746 GLU cc_start: 0.8151 (mp0) cc_final: 0.7651 (mp0) REVERT: h 882 LYS cc_start: 0.8586 (tttm) cc_final: 0.8161 (tptp) REVERT: h 891 LEU cc_start: 0.4345 (mm) cc_final: 0.4143 (mm) REVERT: h 910 LYS cc_start: 0.6828 (tttt) cc_final: 0.6438 (tptt) REVERT: h 937 ILE cc_start: 0.6927 (mm) cc_final: 0.6722 (mm) REVERT: h 965 GLU cc_start: 0.3253 (pt0) cc_final: 0.1469 (tp30) REVERT: h 980 GLN cc_start: 0.7994 (tt0) cc_final: 0.7594 (tt0) REVERT: i 25 MET cc_start: 0.3961 (tmm) cc_final: 0.3433 (tmm) REVERT: i 184 MET cc_start: 0.5014 (pmm) cc_final: 0.4736 (pmm) REVERT: i 379 ILE cc_start: 0.8665 (mt) cc_final: 0.8423 (tt) REVERT: i 429 TYR cc_start: 0.6498 (p90) cc_final: 0.5971 (p90) REVERT: i 441 MET cc_start: 0.7287 (tmm) cc_final: 0.5942 (ttt) REVERT: i 442 LYS cc_start: 0.8634 (ttpt) cc_final: 0.7948 (pttp) REVERT: i 445 TYR cc_start: 0.5537 (t80) cc_final: 0.5317 (t80) REVERT: i 489 MET cc_start: 0.7428 (mmp) cc_final: 0.7127 (mmt) REVERT: k 59 ASP cc_start: 0.8858 (t70) cc_final: 0.8140 (p0) REVERT: k 92 MET cc_start: 0.6737 (pmm) cc_final: 0.6497 (pmm) REVERT: k 437 MET cc_start: 0.8999 (tpt) cc_final: 0.8698 (tpp) REVERT: p 521 MET cc_start: 0.6941 (mmt) cc_final: 0.6350 (mtp) REVERT: q 74 LYS cc_start: 0.8915 (mttp) cc_final: 0.8513 (ttmt) REVERT: q 130 TYR cc_start: 0.7219 (t80) cc_final: 0.6967 (t80) REVERT: q 175 ASP cc_start: 0.7889 (t0) cc_final: 0.6643 (t0) REVERT: q 195 MET cc_start: 0.3303 (ttm) cc_final: 0.3056 (ttt) REVERT: q 234 LEU cc_start: 0.7916 (mt) cc_final: 0.7620 (mt) REVERT: u 92 MET cc_start: -0.4668 (ppp) cc_final: -0.5246 (ptm) REVERT: w 338 MET cc_start: -0.7434 (mmt) cc_final: -0.8145 (mmt) REVERT: w 425 MET cc_start: 0.0103 (pmm) cc_final: -0.1227 (mmt) outliers start: 146 outliers final: 62 residues processed: 1261 average time/residue: 1.0374 time to fit residues: 2328.4507 Evaluate side-chains 978 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 911 time to evaluate : 10.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1711 random chunks: chunk 1537 optimal weight: 3.9990 chunk 1170 optimal weight: 7.9990 chunk 807 optimal weight: 5.9990 chunk 172 optimal weight: 50.0000 chunk 742 optimal weight: 0.7980 chunk 1045 optimal weight: 1.9990 chunk 1562 optimal weight: 10.0000 chunk 1653 optimal weight: 10.0000 chunk 816 optimal weight: 2.9990 chunk 1480 optimal weight: 50.0000 chunk 445 optimal weight: 110.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 GLN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS C 262 GLN ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN K 49 GLN L 26 ASN ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1385 GLN ** a1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1782 HIS ** a1805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a2170 GLN ** b 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 697 GLN b 717 ASN b 747 ASN b 773 GLN b1003 GLN ** b1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 58 GLN ** d 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 568 HIS ** d 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 908 GLN e 452 HIS e 672 GLN e 679 GLN ** e 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 984 HIS ** e 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN f 555 HIS ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 369 ASN ** g 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 538 ASN ** g 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 690 GLN ** g 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 831 ASN ** h 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 970 ASN ** h 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 105 HIS i 116 HIS ** i 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 434 ASN p 237 GLN p 372 GLN ** p 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 545 GLN ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 229 ASN w 219 ASN ** w 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4027 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 132050 Z= 0.304 Angle : 0.690 12.191 180842 Z= 0.354 Chirality : 0.044 0.420 21249 Planarity : 0.005 0.084 22474 Dihedral : 14.750 179.960 21584 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.90 % Favored : 95.08 % Rotamer: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.07), residues: 16602 helix: 0.52 (0.05), residues: 9253 sheet: -1.10 (0.15), residues: 1092 loop : -1.20 (0.08), residues: 6257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP q 250 HIS 0.020 0.001 HIS g 598 PHE 0.042 0.002 PHE e 705 TYR 0.050 0.002 TYR h 928 ARG 0.025 0.001 ARG e 767 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1101 time to evaluate : 10.575 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: A 868 MET cc_start: 0.3431 (mmt) cc_final: 0.3061 (mmp) REVERT: A 1309 MET cc_start: -0.3810 (mmp) cc_final: -0.4154 (mmp) REVERT: A 1412 MET cc_start: -0.0839 (pmm) cc_final: -0.1169 (pmm) REVERT: B 407 MET cc_start: -0.4561 (ptp) cc_final: -0.5488 (mmm) REVERT: B 594 MET cc_start: -0.2045 (mmp) cc_final: -0.2468 (mmt) REVERT: B 796 MET cc_start: 0.2517 (mtt) cc_final: 0.2163 (mtt) REVERT: B 1151 MET cc_start: 0.6247 (ppp) cc_final: 0.6044 (ppp) REVERT: B 1163 MET cc_start: 0.4087 (mtm) cc_final: 0.3627 (ttt) REVERT: E 94 MET cc_start: -0.6278 (ttt) cc_final: -0.6829 (ttt) REVERT: I 108 MET cc_start: -0.2852 (ttt) cc_final: -0.3486 (ttt) REVERT: M 120 MET cc_start: -0.0132 (pmm) cc_final: -0.0371 (mmp) REVERT: O 40 ARG cc_start: -0.0902 (ttt-90) cc_final: -0.1734 (mpt180) REVERT: O 55 ARG cc_start: -0.2714 (mmt180) cc_final: -0.3611 (mmt180) REVERT: U 84 MET cc_start: -0.2411 (tmm) cc_final: -0.4341 (tpt) REVERT: Z 460 MET cc_start: 0.2592 (mmt) cc_final: 0.1461 (tpp) REVERT: Z 508 MET cc_start: -0.1746 (tpt) cc_final: -0.2435 (tpt) REVERT: Z 635 MET cc_start: 0.1580 (tpt) cc_final: 0.0666 (mmt) REVERT: a 1463 MET cc_start: 0.7348 (tpt) cc_final: 0.6939 (tpt) REVERT: a 1502 LEU cc_start: 0.8769 (mt) cc_final: 0.8366 (mt) REVERT: a 1506 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8864 (mm-30) REVERT: a 1624 MET cc_start: 0.9370 (mtp) cc_final: 0.9079 (mtt) REVERT: a 1661 LEU cc_start: 0.8889 (tp) cc_final: 0.8631 (tp) REVERT: a 1950 ARG cc_start: 0.7699 (mmp-170) cc_final: 0.7377 (mmp-170) REVERT: a 2047 MET cc_start: 0.2549 (mtp) cc_final: 0.1874 (mtt) REVERT: a 2069 ASP cc_start: 0.8658 (m-30) cc_final: 0.8143 (m-30) REVERT: a 2092 MET cc_start: 0.7336 (ppp) cc_final: 0.7083 (tmm) REVERT: a 2114 SER cc_start: 0.8391 (t) cc_final: 0.8142 (t) REVERT: a 2121 PHE cc_start: 0.7971 (m-80) cc_final: 0.6711 (t80) REVERT: a 2171 MET cc_start: 0.7393 (ppp) cc_final: 0.7160 (ppp) REVERT: a 2176 GLN cc_start: 0.8446 (mm-40) cc_final: 0.7965 (mp10) REVERT: b 557 ILE cc_start: 0.8858 (mm) cc_final: 0.8521 (mm) REVERT: b 575 ASP cc_start: 0.9296 (m-30) cc_final: 0.8774 (p0) REVERT: b 616 ASN cc_start: 0.9486 (t0) cc_final: 0.9198 (p0) REVERT: b 726 ASP cc_start: 0.8809 (m-30) cc_final: 0.8505 (m-30) REVERT: b 772 MET cc_start: 0.8919 (tmm) cc_final: 0.8412 (tmm) REVERT: b 781 LEU cc_start: 0.9152 (mp) cc_final: 0.8948 (mp) REVERT: b 797 MET cc_start: 0.9243 (ttm) cc_final: 0.8923 (ttm) REVERT: b 818 MET cc_start: 0.8778 (mmt) cc_final: 0.8450 (mmt) REVERT: b 924 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8790 (mp0) REVERT: b 944 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7545 (mt-10) REVERT: b 947 LEU cc_start: 0.8562 (mt) cc_final: 0.8336 (mp) REVERT: b 1023 GLU cc_start: 0.7983 (mp0) cc_final: 0.7776 (mp0) REVERT: b 1070 LEU cc_start: 0.8786 (mm) cc_final: 0.8572 (mm) REVERT: b 1101 MET cc_start: 0.8239 (ttm) cc_final: 0.7932 (tpt) REVERT: d 309 MET cc_start: -0.0390 (ttp) cc_final: -0.1171 (ttp) REVERT: d 316 PHE cc_start: 0.8169 (m-80) cc_final: 0.7913 (m-80) REVERT: d 448 GLN cc_start: 0.7750 (mt0) cc_final: 0.7388 (tt0) REVERT: d 473 CYS cc_start: 0.8513 (m) cc_final: 0.6879 (t) REVERT: d 567 ASP cc_start: 0.8795 (p0) cc_final: 0.8148 (t0) REVERT: d 619 GLU cc_start: 0.8975 (pt0) cc_final: 0.8554 (pp20) REVERT: d 625 GLN cc_start: 0.8396 (tt0) cc_final: 0.8134 (tt0) REVERT: d 642 ASP cc_start: 0.8873 (m-30) cc_final: 0.8618 (m-30) REVERT: d 701 MET cc_start: 0.6967 (tpt) cc_final: 0.6198 (mmt) REVERT: d 705 TYR cc_start: 0.8094 (m-10) cc_final: 0.7779 (m-10) REVERT: d 710 MET cc_start: 0.8213 (tpp) cc_final: 0.7675 (tmm) REVERT: d 776 PHE cc_start: 0.8747 (t80) cc_final: 0.8069 (t80) REVERT: d 803 LEU cc_start: 0.7437 (tp) cc_final: 0.6950 (mt) REVERT: d 859 ASN cc_start: 0.8663 (m110) cc_final: 0.8398 (m110) REVERT: d 878 LYS cc_start: 0.8450 (pttt) cc_final: 0.8241 (ptpt) REVERT: d 892 LEU cc_start: 0.8628 (mp) cc_final: 0.8333 (tt) REVERT: e 415 MET cc_start: 0.3603 (ptt) cc_final: 0.2957 (ptt) REVERT: e 655 PHE cc_start: 0.6468 (t80) cc_final: 0.5867 (t80) REVERT: e 862 LYS cc_start: 0.7565 (mttt) cc_final: 0.6492 (mmmt) REVERT: e 905 GLU cc_start: 0.5971 (OUTLIER) cc_final: 0.5137 (pt0) REVERT: f 55 PHE cc_start: 0.4842 (m-80) cc_final: 0.4512 (m-80) REVERT: f 152 LEU cc_start: 0.8673 (tt) cc_final: 0.8231 (mm) REVERT: f 174 ARG cc_start: 0.6080 (mmt180) cc_final: 0.4875 (mmp-170) REVERT: f 215 MET cc_start: 0.3317 (tpp) cc_final: 0.2545 (tpt) REVERT: f 434 MET cc_start: 0.6517 (mtt) cc_final: 0.6239 (mtm) REVERT: f 587 MET cc_start: 0.4930 (mmp) cc_final: 0.4161 (mmm) REVERT: f 626 MET cc_start: 0.2222 (mmm) cc_final: 0.1904 (tpt) REVERT: g 91 GLU cc_start: 0.8916 (pm20) cc_final: 0.8519 (pm20) REVERT: g 95 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8797 (mp0) REVERT: g 204 MET cc_start: 0.8707 (mmp) cc_final: 0.8163 (mmp) REVERT: g 230 MET cc_start: 0.8855 (mmm) cc_final: 0.8654 (tpp) REVERT: g 297 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9222 (mt-10) REVERT: g 304 TYR cc_start: 0.7304 (m-80) cc_final: 0.7102 (m-80) REVERT: g 409 LEU cc_start: 0.8741 (tp) cc_final: 0.8336 (tp) REVERT: g 416 MET cc_start: 0.6276 (tpp) cc_final: 0.5613 (tpp) REVERT: g 428 GLN cc_start: 0.8872 (tp-100) cc_final: 0.8657 (tm-30) REVERT: g 449 MET cc_start: 0.7046 (ttm) cc_final: 0.6841 (ttm) REVERT: g 467 MET cc_start: 0.5109 (tmm) cc_final: 0.4689 (tmm) REVERT: g 472 MET cc_start: 0.5676 (mmt) cc_final: 0.5468 (mmm) REVERT: g 541 MET cc_start: 0.3333 (ttm) cc_final: 0.1776 (tmm) REVERT: g 604 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6513 (tt) REVERT: g 631 PHE cc_start: 0.7273 (m-80) cc_final: 0.6828 (m-80) REVERT: g 879 GLN cc_start: 0.7696 (tm-30) cc_final: 0.7457 (tm-30) REVERT: g 917 VAL cc_start: 0.8671 (t) cc_final: 0.8227 (p) REVERT: h 340 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7097 (tm-30) REVERT: h 343 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8698 (mm-40) REVERT: h 383 LYS cc_start: 0.8336 (mttp) cc_final: 0.8083 (mmtt) REVERT: h 458 MET cc_start: 0.6835 (ptt) cc_final: 0.6514 (ppp) REVERT: h 508 ASN cc_start: 0.8916 (t0) cc_final: 0.8683 (p0) REVERT: h 648 MET cc_start: -0.0645 (ptt) cc_final: -0.1031 (ptt) REVERT: h 744 GLN cc_start: 0.8907 (tp40) cc_final: 0.8586 (mt0) REVERT: h 882 LYS cc_start: 0.8484 (tttm) cc_final: 0.7965 (tptp) REVERT: h 906 GLU cc_start: 0.6794 (pm20) cc_final: 0.6502 (pm20) REVERT: h 910 LYS cc_start: 0.6733 (tttt) cc_final: 0.6383 (tptt) REVERT: h 937 ILE cc_start: 0.6948 (mm) cc_final: 0.6747 (mm) REVERT: h 965 GLU cc_start: 0.3413 (pt0) cc_final: 0.1354 (tp30) REVERT: h 976 GLN cc_start: 0.8046 (tp40) cc_final: 0.7556 (tp40) REVERT: h 980 GLN cc_start: 0.7907 (tt0) cc_final: 0.7647 (tt0) REVERT: i 25 MET cc_start: 0.3362 (tmm) cc_final: 0.3067 (tmm) REVERT: i 184 MET cc_start: 0.5511 (pmm) cc_final: 0.5236 (pmm) REVERT: i 382 ASP cc_start: 0.8724 (m-30) cc_final: 0.7595 (p0) REVERT: k 59 ASP cc_start: 0.8991 (t70) cc_final: 0.8252 (p0) REVERT: k 288 GLN cc_start: 0.6718 (pp30) cc_final: 0.5440 (mp10) REVERT: k 437 MET cc_start: 0.8995 (tpt) cc_final: 0.8755 (tpp) REVERT: p 448 MET cc_start: 0.5784 (ptm) cc_final: 0.5289 (ttt) REVERT: p 521 MET cc_start: 0.6794 (mmt) cc_final: 0.6110 (mtp) REVERT: q 66 MET cc_start: 0.6580 (mtt) cc_final: 0.5576 (mmm) REVERT: q 145 TYR cc_start: 0.7416 (m-80) cc_final: 0.7182 (m-80) REVERT: q 149 LEU cc_start: 0.4618 (tt) cc_final: 0.4182 (tp) REVERT: q 183 LEU cc_start: 0.5549 (tt) cc_final: 0.4951 (mt) REVERT: q 192 GLU cc_start: 0.7571 (pm20) cc_final: 0.7338 (pm20) REVERT: q 226 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8627 (mp0) REVERT: r 2039 GLU cc_start: 0.6876 (tm-30) cc_final: 0.6515 (tm-30) REVERT: u 92 MET cc_start: -0.4705 (ppp) cc_final: -0.5287 (ptm) REVERT: w 245 MET cc_start: -0.4182 (pmm) cc_final: -0.5265 (ptp) outliers start: 6 outliers final: 0 residues processed: 1106 average time/residue: 1.0493 time to fit residues: 2062.5748 Evaluate side-chains 900 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 898 time to evaluate : 10.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1711 random chunks: chunk 1377 optimal weight: 7.9990 chunk 938 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 1231 optimal weight: 10.0000 chunk 682 optimal weight: 0.0070 chunk 1411 optimal weight: 30.0000 chunk 1143 optimal weight: 4.9990 chunk 1 optimal weight: 50.0000 chunk 844 optimal weight: 1.9990 chunk 1484 optimal weight: 50.0000 chunk 417 optimal weight: 10.0000 overall best weight: 4.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN G 93 ASN ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 HIS ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1102 HIS a1305 HIS ** a1443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a2113 ASN ** a2152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 589 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 747 ASN ** b 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1093 GLN d 492 ASN ** d 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 762 GLN ** d 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 452 HIS e 537 GLN e 662 HIS e 672 GLN ** e 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 993 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 486 GLN ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 371 GLN ** h 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 480 GLN ** h 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 970 ASN ** h 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 51 ASN ** i 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 105 HIS ** i 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 601 HIS ** p 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 219 ASN ** w 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4201 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 132050 Z= 0.393 Angle : 0.762 23.896 180842 Z= 0.389 Chirality : 0.046 0.524 21249 Planarity : 0.006 0.117 22474 Dihedral : 14.720 179.160 21584 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.70 % Favored : 94.26 % Rotamer: Outliers : 0.05 % Allowed : 3.75 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.07), residues: 16602 helix: 0.55 (0.05), residues: 9261 sheet: -1.11 (0.15), residues: 1076 loop : -1.22 (0.08), residues: 6265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.003 TRP e 799 HIS 0.025 0.002 HIS h 588 PHE 0.062 0.002 PHE G 77 TYR 0.076 0.002 TYR h 994 ARG 0.022 0.001 ARG h 482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1048 time to evaluate : 10.472 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: A 329 MET cc_start: 0.1461 (tpt) cc_final: 0.1190 (tpt) REVERT: A 868 MET cc_start: 0.3741 (mmt) cc_final: 0.3412 (mmp) REVERT: A 1292 MET cc_start: -0.4990 (ptt) cc_final: -0.6528 (ttt) REVERT: A 1309 MET cc_start: -0.3766 (mmp) cc_final: -0.4258 (mmp) REVERT: A 1412 MET cc_start: -0.0886 (pmm) cc_final: -0.1224 (pmm) REVERT: B 407 MET cc_start: -0.4151 (ptp) cc_final: -0.5033 (mmm) REVERT: B 796 MET cc_start: 0.2901 (mtt) cc_final: 0.2512 (mtt) REVERT: B 1163 MET cc_start: 0.4056 (mtm) cc_final: 0.3515 (ttt) REVERT: E 94 MET cc_start: -0.6507 (ttt) cc_final: -0.7067 (ttt) REVERT: I 108 MET cc_start: -0.2701 (ttt) cc_final: -0.3424 (ttt) REVERT: O 40 ARG cc_start: -0.0584 (ttt-90) cc_final: -0.1544 (mpt180) REVERT: U 84 MET cc_start: -0.2478 (tmm) cc_final: -0.4313 (tpt) REVERT: Z 460 MET cc_start: 0.2380 (mmt) cc_final: 0.1216 (tpp) REVERT: Z 508 MET cc_start: -0.1596 (tpt) cc_final: -0.2255 (tpt) REVERT: Z 635 MET cc_start: 0.1805 (tpt) cc_final: 0.0664 (mmt) REVERT: a 1317 ASP cc_start: 0.3500 (t70) cc_final: 0.3018 (t0) REVERT: a 1463 MET cc_start: 0.7370 (tpt) cc_final: 0.6853 (tpt) REVERT: a 1502 LEU cc_start: 0.9057 (mt) cc_final: 0.8756 (mt) REVERT: a 1506 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8976 (mm-30) REVERT: a 1661 LEU cc_start: 0.9049 (tp) cc_final: 0.8785 (tp) REVERT: a 1864 MET cc_start: 0.1577 (tpt) cc_final: 0.1337 (tpt) REVERT: a 1931 LEU cc_start: 0.7912 (mt) cc_final: 0.7425 (pp) REVERT: a 1950 ARG cc_start: 0.7597 (mmp-170) cc_final: 0.7109 (mmp-170) REVERT: a 1997 MET cc_start: 0.1796 (ptt) cc_final: 0.1446 (tmm) REVERT: a 2069 ASP cc_start: 0.8725 (m-30) cc_final: 0.8229 (m-30) REVERT: a 2114 SER cc_start: 0.8586 (t) cc_final: 0.8304 (t) REVERT: a 2117 ILE cc_start: 0.9034 (pt) cc_final: 0.8579 (pt) REVERT: a 2121 PHE cc_start: 0.8741 (m-80) cc_final: 0.8169 (m-80) REVERT: a 2127 TYR cc_start: 0.8279 (t80) cc_final: 0.7828 (t80) REVERT: a 2171 MET cc_start: 0.8291 (ppp) cc_final: 0.8018 (ppp) REVERT: a 2176 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8134 (mp10) REVERT: a 2190 MET cc_start: 0.6347 (tmm) cc_final: 0.6096 (tmm) REVERT: b 505 MET cc_start: 0.5893 (ptt) cc_final: 0.5253 (pmm) REVERT: b 556 CYS cc_start: 0.9661 (m) cc_final: 0.9158 (p) REVERT: b 575 ASP cc_start: 0.9477 (m-30) cc_final: 0.9216 (p0) REVERT: b 616 ASN cc_start: 0.9573 (t0) cc_final: 0.9353 (p0) REVERT: b 772 MET cc_start: 0.9035 (tmm) cc_final: 0.8632 (tmm) REVERT: b 776 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8881 (tm-30) REVERT: b 781 LEU cc_start: 0.9085 (mp) cc_final: 0.8849 (mp) REVERT: b 797 MET cc_start: 0.9269 (ttm) cc_final: 0.9061 (ttm) REVERT: b 924 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8879 (mp0) REVERT: b 935 ASP cc_start: 0.8683 (t70) cc_final: 0.8404 (t70) REVERT: b 944 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6975 (tt0) REVERT: b 947 LEU cc_start: 0.8643 (mt) cc_final: 0.8412 (mp) REVERT: b 1023 GLU cc_start: 0.8002 (mp0) cc_final: 0.7792 (mp0) REVERT: b 1070 LEU cc_start: 0.8670 (mm) cc_final: 0.8440 (mm) REVERT: b 1195 GLU cc_start: 0.8290 (tt0) cc_final: 0.7975 (mm-30) REVERT: b 1199 MET cc_start: 0.7056 (tmm) cc_final: 0.6584 (tmm) REVERT: d 309 MET cc_start: 0.0337 (ttp) cc_final: -0.0149 (ttm) REVERT: d 316 PHE cc_start: 0.8363 (m-80) cc_final: 0.8042 (m-80) REVERT: d 419 MET cc_start: 0.4127 (mmt) cc_final: 0.3873 (mtt) REVERT: d 567 ASP cc_start: 0.8817 (p0) cc_final: 0.8123 (t0) REVERT: d 619 GLU cc_start: 0.8986 (pt0) cc_final: 0.8563 (pp20) REVERT: d 642 ASP cc_start: 0.8860 (m-30) cc_final: 0.8638 (m-30) REVERT: d 701 MET cc_start: 0.7598 (tpt) cc_final: 0.7365 (mmt) REVERT: d 752 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8559 (mm-30) REVERT: d 776 PHE cc_start: 0.8769 (t80) cc_final: 0.8493 (t80) REVERT: d 874 MET cc_start: 0.9081 (mmp) cc_final: 0.8830 (mmp) REVERT: d 892 LEU cc_start: 0.8817 (mp) cc_final: 0.8534 (tt) REVERT: e 523 LEU cc_start: 0.8286 (mt) cc_final: 0.7704 (mt) REVERT: e 774 TYR cc_start: 0.7029 (m-80) cc_final: 0.6640 (m-80) REVERT: e 862 LYS cc_start: 0.7565 (mttt) cc_final: 0.6504 (mmmt) REVERT: f 174 ARG cc_start: 0.6343 (mmt180) cc_final: 0.5353 (mmp-170) REVERT: g 27 MET cc_start: 0.9443 (mmm) cc_final: 0.9134 (mmm) REVERT: g 95 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8856 (mp0) REVERT: g 148 ASP cc_start: 0.8481 (p0) cc_final: 0.8249 (p0) REVERT: g 204 MET cc_start: 0.8751 (mmp) cc_final: 0.8381 (mmp) REVERT: g 296 CYS cc_start: 0.9445 (m) cc_final: 0.9088 (t) REVERT: g 297 GLU cc_start: 0.9579 (mt-10) cc_final: 0.9325 (mt-10) REVERT: g 388 PHE cc_start: 0.7444 (m-80) cc_final: 0.7204 (m-80) REVERT: g 409 LEU cc_start: 0.9287 (tp) cc_final: 0.9060 (tp) REVERT: g 416 MET cc_start: 0.7451 (tpp) cc_final: 0.7133 (tpp) REVERT: g 428 GLN cc_start: 0.9180 (tp-100) cc_final: 0.8899 (tp40) REVERT: g 467 MET cc_start: 0.6016 (tmm) cc_final: 0.5807 (tmm) REVERT: g 631 PHE cc_start: 0.7241 (m-80) cc_final: 0.6773 (m-80) REVERT: g 850 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7927 (m) REVERT: g 879 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7454 (tm-30) REVERT: g 886 ASP cc_start: 0.8648 (m-30) cc_final: 0.8131 (t0) REVERT: h 340 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7461 (tm-30) REVERT: h 390 VAL cc_start: 0.8389 (t) cc_final: 0.8114 (p) REVERT: h 458 MET cc_start: 0.7283 (ptt) cc_final: 0.6980 (ppp) REVERT: h 493 LYS cc_start: 0.8093 (pptt) cc_final: 0.7413 (tmtt) REVERT: h 648 MET cc_start: -0.0452 (ptt) cc_final: -0.0901 (ptt) REVERT: h 703 GLU cc_start: 0.9004 (mp0) cc_final: 0.8747 (mp0) REVERT: h 882 LYS cc_start: 0.8384 (tttp) cc_final: 0.8089 (tptp) REVERT: h 906 GLU cc_start: 0.6705 (pm20) cc_final: 0.6464 (pm20) REVERT: h 910 LYS cc_start: 0.6953 (tttt) cc_final: 0.6642 (tptt) REVERT: h 920 ASN cc_start: 0.6829 (t0) cc_final: 0.6481 (t0) REVERT: h 937 ILE cc_start: 0.7138 (mm) cc_final: 0.6933 (mp) REVERT: h 976 GLN cc_start: 0.8071 (tp40) cc_final: 0.7353 (tm-30) REVERT: h 980 GLN cc_start: 0.8037 (tt0) cc_final: 0.7781 (tt0) REVERT: h 994 TYR cc_start: 0.6138 (m-80) cc_final: 0.3508 (m-80) REVERT: i 25 MET cc_start: 0.3680 (tmm) cc_final: 0.3229 (tmm) REVERT: i 184 MET cc_start: 0.5977 (pmm) cc_final: 0.5696 (pmm) REVERT: i 489 MET cc_start: 0.7641 (mmp) cc_final: 0.7348 (mmp) REVERT: k 59 ASP cc_start: 0.9053 (t70) cc_final: 0.7979 (p0) REVERT: k 92 MET cc_start: 0.6758 (pmm) cc_final: 0.6237 (pmm) REVERT: k 288 GLN cc_start: 0.6958 (pp30) cc_final: 0.5691 (mp10) REVERT: k 420 MET cc_start: 0.5227 (mtt) cc_final: 0.4591 (mtt) REVERT: k 437 MET cc_start: 0.9099 (tpt) cc_final: 0.8852 (tpt) REVERT: p 521 MET cc_start: 0.7311 (mmt) cc_final: 0.6623 (mtp) REVERT: q 66 MET cc_start: 0.7144 (mtt) cc_final: 0.6395 (mmm) REVERT: q 80 TYR cc_start: 0.6182 (m-80) cc_final: 0.5884 (m-80) REVERT: q 145 TYR cc_start: 0.7626 (m-80) cc_final: 0.7284 (m-80) REVERT: q 149 LEU cc_start: 0.4777 (tt) cc_final: 0.4568 (tt) REVERT: q 183 LEU cc_start: 0.6297 (tt) cc_final: 0.5848 (mt) REVERT: q 282 LEU cc_start: 0.9193 (tp) cc_final: 0.8840 (tt) REVERT: r 2036 VAL cc_start: 0.7508 (t) cc_final: 0.7258 (t) REVERT: u 92 MET cc_start: -0.4790 (ppp) cc_final: -0.5398 (ptm) REVERT: w 245 MET cc_start: -0.3895 (pmm) cc_final: -0.4827 (ptp) outliers start: 6 outliers final: 2 residues processed: 1053 average time/residue: 1.0339 time to fit residues: 1935.1367 Evaluate side-chains 879 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 876 time to evaluate : 10.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1711 random chunks: chunk 556 optimal weight: 10.0000 chunk 1489 optimal weight: 50.0000 chunk 326 optimal weight: 9.9990 chunk 971 optimal weight: 8.9990 chunk 408 optimal weight: 10.0000 chunk 1655 optimal weight: 9.9990 chunk 1374 optimal weight: 5.9990 chunk 766 optimal weight: 0.6980 chunk 137 optimal weight: 10.0000 chunk 547 optimal weight: 50.0000 chunk 869 optimal weight: 30.0000 overall best weight: 7.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 HIS ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 GLN ** A1417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1555 HIS ** a1904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a1986 HIS a2138 GLN ** a2152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2154 HIS ** b 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 223 ASN ** b 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 448 GLN ** b 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 747 ASN ** b 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 448 GLN ** d 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 492 ASN ** d 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 723 HIS d 733 GLN ** d 810 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 445 HIS ** e 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 452 HIS e 537 GLN ** e 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 854 GLN ** e 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 349 GLN ** g 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 570 HIS ** g 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 142 ASN ** i 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 545 HIS ** i 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 665 ASN ** p 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 14 HIS w 118 HIS ** w 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4443 moved from start: 0.8521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.157 132050 Z= 0.579 Angle : 0.945 20.486 180842 Z= 0.484 Chirality : 0.052 0.578 21249 Planarity : 0.007 0.146 22474 Dihedral : 14.863 178.987 21584 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 29.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.37 % Favored : 93.55 % Rotamer: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.25 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.07), residues: 16602 helix: 0.20 (0.05), residues: 9240 sheet: -1.36 (0.15), residues: 1091 loop : -1.35 (0.08), residues: 6271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP e 799 HIS 0.034 0.002 HIS q 118 PHE 0.090 0.003 PHE e 858 TYR 0.074 0.003 TYR h 928 ARG 0.022 0.001 ARG e 849 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1020 time to evaluate : 10.563 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: symmetry clash revert: symmetry clash REVERT: A 329 MET cc_start: 0.1439 (tpt) cc_final: 0.1187 (tpt) REVERT: A 868 MET cc_start: 0.3976 (mmt) cc_final: 0.3670 (mmp) REVERT: A 986 MET cc_start: 0.3426 (mmp) cc_final: 0.2884 (mmt) REVERT: A 1296 MET cc_start: -0.4049 (ttt) cc_final: -0.5244 (tpt) REVERT: A 1309 MET cc_start: -0.3839 (mmp) cc_final: -0.4287 (mmp) REVERT: A 1412 MET cc_start: -0.0669 (pmm) cc_final: -0.1024 (pmm) REVERT: B 200 MET cc_start: 0.1273 (ppp) cc_final: 0.1069 (ppp) REVERT: B 407 MET cc_start: -0.3038 (ptp) cc_final: -0.3930 (mmm) REVERT: B 796 MET cc_start: 0.3998 (mtt) cc_final: 0.3481 (mtt) REVERT: B 908 MET cc_start: -0.6068 (ptt) cc_final: -0.6756 (ptt) REVERT: E 94 MET cc_start: -0.6233 (ttt) cc_final: -0.6931 (ttt) REVERT: I 108 MET cc_start: -0.2478 (ttt) cc_final: -0.3198 (ttt) REVERT: O 40 ARG cc_start: -0.0432 (ttt-90) cc_final: -0.1353 (mpt180) REVERT: O 55 ARG cc_start: -0.2598 (mmt180) cc_final: -0.3223 (mmt180) REVERT: U 84 MET cc_start: -0.2367 (tmm) cc_final: -0.4227 (tpt) REVERT: Z 460 MET cc_start: 0.2371 (mmt) cc_final: 0.1973 (tpp) REVERT: Z 508 MET cc_start: -0.1889 (tpt) cc_final: -0.2563 (tpt) REVERT: Z 635 MET cc_start: 0.1658 (tpt) cc_final: 0.0493 (mmt) REVERT: a 1131 MET cc_start: -0.0199 (mmt) cc_final: -0.0685 (mmt) REVERT: a 1661 LEU cc_start: 0.9115 (tp) cc_final: 0.8868 (tp) REVERT: a 1864 MET cc_start: 0.3710 (tpt) cc_final: 0.3190 (tpt) REVERT: a 1931 LEU cc_start: 0.8225 (mt) cc_final: 0.7882 (pp) REVERT: a 1950 ARG cc_start: 0.7495 (mmp-170) cc_final: 0.6921 (mmp-170) REVERT: a 1997 MET cc_start: 0.2261 (ptt) cc_final: 0.1721 (tmm) REVERT: a 2069 ASP cc_start: 0.8943 (m-30) cc_final: 0.8643 (t0) REVERT: a 2106 LEU cc_start: 0.8731 (mt) cc_final: 0.8465 (mp) REVERT: a 2133 ASP cc_start: 0.7695 (t70) cc_final: 0.6822 (t0) REVERT: a 2135 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8042 (mp0) REVERT: a 2136 VAL cc_start: 0.8227 (t) cc_final: 0.7451 (t) REVERT: a 2150 LEU cc_start: 0.8949 (mp) cc_final: 0.8669 (mt) REVERT: b 479 MET cc_start: 0.9267 (mpp) cc_final: 0.9055 (mpp) REVERT: b 556 CYS cc_start: 0.9565 (m) cc_final: 0.9199 (p) REVERT: b 739 LEU cc_start: 0.8440 (tp) cc_final: 0.8007 (tp) REVERT: b 743 MET cc_start: 0.8225 (mpp) cc_final: 0.7956 (mpp) REVERT: b 772 MET cc_start: 0.9069 (tmm) cc_final: 0.8850 (tmm) REVERT: b 797 MET cc_start: 0.9295 (ttm) cc_final: 0.8636 (ttm) REVERT: b 1023 GLU cc_start: 0.7949 (mp0) cc_final: 0.7689 (mp0) REVERT: b 1035 MET cc_start: 0.8683 (mmm) cc_final: 0.7312 (mmm) REVERT: b 1070 LEU cc_start: 0.8665 (mm) cc_final: 0.8406 (mm) REVERT: b 1132 CYS cc_start: 0.7847 (m) cc_final: 0.6852 (t) REVERT: b 1140 THR cc_start: 0.7939 (t) cc_final: 0.7693 (m) REVERT: b 1199 MET cc_start: 0.7140 (tmm) cc_final: 0.6786 (tmm) REVERT: d 411 LYS cc_start: 0.8762 (mptt) cc_final: 0.8298 (mtpt) REVERT: d 445 ARG cc_start: 0.9565 (mpp80) cc_final: 0.9095 (mtm110) REVERT: d 448 GLN cc_start: 0.8818 (mt0) cc_final: 0.8239 (mt0) REVERT: d 449 LEU cc_start: 0.9569 (tp) cc_final: 0.9328 (tp) REVERT: d 634 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8085 (mt-10) REVERT: d 642 ASP cc_start: 0.8979 (m-30) cc_final: 0.8755 (m-30) REVERT: d 701 MET cc_start: 0.8038 (tpt) cc_final: 0.7674 (tpp) REVERT: d 702 GLU cc_start: 0.9116 (pt0) cc_final: 0.8827 (tm-30) REVERT: d 703 GLU cc_start: 0.9126 (tp30) cc_final: 0.8771 (tp30) REVERT: d 723 HIS cc_start: 0.8468 (m90) cc_final: 0.7930 (m-70) REVERT: d 727 LEU cc_start: 0.8538 (tp) cc_final: 0.8306 (tt) REVERT: d 748 PHE cc_start: 0.9263 (t80) cc_final: 0.8990 (t80) REVERT: d 874 MET cc_start: 0.8810 (mmp) cc_final: 0.8518 (mmp) REVERT: e 649 ARG cc_start: 0.7155 (pmt-80) cc_final: 0.6859 (pmt-80) REVERT: f 9 ASP cc_start: 0.4686 (OUTLIER) cc_final: 0.4257 (m-30) REVERT: f 14 MET cc_start: 0.7459 (mmp) cc_final: 0.7063 (mmp) REVERT: f 305 PRO cc_start: 0.8738 (Cg_exo) cc_final: 0.8531 (Cg_endo) REVERT: f 485 LYS cc_start: 0.4924 (mmtp) cc_final: 0.4643 (pttt) REVERT: g 27 MET cc_start: 0.9469 (mmm) cc_final: 0.9196 (mmm) REVERT: g 40 GLU cc_start: 0.8771 (mp0) cc_final: 0.8469 (mp0) REVERT: g 95 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8925 (mp0) REVERT: g 204 MET cc_start: 0.8784 (mmp) cc_final: 0.8351 (mmp) REVERT: g 311 MET cc_start: 0.8591 (mtm) cc_final: 0.8388 (mtm) REVERT: g 387 VAL cc_start: 0.9558 (t) cc_final: 0.9219 (t) REVERT: g 388 PHE cc_start: 0.8608 (m-10) cc_final: 0.7955 (m-80) REVERT: g 391 GLU cc_start: 0.9091 (tt0) cc_final: 0.8581 (mt-10) REVERT: g 432 GLU cc_start: 0.8841 (pt0) cc_final: 0.8387 (mm-30) REVERT: g 493 LEU cc_start: 0.8361 (tp) cc_final: 0.8160 (tp) REVERT: g 536 MET cc_start: 0.8680 (mpp) cc_final: 0.8448 (mpp) REVERT: g 560 PHE cc_start: 0.6874 (m-80) cc_final: 0.6669 (m-80) REVERT: g 570 HIS cc_start: 0.7423 (t70) cc_final: 0.6709 (t70) REVERT: g 574 CYS cc_start: 0.8619 (m) cc_final: 0.8343 (m) REVERT: g 596 PHE cc_start: 0.7255 (m-10) cc_final: 0.6826 (m-10) REVERT: g 631 PHE cc_start: 0.7158 (m-80) cc_final: 0.6550 (m-80) REVERT: g 879 GLN cc_start: 0.7718 (tm-30) cc_final: 0.7065 (tm-30) REVERT: g 886 ASP cc_start: 0.8564 (m-30) cc_final: 0.8280 (m-30) REVERT: h 263 GLN cc_start: 0.7301 (mt0) cc_final: 0.6752 (mp10) REVERT: h 343 GLN cc_start: 0.9276 (mm-40) cc_final: 0.8946 (mm-40) REVERT: h 424 ARG cc_start: 0.8537 (ptt180) cc_final: 0.8293 (ptt90) REVERT: h 462 HIS cc_start: 0.8870 (t-90) cc_final: 0.8591 (t70) REVERT: h 493 LYS cc_start: 0.8392 (pptt) cc_final: 0.7830 (tmtt) REVERT: h 648 MET cc_start: -0.0470 (ptt) cc_final: -0.1186 (ptt) REVERT: h 728 SER cc_start: 0.7159 (p) cc_final: 0.6933 (m) REVERT: h 910 LYS cc_start: 0.7751 (tttt) cc_final: 0.7295 (tptt) REVERT: h 937 ILE cc_start: 0.7277 (mm) cc_final: 0.6840 (mm) REVERT: h 976 GLN cc_start: 0.8082 (tp40) cc_final: 0.7460 (tp40) REVERT: h 977 LEU cc_start: 0.7077 (tp) cc_final: 0.6860 (tt) REVERT: h 980 GLN cc_start: 0.8020 (tt0) cc_final: 0.7493 (tm-30) REVERT: h 994 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.3704 (m-80) REVERT: i 137 MET cc_start: 0.5263 (mtt) cc_final: 0.3984 (mmp) REVERT: i 184 MET cc_start: 0.6982 (pmm) cc_final: 0.6721 (pmm) REVERT: k 92 MET cc_start: 0.7219 (pmm) cc_final: 0.6876 (pmm) REVERT: k 288 GLN cc_start: 0.7100 (pp30) cc_final: 0.6609 (mp10) REVERT: k 420 MET cc_start: 0.5655 (mtt) cc_final: 0.4609 (tpp) REVERT: k 437 MET cc_start: 0.9112 (tpt) cc_final: 0.8335 (tpt) REVERT: q 65 LEU cc_start: 0.9233 (tp) cc_final: 0.8966 (tt) REVERT: q 66 MET cc_start: 0.8283 (mtt) cc_final: 0.7857 (mmm) REVERT: q 145 TYR cc_start: 0.7931 (m-80) cc_final: 0.7579 (m-80) REVERT: q 245 MET cc_start: 0.5729 (mmt) cc_final: 0.5419 (mmt) REVERT: u 92 MET cc_start: -0.4748 (ppp) cc_final: -0.5334 (ptm) REVERT: w 244 MET cc_start: 0.0070 (pmm) cc_final: -0.1054 (pmm) REVERT: w 245 MET cc_start: -0.4061 (pmm) cc_final: -0.5817 (ptt) REVERT: w 338 MET cc_start: -0.7704 (mmt) cc_final: -0.8185 (mmt) REVERT: w 425 MET cc_start: -0.0024 (pmm) cc_final: -0.1045 (tpp) outliers start: 5 outliers final: 1 residues processed: 1023 average time/residue: 1.0833 time to fit residues: 1982.1860 Evaluate side-chains 855 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 852 time to evaluate : 11.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1711 random chunks: chunk 1596 optimal weight: 6.9990 chunk 186 optimal weight: 30.0000 chunk 943 optimal weight: 7.9990 chunk 1208 optimal weight: 10.0000 chunk 936 optimal weight: 0.6980 chunk 1393 optimal weight: 40.0000 chunk 924 optimal weight: 2.9990 chunk 1649 optimal weight: 8.9990 chunk 1032 optimal weight: 0.8980 chunk 1005 optimal weight: 0.0370 chunk 761 optimal weight: 3.9990 overall best weight: 1.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN B 525 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN H 133 HIS ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 HIS K 69 HIS ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a2087 ASN ** a2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a2152 GLN ** b 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1093 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1127 GLN ** b1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 381 HIS d 421 ASN d 475 ASN d 492 ASN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 644 GLN ** d 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 728 GLN d 762 GLN ** d 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 876 HIS ** d 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 445 HIS ** e 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 770 GLN ** e 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 933 GLN e 963 GLN e 984 HIS e 993 HIS e1007 GLN g 150 HIS ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 414 ASN ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 552 GLN g 579 GLN g 753 ASN ** g 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 228 GLN ** i 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2040 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 14 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4296 moved from start: 0.8563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 132050 Z= 0.248 Angle : 0.680 14.910 180842 Z= 0.346 Chirality : 0.044 0.398 21249 Planarity : 0.005 0.099 22474 Dihedral : 14.687 179.006 21584 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.15 % Favored : 94.83 % Rotamer: Outliers : 0.02 % Allowed : 1.60 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.07), residues: 16602 helix: 0.61 (0.05), residues: 9285 sheet: -1.22 (0.15), residues: 1082 loop : -1.21 (0.08), residues: 6235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.115 0.002 TRP r2037 HIS 0.022 0.001 HIS e 984 PHE 0.043 0.002 PHE a2104 TYR 0.042 0.002 TYR h 994 ARG 0.015 0.001 ARG a2053 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1063 time to evaluate : 10.555 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: A 58 MET cc_start: 0.8528 (tmm) cc_final: 0.8281 (tmm) REVERT: A 329 MET cc_start: 0.1143 (tpt) cc_final: 0.0905 (tpt) REVERT: A 986 MET cc_start: 0.3100 (mmp) cc_final: 0.2559 (mmt) REVERT: A 1309 MET cc_start: -0.3670 (mmp) cc_final: -0.4249 (mmt) REVERT: A 1412 MET cc_start: -0.0839 (pmm) cc_final: -0.1155 (pmm) REVERT: B 407 MET cc_start: -0.3193 (ptp) cc_final: -0.3758 (mmm) REVERT: B 550 MET cc_start: -0.1655 (mtp) cc_final: -0.1858 (mtp) REVERT: B 796 MET cc_start: 0.3819 (mtt) cc_final: 0.3285 (mtt) REVERT: B 976 MET cc_start: 0.6349 (tpt) cc_final: 0.5706 (tpt) REVERT: B 1163 MET cc_start: 0.4215 (mtm) cc_final: 0.3636 (ttt) REVERT: E 94 MET cc_start: -0.6524 (ttt) cc_final: -0.7160 (ttt) REVERT: I 108 MET cc_start: -0.2578 (ttt) cc_final: -0.3266 (ttt) REVERT: O 40 ARG cc_start: -0.0458 (ttt-90) cc_final: -0.1332 (mpt180) REVERT: U 84 MET cc_start: -0.2544 (tmm) cc_final: -0.4372 (tpt) REVERT: Z 460 MET cc_start: 0.2331 (mmt) cc_final: 0.1927 (tpp) REVERT: Z 508 MET cc_start: -0.1700 (tpt) cc_final: -0.2380 (tpt) REVERT: Z 635 MET cc_start: 0.1676 (tpt) cc_final: 0.0527 (mmt) REVERT: a 1463 MET cc_start: 0.7620 (tpt) cc_final: 0.7055 (tpt) REVERT: a 1502 LEU cc_start: 0.9234 (mt) cc_final: 0.8964 (mt) REVERT: a 1506 GLU cc_start: 0.9318 (mp0) cc_final: 0.8895 (mp0) REVERT: a 1661 LEU cc_start: 0.9016 (tp) cc_final: 0.8722 (tp) REVERT: a 1931 LEU cc_start: 0.8229 (mt) cc_final: 0.7776 (pp) REVERT: a 1950 ARG cc_start: 0.7638 (mmp-170) cc_final: 0.7116 (mmp-170) REVERT: a 1997 MET cc_start: 0.2223 (ptt) cc_final: 0.1864 (tmm) REVERT: a 2106 LEU cc_start: 0.8503 (mt) cc_final: 0.8220 (mt) REVERT: a 2150 LEU cc_start: 0.8769 (mp) cc_final: 0.8424 (mt) REVERT: b 415 MET cc_start: 0.7824 (mtm) cc_final: 0.7097 (ptp) REVERT: b 435 MET cc_start: 0.9277 (tpt) cc_final: 0.8604 (tmm) REVERT: b 436 LEU cc_start: 0.8842 (mt) cc_final: 0.8388 (mt) REVERT: b 479 MET cc_start: 0.9223 (mpp) cc_final: 0.8994 (mpp) REVERT: b 556 CYS cc_start: 0.9557 (m) cc_final: 0.9172 (p) REVERT: b 702 GLU cc_start: 0.8080 (mp0) cc_final: 0.7696 (mp0) REVERT: b 743 MET cc_start: 0.8158 (mpp) cc_final: 0.7812 (mpp) REVERT: b 818 MET cc_start: 0.8711 (mmt) cc_final: 0.8372 (mmt) REVERT: b 831 MET cc_start: 0.8458 (ppp) cc_final: 0.8243 (ppp) REVERT: b 1035 MET cc_start: 0.8615 (mmm) cc_final: 0.6796 (mmm) REVERT: b 1051 LEU cc_start: 0.8835 (mm) cc_final: 0.8629 (mm) REVERT: b 1070 LEU cc_start: 0.8647 (mm) cc_final: 0.8334 (mm) REVERT: b 1101 MET cc_start: 0.8005 (tpt) cc_final: 0.7784 (tpp) REVERT: b 1132 CYS cc_start: 0.7677 (m) cc_final: 0.7109 (p) REVERT: b 1147 ILE cc_start: 0.6380 (pt) cc_final: 0.3836 (pt) REVERT: b 1152 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8021 (pm20) REVERT: b 1182 ASP cc_start: 0.6603 (m-30) cc_final: 0.6155 (m-30) REVERT: b 1199 MET cc_start: 0.7180 (tmm) cc_final: 0.6822 (tmm) REVERT: d 379 PHE cc_start: 0.5717 (m-80) cc_final: 0.5199 (m-10) REVERT: d 411 LYS cc_start: 0.8692 (mptt) cc_final: 0.8212 (mtpt) REVERT: d 461 ARG cc_start: 0.8162 (tmt-80) cc_final: 0.7892 (tpt90) REVERT: d 567 ASP cc_start: 0.8601 (p0) cc_final: 0.8145 (t0) REVERT: d 642 ASP cc_start: 0.8923 (m-30) cc_final: 0.8586 (m-30) REVERT: d 701 MET cc_start: 0.8040 (tpt) cc_final: 0.7691 (mmt) REVERT: d 703 GLU cc_start: 0.9092 (tp30) cc_final: 0.8709 (tp30) REVERT: d 724 HIS cc_start: 0.4627 (t-90) cc_final: 0.3799 (p-80) REVERT: d 727 LEU cc_start: 0.8367 (tp) cc_final: 0.8153 (tt) REVERT: d 776 PHE cc_start: 0.8926 (t80) cc_final: 0.7938 (t80) REVERT: d 802 MET cc_start: 0.8676 (ttp) cc_final: 0.8464 (ttt) REVERT: d 874 MET cc_start: 0.8988 (mmp) cc_final: 0.8758 (mmp) REVERT: d 892 LEU cc_start: 0.8586 (mp) cc_final: 0.8313 (tt) REVERT: e 433 GLU cc_start: 0.9103 (mp0) cc_final: 0.8841 (pp20) REVERT: e 561 VAL cc_start: 0.8414 (t) cc_final: 0.8197 (t) REVERT: e 671 CYS cc_start: 0.8745 (m) cc_final: 0.8373 (m) REVERT: e 785 HIS cc_start: 0.4591 (m90) cc_final: 0.4281 (m90) REVERT: e 843 ARG cc_start: 0.1659 (ttp-170) cc_final: 0.1296 (tmt170) REVERT: e 862 LYS cc_start: 0.7612 (mttt) cc_final: 0.6767 (mmtt) REVERT: e 963 GLN cc_start: 0.5257 (OUTLIER) cc_final: 0.4343 (pm20) REVERT: f 152 LEU cc_start: 0.8434 (tt) cc_final: 0.8038 (mm) REVERT: f 174 ARG cc_start: 0.6620 (mmt180) cc_final: 0.5945 (mmp80) REVERT: f 215 MET cc_start: 0.4721 (tpp) cc_final: 0.3848 (tpp) REVERT: f 434 MET cc_start: 0.6339 (mtm) cc_final: 0.5956 (ttp) REVERT: g 27 MET cc_start: 0.9473 (mmm) cc_final: 0.9158 (mmm) REVERT: g 40 GLU cc_start: 0.8768 (mp0) cc_final: 0.8445 (mp0) REVERT: g 55 TYR cc_start: 0.8607 (m-10) cc_final: 0.8358 (m-10) REVERT: g 95 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8869 (mp0) REVERT: g 204 MET cc_start: 0.8718 (mmp) cc_final: 0.8372 (mmp) REVERT: g 230 MET cc_start: 0.8633 (mmm) cc_final: 0.8403 (tpp) REVERT: g 283 THR cc_start: 0.8766 (p) cc_final: 0.8533 (p) REVERT: g 304 TYR cc_start: 0.7923 (m-80) cc_final: 0.7554 (m-80) REVERT: g 387 VAL cc_start: 0.9487 (t) cc_final: 0.9047 (t) REVERT: g 388 PHE cc_start: 0.8571 (m-80) cc_final: 0.7927 (m-80) REVERT: g 391 GLU cc_start: 0.9000 (tt0) cc_final: 0.8418 (mt-10) REVERT: g 432 GLU cc_start: 0.8774 (pt0) cc_final: 0.8328 (mm-30) REVERT: g 449 MET cc_start: 0.8400 (ttm) cc_final: 0.8134 (ttp) REVERT: g 467 MET cc_start: 0.7590 (tmm) cc_final: 0.7354 (tmm) REVERT: g 541 MET cc_start: 0.6576 (tmm) cc_final: 0.6025 (tmm) REVERT: g 570 HIS cc_start: 0.7215 (t70) cc_final: 0.6601 (t70) REVERT: g 574 CYS cc_start: 0.8486 (m) cc_final: 0.8229 (m) REVERT: g 596 PHE cc_start: 0.7076 (m-10) cc_final: 0.6661 (m-10) REVERT: g 631 PHE cc_start: 0.7168 (m-80) cc_final: 0.6750 (m-80) REVERT: g 675 MET cc_start: 0.7198 (tpp) cc_final: 0.6749 (tpt) REVERT: g 879 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7136 (tm-30) REVERT: g 914 ASN cc_start: 0.9292 (m-40) cc_final: 0.8956 (m-40) REVERT: h 343 GLN cc_start: 0.9228 (mm-40) cc_final: 0.8862 (mm-40) REVERT: h 416 ASP cc_start: 0.7887 (m-30) cc_final: 0.7607 (m-30) REVERT: h 493 LYS cc_start: 0.8323 (pptt) cc_final: 0.7766 (tmtt) REVERT: h 611 MET cc_start: 0.4307 (mpp) cc_final: 0.3662 (mmt) REVERT: h 615 MET cc_start: 0.8345 (mpp) cc_final: 0.8119 (mpp) REVERT: h 648 MET cc_start: -0.0739 (ptt) cc_final: -0.1641 (ptt) REVERT: h 882 LYS cc_start: 0.7872 (tptt) cc_final: 0.7461 (tptp) REVERT: h 910 LYS cc_start: 0.7144 (tttt) cc_final: 0.6733 (tptt) REVERT: h 925 MET cc_start: 0.8365 (mtm) cc_final: 0.8128 (mtm) REVERT: h 936 THR cc_start: 0.7244 (m) cc_final: 0.7043 (p) REVERT: h 976 GLN cc_start: 0.7979 (tp40) cc_final: 0.7711 (mm-40) REVERT: h 980 GLN cc_start: 0.7963 (tt0) cc_final: 0.7064 (mm-40) REVERT: h 982 ARG cc_start: 0.7104 (mpt180) cc_final: 0.6177 (mmt-90) REVERT: h 994 TYR cc_start: 0.6353 (m-80) cc_final: 0.4809 (m-80) REVERT: h 995 PHE cc_start: 0.4575 (m-10) cc_final: 0.3997 (m-10) REVERT: i 184 MET cc_start: 0.6920 (pmm) cc_final: 0.6625 (pmm) REVERT: i 382 ASP cc_start: 0.9400 (m-30) cc_final: 0.8737 (p0) REVERT: k 92 MET cc_start: 0.7092 (pmm) cc_final: 0.6779 (pmm) REVERT: k 163 MET cc_start: 0.7422 (tpp) cc_final: 0.6791 (tpp) REVERT: k 288 GLN cc_start: 0.7049 (pp30) cc_final: 0.6080 (mp10) REVERT: k 420 MET cc_start: 0.5628 (mtt) cc_final: 0.4364 (tpp) REVERT: k 437 MET cc_start: 0.9079 (tpt) cc_final: 0.8158 (tpt) REVERT: q 17 LEU cc_start: 0.7628 (mt) cc_final: 0.7353 (mt) REVERT: q 66 MET cc_start: 0.8002 (mtt) cc_final: 0.7702 (mmm) REVERT: q 145 TYR cc_start: 0.7666 (m-80) cc_final: 0.7353 (m-80) REVERT: q 149 LEU cc_start: 0.4816 (tt) cc_final: 0.4579 (tp) REVERT: q 282 LEU cc_start: 0.9126 (tp) cc_final: 0.8865 (tt) REVERT: u 92 MET cc_start: -0.4690 (ppp) cc_final: -0.5290 (ptm) REVERT: w 244 MET cc_start: 0.0005 (pmm) cc_final: -0.1094 (pmm) REVERT: w 245 MET cc_start: -0.4016 (pmm) cc_final: -0.5632 (ptt) outliers start: 2 outliers final: 0 residues processed: 1064 average time/residue: 1.0543 time to fit residues: 2005.5881 Evaluate side-chains 884 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 883 time to evaluate : 10.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1711 random chunks: chunk 1020 optimal weight: 0.6980 chunk 658 optimal weight: 9.9990 chunk 984 optimal weight: 4.9990 chunk 496 optimal weight: 50.0000 chunk 324 optimal weight: 0.0020 chunk 319 optimal weight: 40.0000 chunk 1048 optimal weight: 0.5980 chunk 1123 optimal weight: 8.9990 chunk 815 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 1296 optimal weight: 50.0000 overall best weight: 2.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN A1417 HIS ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 GLN I 121 HIS K 69 HIS ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 85 GLN ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 529 GLN ** b 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 802 ASN ** b 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 GLN d 261 GLN d 381 HIS d 475 ASN d 492 ASN ** d 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 218 GLN ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 451 HIS ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 538 ASN ** g 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 552 GLN ** g 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 837 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 18 ASN q 44 ASN ** q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 272 GLN ** r2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 263 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4354 moved from start: 0.8884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 132050 Z= 0.297 Angle : 0.686 13.991 180842 Z= 0.350 Chirality : 0.044 0.332 21249 Planarity : 0.005 0.070 22474 Dihedral : 14.633 178.798 21584 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.07), residues: 16602 helix: 0.72 (0.06), residues: 9316 sheet: -1.15 (0.16), residues: 1079 loop : -1.19 (0.08), residues: 6207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP q 143 HIS 0.020 0.001 HIS g 598 PHE 0.040 0.002 PHE a2104 TYR 0.037 0.002 TYR h 994 ARG 0.016 0.001 ARG q 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1013 time to evaluate : 10.456 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: A 238 MET cc_start: 0.4793 (ttp) cc_final: 0.4445 (ttp) REVERT: A 248 MET cc_start: 0.7444 (mpp) cc_final: 0.6426 (mmt) REVERT: A 501 MET cc_start: -0.3079 (tpp) cc_final: -0.3609 (tpt) REVERT: A 986 MET cc_start: 0.3187 (mmp) cc_final: 0.2677 (mmt) REVERT: A 1296 MET cc_start: -0.3700 (ttt) cc_final: -0.4524 (tpt) REVERT: A 1309 MET cc_start: -0.3783 (mmp) cc_final: -0.4214 (mmt) REVERT: A 1412 MET cc_start: -0.0846 (pmm) cc_final: -0.1153 (pmm) REVERT: B 407 MET cc_start: -0.2916 (ptp) cc_final: -0.3482 (mmm) REVERT: B 702 MET cc_start: -0.4637 (tmm) cc_final: -0.6506 (mtt) REVERT: B 796 MET cc_start: 0.3667 (mtt) cc_final: 0.3171 (mtt) REVERT: B 1163 MET cc_start: 0.4156 (mtm) cc_final: 0.3541 (ttt) REVERT: B 1172 MET cc_start: 0.7452 (mmp) cc_final: 0.7144 (mpp) REVERT: E 94 MET cc_start: -0.6461 (ttt) cc_final: -0.7114 (ttt) REVERT: I 108 MET cc_start: -0.2588 (ttt) cc_final: -0.3257 (ttt) REVERT: O 40 ARG cc_start: -0.0424 (ttt-90) cc_final: -0.1334 (mpt180) REVERT: O 55 ARG cc_start: -0.2730 (mmt180) cc_final: -0.3225 (mmt180) REVERT: U 84 MET cc_start: -0.2488 (tmm) cc_final: -0.4338 (tpt) REVERT: Z 460 MET cc_start: 0.2475 (mmt) cc_final: 0.2003 (tpp) REVERT: Z 508 MET cc_start: -0.1783 (tpt) cc_final: -0.2429 (tpt) REVERT: Z 635 MET cc_start: 0.2310 (tpt) cc_final: 0.0595 (mmt) REVERT: a 1412 LEU cc_start: 0.7901 (tt) cc_final: 0.7638 (pp) REVERT: a 1463 MET cc_start: 0.8098 (tpt) cc_final: 0.7894 (tpt) REVERT: a 1502 LEU cc_start: 0.9349 (mt) cc_final: 0.9070 (mt) REVERT: a 1506 GLU cc_start: 0.9406 (mp0) cc_final: 0.8956 (mp0) REVERT: a 1661 LEU cc_start: 0.9009 (tp) cc_final: 0.8703 (tp) REVERT: a 1931 LEU cc_start: 0.8362 (mt) cc_final: 0.7863 (pp) REVERT: a 1950 ARG cc_start: 0.7522 (mmp-170) cc_final: 0.6979 (mmp-170) REVERT: a 1997 MET cc_start: 0.2360 (ptt) cc_final: 0.1995 (tmm) REVERT: a 2102 LEU cc_start: 0.7505 (tp) cc_final: 0.7192 (tt) REVERT: a 2106 LEU cc_start: 0.8739 (mt) cc_final: 0.8472 (mt) REVERT: a 2150 LEU cc_start: 0.8967 (mp) cc_final: 0.8622 (mt) REVERT: b 267 MET cc_start: 0.8171 (tpt) cc_final: 0.7511 (ttp) REVERT: b 415 MET cc_start: 0.8003 (mtm) cc_final: 0.7597 (ptp) REVERT: b 435 MET cc_start: 0.9302 (tpt) cc_final: 0.8734 (tmm) REVERT: b 436 LEU cc_start: 0.8925 (mt) cc_final: 0.8496 (mt) REVERT: b 479 MET cc_start: 0.9185 (mpp) cc_final: 0.8947 (mpp) REVERT: b 517 MET cc_start: 0.8701 (mmt) cc_final: 0.8465 (mmm) REVERT: b 556 CYS cc_start: 0.9605 (m) cc_final: 0.9388 (m) REVERT: b 574 LYS cc_start: 0.8124 (tmmt) cc_final: 0.7841 (ptmm) REVERT: b 583 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8334 (mm-30) REVERT: b 702 GLU cc_start: 0.8097 (mp0) cc_final: 0.7711 (mp0) REVERT: b 743 MET cc_start: 0.8284 (mpp) cc_final: 0.7944 (mpp) REVERT: b 772 MET cc_start: 0.9122 (tmm) cc_final: 0.8800 (tmm) REVERT: b 935 ASP cc_start: 0.8426 (t70) cc_final: 0.8187 (t70) REVERT: b 1051 LEU cc_start: 0.8762 (mm) cc_final: 0.8546 (mm) REVERT: b 1070 LEU cc_start: 0.8659 (mm) cc_final: 0.8344 (mm) REVERT: b 1132 CYS cc_start: 0.7653 (m) cc_final: 0.7041 (p) REVERT: b 1135 ASP cc_start: 0.7810 (t70) cc_final: 0.7532 (t70) REVERT: b 1199 MET cc_start: 0.7179 (tmm) cc_final: 0.6828 (tmm) REVERT: d 309 MET cc_start: 0.0654 (ttp) cc_final: 0.0257 (ttt) REVERT: d 379 PHE cc_start: 0.6133 (m-80) cc_final: 0.5501 (m-10) REVERT: d 400 MET cc_start: 0.9434 (mmp) cc_final: 0.9217 (mmm) REVERT: d 461 ARG cc_start: 0.8189 (tmt-80) cc_final: 0.7900 (tpt90) REVERT: d 642 ASP cc_start: 0.8909 (m-30) cc_final: 0.8573 (m-30) REVERT: d 701 MET cc_start: 0.8130 (tpt) cc_final: 0.7803 (mmt) REVERT: d 724 HIS cc_start: 0.4995 (t-90) cc_final: 0.4680 (p-80) REVERT: d 727 LEU cc_start: 0.8586 (tp) cc_final: 0.8381 (tt) REVERT: d 772 LEU cc_start: 0.8659 (mt) cc_final: 0.8448 (mt) REVERT: d 776 PHE cc_start: 0.8764 (t80) cc_final: 0.7278 (t80) REVERT: d 802 MET cc_start: 0.8848 (ttp) cc_final: 0.8637 (ttt) REVERT: d 803 LEU cc_start: 0.8454 (tp) cc_final: 0.8138 (mt) REVERT: d 863 VAL cc_start: 0.8966 (t) cc_final: 0.8706 (p) REVERT: e 561 VAL cc_start: 0.8745 (t) cc_final: 0.8530 (t) REVERT: e 607 LEU cc_start: 0.7570 (mt) cc_final: 0.7202 (mt) REVERT: e 671 CYS cc_start: 0.8957 (m) cc_final: 0.8527 (m) REVERT: e 862 LYS cc_start: 0.7790 (mttt) cc_final: 0.7191 (pttm) REVERT: f 14 MET cc_start: 0.7109 (mmp) cc_final: 0.6856 (mmp) REVERT: f 174 ARG cc_start: 0.6330 (mmt180) cc_final: 0.5830 (mmp-170) REVERT: f 215 MET cc_start: 0.5401 (tpp) cc_final: 0.5030 (tpp) REVERT: f 434 MET cc_start: 0.6054 (mtm) cc_final: 0.5609 (ttp) REVERT: f 587 MET cc_start: 0.7323 (tpt) cc_final: 0.6802 (mmm) REVERT: g 27 MET cc_start: 0.9450 (mmm) cc_final: 0.9203 (mmm) REVERT: g 40 GLU cc_start: 0.8776 (mp0) cc_final: 0.8455 (mp0) REVERT: g 55 TYR cc_start: 0.8700 (m-10) cc_final: 0.8406 (m-10) REVERT: g 95 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8810 (mp0) REVERT: g 204 MET cc_start: 0.8701 (mmp) cc_final: 0.8359 (mmp) REVERT: g 230 MET cc_start: 0.8693 (mmm) cc_final: 0.8451 (tpp) REVERT: g 283 THR cc_start: 0.8790 (p) cc_final: 0.8559 (p) REVERT: g 304 TYR cc_start: 0.8061 (m-80) cc_final: 0.7661 (m-80) REVERT: g 387 VAL cc_start: 0.9569 (t) cc_final: 0.9230 (t) REVERT: g 388 PHE cc_start: 0.8629 (m-80) cc_final: 0.8059 (m-80) REVERT: g 391 GLU cc_start: 0.9094 (tt0) cc_final: 0.8554 (mt-10) REVERT: g 432 GLU cc_start: 0.8848 (pt0) cc_final: 0.8400 (mm-30) REVERT: g 541 MET cc_start: 0.7413 (tmm) cc_final: 0.6832 (tmm) REVERT: g 570 HIS cc_start: 0.7385 (t70) cc_final: 0.6997 (t70) REVERT: g 631 PHE cc_start: 0.7168 (m-80) cc_final: 0.6812 (m-80) REVERT: g 699 THR cc_start: 0.7913 (m) cc_final: 0.7708 (p) REVERT: g 879 GLN cc_start: 0.7769 (tm-30) cc_final: 0.7214 (tm-30) REVERT: g 914 ASN cc_start: 0.9306 (m-40) cc_final: 0.9027 (m-40) REVERT: h 263 GLN cc_start: 0.7228 (mt0) cc_final: 0.6650 (mp10) REVERT: h 358 PHE cc_start: 0.4313 (t80) cc_final: 0.3655 (t80) REVERT: h 458 MET cc_start: 0.7957 (ptt) cc_final: 0.7285 (ppp) REVERT: h 493 LYS cc_start: 0.8468 (pptt) cc_final: 0.7773 (tptp) REVERT: h 609 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8782 (tm-30) REVERT: h 648 MET cc_start: -0.0301 (ptt) cc_final: -0.1287 (ptt) REVERT: h 824 TYR cc_start: 0.2516 (t80) cc_final: 0.1741 (t80) REVERT: h 841 ASP cc_start: 0.5646 (m-30) cc_final: 0.4778 (t0) REVERT: h 867 PHE cc_start: 0.5612 (m-80) cc_final: 0.5273 (m-80) REVERT: h 882 LYS cc_start: 0.7776 (tptt) cc_final: 0.7462 (tptp) REVERT: h 910 LYS cc_start: 0.7442 (tttt) cc_final: 0.6989 (tptt) REVERT: h 925 MET cc_start: 0.8451 (mtm) cc_final: 0.8248 (mtm) REVERT: h 930 ASP cc_start: 0.7011 (p0) cc_final: 0.6352 (p0) REVERT: h 943 TYR cc_start: 0.8006 (t80) cc_final: 0.7662 (t80) REVERT: h 945 HIS cc_start: 0.6685 (m90) cc_final: 0.6248 (m90) REVERT: h 980 GLN cc_start: 0.8083 (tt0) cc_final: 0.7693 (tm-30) REVERT: h 982 ARG cc_start: 0.7054 (mpt180) cc_final: 0.6122 (mmt-90) REVERT: h 988 GLN cc_start: 0.5807 (mt0) cc_final: 0.4159 (mm-40) REVERT: h 992 LYS cc_start: 0.7807 (tppt) cc_final: 0.7266 (mtpt) REVERT: h 995 PHE cc_start: 0.4785 (m-10) cc_final: 0.4159 (m-10) REVERT: i 184 MET cc_start: 0.6912 (pmm) cc_final: 0.6647 (pmm) REVERT: i 382 ASP cc_start: 0.9443 (m-30) cc_final: 0.8790 (p0) REVERT: k 92 MET cc_start: 0.7136 (pmm) cc_final: 0.6931 (pmm) REVERT: k 163 MET cc_start: 0.7408 (tpp) cc_final: 0.6745 (tpp) REVERT: k 288 GLN cc_start: 0.7218 (pp30) cc_final: 0.6210 (mp10) REVERT: k 299 MET cc_start: 0.4069 (mmp) cc_final: 0.2974 (mtm) REVERT: k 420 MET cc_start: 0.5616 (mtt) cc_final: 0.4823 (mtt) REVERT: k 437 MET cc_start: 0.9141 (tpt) cc_final: 0.8934 (tpt) REVERT: m 687 GLN cc_start: 0.6120 (mp10) cc_final: 0.5678 (mp10) REVERT: p 350 MET cc_start: 0.2193 (ttt) cc_final: 0.1381 (ttp) REVERT: q 145 TYR cc_start: 0.7743 (m-80) cc_final: 0.7397 (m-80) REVERT: q 282 LEU cc_start: 0.9153 (tp) cc_final: 0.8911 (tt) REVERT: u 92 MET cc_start: -0.4764 (ppp) cc_final: -0.5310 (ptm) REVERT: w 245 MET cc_start: -0.4016 (pmm) cc_final: -0.4792 (ptp) REVERT: w 338 MET cc_start: -0.7517 (mmt) cc_final: -0.8079 (mmt) REVERT: w 425 MET cc_start: -0.0010 (pmm) cc_final: -0.1103 (tpp) outliers start: 0 outliers final: 0 residues processed: 1013 average time/residue: 1.0423 time to fit residues: 1890.3400 Evaluate side-chains 854 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 854 time to evaluate : 10.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1711 random chunks: chunk 1500 optimal weight: 0.3980 chunk 1579 optimal weight: 0.8980 chunk 1441 optimal weight: 7.9990 chunk 1536 optimal weight: 40.0000 chunk 924 optimal weight: 1.9990 chunk 669 optimal weight: 0.9990 chunk 1206 optimal weight: 10.0000 chunk 471 optimal weight: 50.0000 chunk 1388 optimal weight: 10.0000 chunk 1453 optimal weight: 40.0000 chunk 1531 optimal weight: 7.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 HIS K 69 HIS ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1243 GLN a1441 GLN ** a1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1928 GLN ** a1970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 580 GLN ** b 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 879 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 475 ASN d 492 ASN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 537 GLN ** e 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 236 HIS ** g 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 375 GLN g 414 ASN g 451 HIS ** g 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 715 HIS ** g 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 837 HIS ** h 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 976 GLN i 103 ASN ** k 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 72 GLN ** p 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 44 ASN ** q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4356 moved from start: 0.9224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 132050 Z= 0.264 Angle : 0.664 15.144 180842 Z= 0.338 Chirality : 0.043 0.316 21249 Planarity : 0.005 0.104 22474 Dihedral : 14.584 178.748 21584 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.97 % Favored : 95.01 % Rotamer: Outliers : 0.01 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.07), residues: 16602 helix: 0.84 (0.06), residues: 9313 sheet: -1.07 (0.16), residues: 1071 loop : -1.13 (0.08), residues: 6218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP r2037 HIS 0.016 0.001 HIS g 140 PHE 0.041 0.002 PHE a2104 TYR 0.042 0.002 TYR e 774 ARG 0.013 0.001 ARG q 239 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1014 time to evaluate : 10.573 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: A 238 MET cc_start: 0.4640 (ttp) cc_final: 0.4418 (ttp) REVERT: A 248 MET cc_start: 0.7282 (mpp) cc_final: 0.6149 (mmt) REVERT: A 501 MET cc_start: -0.2927 (tpp) cc_final: -0.3370 (tpt) REVERT: A 986 MET cc_start: 0.3062 (mmp) cc_final: 0.2564 (mmt) REVERT: A 1309 MET cc_start: -0.3861 (mmp) cc_final: -0.4245 (mmt) REVERT: A 1412 MET cc_start: -0.1021 (pmm) cc_final: -0.1317 (pmm) REVERT: B 407 MET cc_start: -0.2932 (ptp) cc_final: -0.3417 (mmm) REVERT: B 796 MET cc_start: 0.3936 (mtt) cc_final: 0.3534 (mtt) REVERT: B 976 MET cc_start: 0.6433 (tpt) cc_final: 0.6130 (tpt) REVERT: B 1163 MET cc_start: 0.4254 (mtm) cc_final: 0.3614 (ttt) REVERT: B 1172 MET cc_start: 0.7509 (mmp) cc_final: 0.7131 (mpp) REVERT: E 94 MET cc_start: -0.6664 (ttt) cc_final: -0.7273 (ttt) REVERT: I 108 MET cc_start: -0.2631 (ttt) cc_final: -0.3283 (ttt) REVERT: O 40 ARG cc_start: -0.0544 (ttt-90) cc_final: -0.1384 (mpt180) REVERT: O 55 ARG cc_start: -0.2697 (mmt180) cc_final: -0.3262 (mmt180) REVERT: O 92 ARG cc_start: -0.4656 (mtp180) cc_final: -0.5934 (mtt180) REVERT: U 84 MET cc_start: -0.2435 (tmm) cc_final: -0.4313 (tpt) REVERT: Z 460 MET cc_start: 0.2195 (mmt) cc_final: 0.1778 (tpp) REVERT: Z 474 MET cc_start: 0.4081 (tmm) cc_final: 0.3812 (tmm) REVERT: Z 508 MET cc_start: -0.1813 (tpt) cc_final: -0.2411 (tpt) REVERT: Z 635 MET cc_start: 0.2283 (tpt) cc_final: 0.0659 (mmt) REVERT: a 1412 LEU cc_start: 0.8157 (tt) cc_final: 0.7930 (pp) REVERT: a 1502 LEU cc_start: 0.9369 (mt) cc_final: 0.9136 (mt) REVERT: a 1506 GLU cc_start: 0.9351 (mp0) cc_final: 0.9076 (mp0) REVERT: a 1661 LEU cc_start: 0.8992 (tp) cc_final: 0.8640 (tp) REVERT: a 1931 LEU cc_start: 0.8408 (mt) cc_final: 0.7918 (pp) REVERT: a 1950 ARG cc_start: 0.7532 (mmp-170) cc_final: 0.6915 (mmp-170) REVERT: a 1997 MET cc_start: 0.2442 (ptt) cc_final: 0.2086 (tmm) REVERT: a 2102 LEU cc_start: 0.7866 (tp) cc_final: 0.7606 (tp) REVERT: a 2106 LEU cc_start: 0.8941 (mt) cc_final: 0.8713 (mt) REVERT: a 2111 MET cc_start: 0.8605 (ptp) cc_final: 0.8315 (ptt) REVERT: a 2150 LEU cc_start: 0.9000 (mp) cc_final: 0.8680 (mt) REVERT: b 267 MET cc_start: 0.8215 (tpt) cc_final: 0.7851 (ttt) REVERT: b 435 MET cc_start: 0.9350 (tpt) cc_final: 0.9042 (tpt) REVERT: b 450 GLN cc_start: 0.9575 (tp40) cc_final: 0.9342 (tm-30) REVERT: b 452 MET cc_start: 0.9162 (tmm) cc_final: 0.8476 (ptm) REVERT: b 574 LYS cc_start: 0.8131 (tmmt) cc_final: 0.7834 (ptmm) REVERT: b 616 ASN cc_start: 0.9595 (t0) cc_final: 0.9346 (p0) REVERT: b 702 GLU cc_start: 0.8140 (mp0) cc_final: 0.7764 (mp0) REVERT: b 772 MET cc_start: 0.9127 (tmm) cc_final: 0.8815 (tmm) REVERT: b 818 MET cc_start: 0.8791 (mmt) cc_final: 0.8411 (mmt) REVERT: b 892 LEU cc_start: 0.9035 (mm) cc_final: 0.8807 (mm) REVERT: b 935 ASP cc_start: 0.8262 (t70) cc_final: 0.7825 (t70) REVERT: b 1044 GLU cc_start: 0.8252 (pm20) cc_final: 0.7934 (pm20) REVERT: b 1070 LEU cc_start: 0.8705 (mm) cc_final: 0.8381 (mm) REVERT: b 1101 MET cc_start: 0.7844 (tpt) cc_final: 0.7445 (tpt) REVERT: b 1132 CYS cc_start: 0.7587 (m) cc_final: 0.6998 (p) REVERT: b 1135 ASP cc_start: 0.7904 (t70) cc_final: 0.7565 (t0) REVERT: b 1199 MET cc_start: 0.7118 (tmm) cc_final: 0.6775 (tmm) REVERT: d 289 HIS cc_start: 0.7865 (t70) cc_final: 0.7586 (t-170) REVERT: d 400 MET cc_start: 0.9465 (mmp) cc_final: 0.9243 (mmm) REVERT: d 461 ARG cc_start: 0.8146 (tmt-80) cc_final: 0.7804 (tpt90) REVERT: d 634 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8022 (mt-10) REVERT: d 637 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8427 (tm-30) REVERT: d 642 ASP cc_start: 0.8902 (m-30) cc_final: 0.8535 (m-30) REVERT: d 686 TYR cc_start: 0.7235 (t80) cc_final: 0.6809 (t80) REVERT: d 701 MET cc_start: 0.8258 (tpt) cc_final: 0.7925 (mmm) REVERT: d 776 PHE cc_start: 0.8477 (t80) cc_final: 0.7640 (t80) REVERT: e 474 LEU cc_start: 0.9340 (tp) cc_final: 0.9068 (tt) REVERT: e 671 CYS cc_start: 0.9002 (m) cc_final: 0.8581 (m) REVERT: e 862 LYS cc_start: 0.7665 (mttt) cc_final: 0.7127 (pttm) REVERT: f 14 MET cc_start: 0.7067 (mmp) cc_final: 0.6847 (mmp) REVERT: f 174 ARG cc_start: 0.5925 (mmt180) cc_final: 0.5423 (mmp80) REVERT: f 215 MET cc_start: 0.5400 (tpp) cc_final: 0.4997 (tpp) REVERT: f 434 MET cc_start: 0.6398 (mtm) cc_final: 0.5984 (ttp) REVERT: f 563 LEU cc_start: 0.9222 (tt) cc_final: 0.8938 (tp) REVERT: g 27 MET cc_start: 0.9454 (mmm) cc_final: 0.9202 (mmm) REVERT: g 55 TYR cc_start: 0.8677 (m-10) cc_final: 0.8439 (m-10) REVERT: g 95 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8790 (mp0) REVERT: g 204 MET cc_start: 0.8710 (mmp) cc_final: 0.8404 (mmp) REVERT: g 283 THR cc_start: 0.8762 (p) cc_final: 0.8519 (p) REVERT: g 304 TYR cc_start: 0.8142 (m-80) cc_final: 0.7628 (m-80) REVERT: g 431 VAL cc_start: 0.8979 (t) cc_final: 0.8688 (t) REVERT: g 432 GLU cc_start: 0.8931 (pt0) cc_final: 0.8513 (mm-30) REVERT: g 489 LEU cc_start: 0.9385 (mt) cc_final: 0.9165 (mt) REVERT: g 631 PHE cc_start: 0.7314 (m-80) cc_final: 0.6983 (m-80) REVERT: g 778 CYS cc_start: 0.8737 (m) cc_final: 0.8124 (t) REVERT: g 845 ARG cc_start: 0.6162 (mmt-90) cc_final: 0.5825 (mmt180) REVERT: g 879 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7019 (tm-30) REVERT: g 914 ASN cc_start: 0.9281 (m-40) cc_final: 0.9011 (m-40) REVERT: h 358 PHE cc_start: 0.4714 (t80) cc_final: 0.4109 (t80) REVERT: h 420 GLU cc_start: 0.8457 (pt0) cc_final: 0.8026 (tp30) REVERT: h 493 LYS cc_start: 0.8500 (pptt) cc_final: 0.7998 (tmtt) REVERT: h 648 MET cc_start: -0.0189 (ptt) cc_final: -0.1545 (ptt) REVERT: h 824 TYR cc_start: 0.2925 (t80) cc_final: 0.2196 (t80) REVERT: h 910 LYS cc_start: 0.7468 (tttt) cc_final: 0.7013 (tptt) REVERT: h 930 ASP cc_start: 0.6787 (p0) cc_final: 0.5784 (p0) REVERT: h 941 LEU cc_start: 0.8494 (mt) cc_final: 0.8090 (mt) REVERT: h 980 GLN cc_start: 0.8051 (tt0) cc_final: 0.7733 (tm-30) REVERT: h 982 ARG cc_start: 0.6630 (mpt180) cc_final: 0.6392 (mmt-90) REVERT: h 988 GLN cc_start: 0.5760 (mt0) cc_final: 0.3935 (mm-40) REVERT: i 184 MET cc_start: 0.7227 (pmm) cc_final: 0.7022 (pmm) REVERT: i 382 ASP cc_start: 0.9540 (m-30) cc_final: 0.8907 (p0) REVERT: i 441 MET cc_start: 0.9040 (tmm) cc_final: 0.8680 (ttt) REVERT: k 163 MET cc_start: 0.7437 (tpp) cc_final: 0.6828 (tpp) REVERT: k 288 GLN cc_start: 0.7223 (pp30) cc_final: 0.6461 (mp10) REVERT: k 299 MET cc_start: 0.4262 (mmp) cc_final: 0.3207 (mtm) REVERT: k 420 MET cc_start: 0.5576 (mtt) cc_final: 0.4928 (mtt) REVERT: k 437 MET cc_start: 0.9194 (tpt) cc_final: 0.8676 (tpp) REVERT: p 11 TYR cc_start: 0.9066 (t80) cc_final: 0.8799 (t80) REVERT: p 350 MET cc_start: 0.1733 (ttt) cc_final: 0.1076 (ttp) REVERT: q 66 MET cc_start: 0.9167 (mmp) cc_final: 0.8664 (mmm) REVERT: q 145 TYR cc_start: 0.7654 (m-80) cc_final: 0.7321 (m-80) REVERT: q 205 ASP cc_start: 0.8804 (m-30) cc_final: 0.8241 (p0) REVERT: q 282 LEU cc_start: 0.9182 (tp) cc_final: 0.8953 (tt) REVERT: u 92 MET cc_start: -0.4973 (ppp) cc_final: -0.5464 (ptm) REVERT: w 244 MET cc_start: 0.0390 (pmm) cc_final: -0.0365 (pmm) REVERT: w 245 MET cc_start: -0.4087 (pmm) cc_final: -0.4856 (ptp) REVERT: w 338 MET cc_start: -0.7567 (mmt) cc_final: -0.8104 (mmt) REVERT: w 425 MET cc_start: 0.0130 (pmm) cc_final: -0.1112 (tpp) outliers start: 1 outliers final: 0 residues processed: 1015 average time/residue: 1.0190 time to fit residues: 1847.1200 Evaluate side-chains 858 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 858 time to evaluate : 9.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1711 random chunks: chunk 1009 optimal weight: 0.9980 chunk 1625 optimal weight: 8.9990 chunk 991 optimal weight: 10.0000 chunk 770 optimal weight: 0.9990 chunk 1129 optimal weight: 0.8980 chunk 1704 optimal weight: 10.0000 chunk 1568 optimal weight: 2.9990 chunk 1357 optimal weight: 40.0000 chunk 140 optimal weight: 4.9990 chunk 1048 optimal weight: 0.9990 chunk 832 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN B 577 HIS ** B1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 HIS K 69 HIS ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1055 HIS a1385 GLN ** a1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1889 HIS ** a1904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1970 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2089 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 555 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 223 HIS d 261 GLN d 475 ASN d 492 ASN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 724 HIS ** d 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 537 GLN ** e 662 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 369 ASN g 414 ASN ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 532 GLN g 552 GLN ** g 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 103 ASN i 188 ASN ** k 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 465 ASN ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4310 moved from start: 0.9273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 132050 Z= 0.198 Angle : 0.635 15.984 180842 Z= 0.321 Chirality : 0.042 0.537 21249 Planarity : 0.004 0.086 22474 Dihedral : 14.522 178.571 21584 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 0.01 % Allowed : 0.25 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.07), residues: 16602 helix: 0.97 (0.06), residues: 9343 sheet: -0.97 (0.16), residues: 1082 loop : -1.08 (0.08), residues: 6177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP r2037 HIS 0.016 0.001 HIS g 140 PHE 0.061 0.002 PHE e 851 TYR 0.063 0.002 TYR b1005 ARG 0.017 0.000 ARG e 951 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 33204 Ramachandran restraints generated. 16602 Oldfield, 0 Emsley, 16602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1038 time to evaluate : 10.488 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: A 238 MET cc_start: 0.4648 (ttp) cc_final: 0.4448 (ttp) REVERT: A 248 MET cc_start: 0.7123 (mpp) cc_final: 0.6007 (mmt) REVERT: A 329 MET cc_start: 0.1283 (tpt) cc_final: 0.1056 (tpt) REVERT: A 501 MET cc_start: -0.3075 (tpp) cc_final: -0.3485 (tpt) REVERT: A 986 MET cc_start: 0.3063 (mmp) cc_final: 0.2552 (mmt) REVERT: A 1309 MET cc_start: -0.3937 (mmp) cc_final: -0.4299 (mmt) REVERT: A 1412 MET cc_start: -0.1017 (pmm) cc_final: -0.1338 (pmm) REVERT: B 407 MET cc_start: -0.2927 (ptp) cc_final: -0.3382 (mmm) REVERT: B 796 MET cc_start: 0.3304 (mtt) cc_final: 0.2924 (mtt) REVERT: B 976 MET cc_start: 0.6523 (tpt) cc_final: 0.6077 (tpt) REVERT: B 1163 MET cc_start: 0.4236 (mtm) cc_final: 0.3587 (ttt) REVERT: B 1172 MET cc_start: 0.7469 (mmp) cc_final: 0.7097 (mpp) REVERT: E 94 MET cc_start: -0.7041 (ttt) cc_final: -0.7559 (ttt) REVERT: I 108 MET cc_start: -0.2889 (ttt) cc_final: -0.3461 (ttt) REVERT: O 40 ARG cc_start: -0.0361 (ttt-90) cc_final: -0.1257 (mpt180) REVERT: O 55 ARG cc_start: -0.2826 (mmt180) cc_final: -0.3362 (mmt180) REVERT: O 92 ARG cc_start: -0.4736 (mtp180) cc_final: -0.6004 (mtt180) REVERT: U 84 MET cc_start: -0.2328 (tmm) cc_final: -0.4268 (tpt) REVERT: Z 460 MET cc_start: 0.2223 (mmt) cc_final: 0.1749 (tpp) REVERT: Z 508 MET cc_start: -0.2013 (tpt) cc_final: -0.2578 (tpt) REVERT: Z 635 MET cc_start: 0.2268 (tpt) cc_final: 0.0708 (mmt) REVERT: a 1412 LEU cc_start: 0.8154 (tt) cc_final: 0.7913 (pp) REVERT: a 1624 MET cc_start: 0.9326 (mtt) cc_final: 0.9015 (mtm) REVERT: a 1661 LEU cc_start: 0.8940 (tp) cc_final: 0.8617 (tt) REVERT: a 1931 LEU cc_start: 0.8416 (mt) cc_final: 0.7755 (pp) REVERT: a 1950 ARG cc_start: 0.7586 (mmp-170) cc_final: 0.7016 (mmp-170) REVERT: a 1997 MET cc_start: 0.2479 (ptt) cc_final: 0.2129 (tmm) REVERT: a 2051 MET cc_start: 0.5731 (mmm) cc_final: 0.5067 (mmm) REVERT: a 2111 MET cc_start: 0.8492 (ptp) cc_final: 0.8182 (ptt) REVERT: a 2127 TYR cc_start: 0.8954 (t80) cc_final: 0.8625 (t80) REVERT: a 2150 LEU cc_start: 0.8983 (mp) cc_final: 0.8687 (mt) REVERT: b 267 MET cc_start: 0.7759 (tpt) cc_final: 0.6926 (ttt) REVERT: b 435 MET cc_start: 0.9290 (tpt) cc_final: 0.8937 (tpt) REVERT: b 450 GLN cc_start: 0.9582 (tp40) cc_final: 0.9296 (tm-30) REVERT: b 479 MET cc_start: 0.9178 (mpp) cc_final: 0.8971 (mpp) REVERT: b 485 MET cc_start: 0.9032 (tmm) cc_final: 0.8681 (tmm) REVERT: b 574 LYS cc_start: 0.8136 (tmmt) cc_final: 0.7868 (ptmm) REVERT: b 616 ASN cc_start: 0.9589 (t0) cc_final: 0.9338 (p0) REVERT: b 702 GLU cc_start: 0.8182 (mp0) cc_final: 0.7821 (mp0) REVERT: b 743 MET cc_start: 0.8121 (mpp) cc_final: 0.7916 (mpp) REVERT: b 744 LEU cc_start: 0.8942 (mm) cc_final: 0.8633 (mp) REVERT: b 772 MET cc_start: 0.9120 (tmm) cc_final: 0.8834 (tmm) REVERT: b 1044 GLU cc_start: 0.8171 (pm20) cc_final: 0.7816 (pm20) REVERT: b 1051 LEU cc_start: 0.8772 (mm) cc_final: 0.8567 (mm) REVERT: b 1070 LEU cc_start: 0.8670 (mm) cc_final: 0.8428 (mt) REVERT: b 1101 MET cc_start: 0.7854 (tpt) cc_final: 0.7628 (tpp) REVERT: b 1132 CYS cc_start: 0.7430 (m) cc_final: 0.7017 (p) REVERT: b 1135 ASP cc_start: 0.8031 (t70) cc_final: 0.7779 (t70) REVERT: b 1195 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7893 (mm-30) REVERT: b 1199 MET cc_start: 0.7216 (tmm) cc_final: 0.6918 (tmm) REVERT: d 400 MET cc_start: 0.9454 (mmp) cc_final: 0.9222 (mmm) REVERT: d 415 PHE cc_start: 0.7826 (m-80) cc_final: 0.7540 (m-80) REVERT: d 461 ARG cc_start: 0.8173 (tmt-80) cc_final: 0.7956 (tpt170) REVERT: d 634 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8176 (mt-10) REVERT: d 637 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8357 (tm-30) REVERT: d 642 ASP cc_start: 0.8879 (m-30) cc_final: 0.8579 (m-30) REVERT: d 701 MET cc_start: 0.8235 (tpt) cc_final: 0.7980 (mmm) REVERT: d 776 PHE cc_start: 0.8150 (t80) cc_final: 0.6853 (t80) REVERT: e 609 ASP cc_start: 0.8238 (m-30) cc_final: 0.7903 (m-30) REVERT: e 631 ILE cc_start: 0.7976 (pt) cc_final: 0.7744 (mp) REVERT: e 671 CYS cc_start: 0.8922 (m) cc_final: 0.8490 (m) REVERT: e 689 LEU cc_start: 0.9192 (mm) cc_final: 0.8892 (mm) REVERT: e 862 LYS cc_start: 0.7613 (mttt) cc_final: 0.7073 (pttm) REVERT: f 76 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8467 (mt-10) REVERT: f 174 ARG cc_start: 0.5902 (mmt180) cc_final: 0.5406 (mmp80) REVERT: f 215 MET cc_start: 0.5373 (tpp) cc_final: 0.4996 (tpp) REVERT: f 434 MET cc_start: 0.6274 (mtm) cc_final: 0.5848 (ttp) REVERT: f 563 LEU cc_start: 0.9101 (tt) cc_final: 0.8766 (tp) REVERT: f 587 MET cc_start: 0.5924 (mmp) cc_final: 0.5429 (mmp) REVERT: g 74 VAL cc_start: 0.8262 (t) cc_final: 0.7963 (m) REVERT: g 95 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8721 (mp0) REVERT: g 204 MET cc_start: 0.8561 (mmp) cc_final: 0.8302 (mmp) REVERT: g 275 ASP cc_start: 0.8364 (m-30) cc_final: 0.8155 (m-30) REVERT: g 283 THR cc_start: 0.8709 (p) cc_final: 0.8453 (p) REVERT: g 304 TYR cc_start: 0.8041 (m-80) cc_final: 0.7537 (m-80) REVERT: g 431 VAL cc_start: 0.8923 (t) cc_final: 0.8643 (t) REVERT: g 432 GLU cc_start: 0.8887 (pt0) cc_final: 0.8506 (mm-30) REVERT: g 631 PHE cc_start: 0.7476 (m-80) cc_final: 0.7086 (m-80) REVERT: g 689 TYR cc_start: 0.5412 (t80) cc_final: 0.4576 (t80) REVERT: g 700 LEU cc_start: 0.7047 (mt) cc_final: 0.6273 (tt) REVERT: g 707 GLN cc_start: 0.7369 (pm20) cc_final: 0.6758 (pp30) REVERT: g 879 GLN cc_start: 0.7672 (tm-30) cc_final: 0.6998 (tm-30) REVERT: g 914 ASN cc_start: 0.9265 (m-40) cc_final: 0.8986 (m-40) REVERT: h 358 PHE cc_start: 0.4597 (t80) cc_final: 0.4032 (t80) REVERT: h 493 LYS cc_start: 0.8403 (pptt) cc_final: 0.7804 (tptp) REVERT: h 648 MET cc_start: -0.0230 (ptt) cc_final: -0.1598 (ptt) REVERT: h 824 TYR cc_start: 0.3091 (t80) cc_final: 0.2482 (t80) REVERT: h 910 LYS cc_start: 0.7335 (tttt) cc_final: 0.6969 (tptt) REVERT: h 925 MET cc_start: 0.8524 (mtm) cc_final: 0.8124 (mtm) REVERT: h 928 TYR cc_start: 0.8594 (m-80) cc_final: 0.8332 (m-10) REVERT: h 936 THR cc_start: 0.8108 (m) cc_final: 0.7630 (p) REVERT: h 937 ILE cc_start: 0.8344 (tt) cc_final: 0.7888 (tp) REVERT: h 980 GLN cc_start: 0.8008 (tt0) cc_final: 0.7742 (tm-30) REVERT: h 988 GLN cc_start: 0.5592 (mt0) cc_final: 0.4793 (pt0) REVERT: i 108 MET cc_start: 0.5567 (mmp) cc_final: 0.4934 (ttt) REVERT: i 136 LEU cc_start: 0.7623 (mm) cc_final: 0.7365 (pp) REVERT: i 382 ASP cc_start: 0.9491 (m-30) cc_final: 0.8806 (p0) REVERT: i 441 MET cc_start: 0.8930 (tmm) cc_final: 0.8721 (ttt) REVERT: k 92 MET cc_start: 0.6768 (pmm) cc_final: 0.6263 (pmm) REVERT: k 163 MET cc_start: 0.7406 (tpp) cc_final: 0.6823 (tpp) REVERT: k 288 GLN cc_start: 0.7301 (pp30) cc_final: 0.6498 (mp10) REVERT: k 299 MET cc_start: 0.4235 (mmp) cc_final: 0.3160 (mtm) REVERT: k 420 MET cc_start: 0.5698 (mtt) cc_final: 0.5103 (mtt) REVERT: k 437 MET cc_start: 0.9200 (tpt) cc_final: 0.8706 (tpp) REVERT: p 350 MET cc_start: 0.1526 (ttt) cc_final: 0.0998 (ttp) REVERT: q 66 MET cc_start: 0.9200 (mmp) cc_final: 0.8758 (mmm) REVERT: q 145 TYR cc_start: 0.7564 (m-80) cc_final: 0.7226 (m-80) REVERT: q 205 ASP cc_start: 0.8736 (m-30) cc_final: 0.8154 (p0) REVERT: q 282 LEU cc_start: 0.9199 (tp) cc_final: 0.8962 (tt) REVERT: u 92 MET cc_start: -0.4825 (ppp) cc_final: -0.5380 (ptm) REVERT: w 244 MET cc_start: 0.0374 (pmm) cc_final: -0.0358 (pmm) REVERT: w 245 MET cc_start: -0.3876 (pmm) cc_final: -0.4590 (ptp) REVERT: w 338 MET cc_start: -0.7656 (mmt) cc_final: -0.8183 (mmt) REVERT: w 425 MET cc_start: 0.0177 (pmm) cc_final: -0.1164 (tpp) outliers start: 1 outliers final: 0 residues processed: 1039 average time/residue: 1.0332 time to fit residues: 1912.3553 Evaluate side-chains 873 residues out of total 14932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 873 time to evaluate : 10.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1711 random chunks: chunk 1078 optimal weight: 8.9990 chunk 1445 optimal weight: 50.0000 chunk 415 optimal weight: 50.0000 chunk 1251 optimal weight: 30.0000 chunk 200 optimal weight: 8.9990 chunk 377 optimal weight: 20.0000 chunk 1359 optimal weight: 50.0000 chunk 568 optimal weight: 40.0000 chunk 1396 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 250 optimal weight: 7.9990 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 372 ASN ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 HIS K 69 HIS ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1873 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1889 HIS ** a1904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1970 ASN a2113 ASN ** b 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 616 ASN ** b 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 900 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 698 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 836 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 888 HIS ** e 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 953 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 538 ASN g 539 HIS ** g 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 621 HIS ** h 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 879 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 919 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 37 ASN ** i 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 105 HIS ** i 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 188 ASN ** k 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 87 HIS ** p 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r2051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 54 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.134598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.117852 restraints weight = 1049651.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.116686 restraints weight = 961259.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.116923 restraints weight = 742558.326| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5456 moved from start: 1.0580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.171 132050 Z= 0.683 Angle : 1.007 23.073 180842 Z= 0.518 Chirality : 0.054 0.693 21249 Planarity : 0.007 0.136 22474 Dihedral : 14.799 178.731 21584 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 33.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.74 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.07), residues: 16602 helix: 0.36 (0.06), residues: 9206 sheet: -1.14 (0.16), residues: 1026 loop : -1.29 (0.08), residues: 6370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP r2041 HIS 0.041 0.003 HIS h 945 PHE 0.113 0.004 PHE a2104 TYR 0.092 0.003 TYR h 940 ARG 0.044 0.001 ARG b 227 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31501.23 seconds wall clock time: 551 minutes 31.49 seconds (33091.49 seconds total)