Starting phenix.real_space_refine on Wed Mar 27 16:32:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aaf_15296/03_2024/8aaf_15296_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aaf_15296/03_2024/8aaf_15296.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aaf_15296/03_2024/8aaf_15296_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aaf_15296/03_2024/8aaf_15296_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aaf_15296/03_2024/8aaf_15296_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aaf_15296/03_2024/8aaf_15296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aaf_15296/03_2024/8aaf_15296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aaf_15296/03_2024/8aaf_15296_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aaf_15296/03_2024/8aaf_15296_updated.pdb" } resolution = 2.5 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= 0.007 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 3643 5.49 5 Mg 13 5.21 5 S 177 5.16 5 C 81340 2.51 5 N 27609 2.21 5 O 38588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "G GLU 86": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "H PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "J GLU 4": "OE1" <-> "OE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "L GLU 67": "OE1" <-> "OE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M GLU 108": "OE1" <-> "OE2" Residue "M GLU 109": "OE1" <-> "OE2" Residue "M GLU 119": "OE1" <-> "OE2" Residue "P GLU 55": "OE1" <-> "OE2" Residue "P GLU 76": "OE1" <-> "OE2" Residue "Q GLU 35": "OE1" <-> "OE2" Residue "Q GLU 68": "OE1" <-> "OE2" Residue "Q GLU 81": "OE1" <-> "OE2" Residue "R GLU 83": "OE1" <-> "OE2" Residue "S GLU 58": "OE1" <-> "OE2" Residue "T GLU 87": "OE1" <-> "OE2" Residue "U GLU 8": "OE1" <-> "OE2" Residue "U GLU 15": "OE1" <-> "OE2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U GLU 60": "OE1" <-> "OE2" Residue "U GLU 64": "OE1" <-> "OE2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "b GLU 96": "OE1" <-> "OE2" Residue "c GLU 88": "OE1" <-> "OE2" Residue "j GLU 74": "OE1" <-> "OE2" Residue "j GLU 118": "OE1" <-> "OE2" Residue "k GLU 71": "OE1" <-> "OE2" Residue "k GLU 190": "OE1" <-> "OE2" Residue "k GLU 291": "OE1" <-> "OE2" Residue "k GLU 353": "OE1" <-> "OE2" Residue "l TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 117": "OE1" <-> "OE2" Residue "l TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 337": "OE1" <-> "OE2" Residue "m TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 148": "OE1" <-> "OE2" Residue "q GLU 143": "OE1" <-> "OE2" Residue "r GLU 45": "OE1" <-> "OE2" Residue "r GLU 58": "OE1" <-> "OE2" Residue "s GLU 15": "OE1" <-> "OE2" Residue "s GLU 38": "OE1" <-> "OE2" Residue "u GLU 37": "OE1" <-> "OE2" Residue "a ARG 99": "NH1" <-> "NH2" Residue "a GLU 162": "OE1" <-> "OE2" Residue "a PHE 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 203": "OE1" <-> "OE2" Residue "e GLU 205": "OE1" <-> "OE2" Residue "e PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 900": "OE1" <-> "OE2" Residue "e GLU 937": "OE1" <-> "OE2" Residue "e GLU 972": "OE1" <-> "OE2" Residue "e GLU 989": "OE1" <-> "OE2" Residue "e GLU 991": "OE1" <-> "OE2" Residue "e GLU 996": "OE1" <-> "OE2" Residue "v GLU 71": "OE1" <-> "OE2" Residue "0 ARG 61": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 151377 Number of models: 1 Model: "" Number of chains: 69 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "B" Number of atoms: 1555 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "C" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1416 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "E" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1258 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "F" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "G" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1272 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "I" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "J" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 518 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "M" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "N" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1169 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "P" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 737 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "Q" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "T" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "V" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 645 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 78} Chain: "X" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Z" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 410 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 824 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "d" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 207 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "f" Number of atoms: 68802 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3216, 68782 Classifications: {'RNA': 3216} Modifications used: {'rna2p_pur': 330, 'rna2p_pyr': 220, 'rna3p_pur': 1449, 'rna3p_pyr': 1217} Link IDs: {'rna2p': 550, 'rna3p': 2665} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 3216, 68782 Classifications: {'RNA': 3216} Modifications used: {'rna2p_pur': 330, 'rna2p_pyr': 219, 'rna3p_pur': 1449, 'rna3p_pyr': 1218} Link IDs: {'rna2p': 549, 'rna3p': 2666} Chain breaks: 3 bond proxies already assigned to first conformer: 76966 Chain: "h" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "i" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 14, 'rna3p_pur': 63, 'rna3p_pyr': 66} Link IDs: {'rna2p': 28, 'rna3p': 129} Chain: "j" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1874 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 234} Chain: "k" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2351 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "n" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1307 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 157} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "o" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "p" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1804 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 220} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "q" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1508 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "r" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1764 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "s" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1346 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "t" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "u" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "a" Number of atoms: 6582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6582 Classifications: {'peptide': 848} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 29, 'TRANS': 818} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 311 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 158 Chain: "e" Number of atoms: 11509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1527, 11509 Classifications: {'peptide': 1527} Incomplete info: {'truncation_to_alanine': 271} Link IDs: {'PTRANS': 38, 'TRANS': 1488} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 981 Unresolved non-hydrogen angles: 1251 Unresolved non-hydrogen dihedrals: 815 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 12, 'ASN:plan1': 24, 'TRP:plan': 1, 'ASP:plan': 21, 'PHE:plan': 27, 'GLU:plan': 25, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 569 Chain: "g" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1651 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "v" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1085 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 136} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'5CT:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "w" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1709 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain: "x" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1579 Classifications: {'RNA': 74} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p': 1, 'rna3p_pur': 27, 'rna3p_pyr': 30} Link IDs: {'rna2p': 16, 'rna3p': 57} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "y" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1556 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p': 1, 'rna3p_pur': 29, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 63} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "z" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 734 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 409 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 176 Chain: "0" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 967 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "1" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 13 Unusual residues: {' MG': 3, 'SPD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20901 SG CYS T 44 120.633 171.844 212.408 1.00 54.16 S ATOM 20919 SG CYS T 47 122.711 169.178 211.323 1.00 59.61 S ATOM 21191 SG CYS T 84 123.920 171.662 214.134 1.00 57.91 S ATOM 23302 SG CYS W 19 85.286 189.500 170.105 1.00 40.18 S ATOM 23327 SG CYS W 22 83.532 189.576 166.826 1.00 41.00 S ATOM 23427 SG CYS W 34 87.263 189.561 166.864 1.00 38.42 S ATOM 23445 SG CYS W 37 85.315 192.664 168.016 1.00 40.17 S ATOM 25002 SG CYS Z 96 133.219 140.262 76.511 1.00 54.37 S ATOM 25028 SG CYS Z 99 130.591 138.597 78.531 1.00 53.18 S ATOM 25115 SG CYS Z 110 130.455 138.056 74.853 1.00 52.08 S ATOM 25161 SG CYS Z 115 129.414 141.289 76.089 1.00 52.77 S ATOM 25359 SG CYS b 12 132.774 247.857 109.843 1.00 63.95 S ATOM 25394 SG CYS b 17 134.070 251.385 108.931 1.00 72.10 S ATOM 25858 SG CYS b 74 136.274 248.863 111.064 1.00 60.93 S ATOM 25880 SG CYS b 77 133.187 250.722 112.242 1.00 66.15 S ATOM 26403 SG CYS c 39 139.254 169.238 205.546 1.00 58.71 S ATOM 26426 SG CYS c 42 138.627 166.267 207.649 1.00 62.48 S ATOM 26535 SG CYS c 57 136.406 166.785 204.660 1.00 55.64 S ATOM 26553 SG CYS c 60 136.003 169.261 207.408 1.00 57.82 S ATOM A0W74 SG CYS e1527 39.614 126.447 188.667 1.00285.10 S ATOM A0W7O SG CYS e1530 37.155 124.007 187.646 1.00279.23 S ATOM A0WCG SG CYS e1551 37.823 127.179 185.542 1.00286.27 S ATOM A0WD1 SG CYS e1554 36.035 127.908 188.625 1.00284.05 S ATOM A0W32 SG CYS e1508 41.402 120.765 178.073 1.00285.58 S ATOM A0W3L SG CYS e1511 41.259 119.402 174.692 1.00284.14 S ATOM A0W9E SG CYS e1538 43.114 123.016 174.944 1.00281.30 S Residues with excluded nonbonded symmetry interactions: 198 residue: pdb=" N AVAL B 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 3 " occ=0.50 residue: pdb=" N AGLU B 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2AGLU B 4 " occ=0.50 residue: pdb=" N APRO B 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD APRO B 5 " occ=0.50 residue: pdb=" N AVAL B 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 6 " occ=0.50 residue: pdb=" N AVAL B 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 7 " occ=0.50 residue: pdb=" N AVAL B 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 8 " occ=0.50 residue: pdb=" N AILE B 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1AILE B 9 " occ=0.50 residue: pdb=" N AASP B 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2AASP B 10 " occ=0.50 residue: pdb=" N AGLY B 11 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLY B 11 " occ=0.50 residue: pdb=" N ALYS B 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ ALYS B 12 " occ=0.50 residue: pdb=" N AGLY B 13 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLY B 13 " occ=0.50 residue: pdb=" N AHIS B 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2AHIS B 14 " occ=0.50 ... (remaining 186 not shown) Time building chain proxies: 82.24, per 1000 atoms: 0.54 Number of scatterers: 151377 At special positions: 0 Unit cell: (232.98, 283.812, 262.632, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 177 16.00 P 3643 15.00 Mg 13 11.99 O 38588 8.00 N 27609 7.00 C 81340 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: 60.19 Conformation dependent library (CDL) restraints added in 11.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 47 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 84 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 44 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 22 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 19 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 37 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 34 " pdb=" ZN Z 201 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 99 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 110 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 115 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 96 " pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 12 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 17 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 39 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 57 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 42 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 60 " pdb=" ZN e2001 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1551 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1530 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1554 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1527 " pdb=" ZN e2002 " pdb="ZN ZN e2002 " - pdb=" ND1 HIS e1535 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1508 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1511 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1538 " Number of angles added : 33 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17764 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 365 helices and 88 sheets defined 48.7% alpha, 13.0% beta 1185 base pairs and 2012 stacking pairs defined. Time for finding SS restraints: 90.99 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 4.806A pdb=" N TYR A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LYS A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 34 removed outlier: 3.753A pdb=" N TRP A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASN A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 83 through 88 removed outlier: 3.844A pdb=" N GLN A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLY A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 88' Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 139 through 145 removed outlier: 4.410A pdb=" N ASP A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 153 removed outlier: 5.054A pdb=" N TRP A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N CYS A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 153' Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 186 through 196 Processing helix chain 'B' and resid 15 through 30 removed outlier: 3.689A pdb=" N ALYS B 25 " --> pdb=" O ASER B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 60 removed outlier: 4.078A pdb=" N ALYS B 60 " --> pdb=" O AASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 4.023A pdb=" N AGLY B 69 " --> pdb=" O AASN B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix No H-bonds generated for 'chain 'B' and resid 65 through 70' Processing helix chain 'B' and resid 75 through 89 removed outlier: 3.835A pdb=" N AMET B 87 " --> pdb=" O AALA B 83 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASER B 89 " --> pdb=" O AARG B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 removed outlier: 3.927A pdb=" N AARG B 101 " --> pdb=" O AALA B 97 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALEU B 102 " --> pdb=" O AALA B 98 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ALYS B 103 " --> pdb=" O ALEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 4.914A pdb=" N ALYS B 114 " --> pdb=" O APRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 151 through 186 removed outlier: 3.813A pdb=" N ALYS B 170 " --> pdb=" O AGLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.729A pdb=" N SER C 14 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ALA C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' Processing helix chain 'C' and resid 25 through 37 removed outlier: 3.640A pdb=" N GLU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 Processing helix chain 'C' and resid 84 through 106 Processing helix chain 'C' and resid 169 through 183 Processing helix chain 'C' and resid 70 through 76 removed outlier: 3.764A pdb=" N GLY C 73 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU C 75 " --> pdb=" O GLN C 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 40 Processing helix chain 'D' and resid 42 through 54 removed outlier: 3.961A pdb=" N LYS D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Proline residue: D 60 - end of helix Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.812A pdb=" N GLN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 118 Processing helix chain 'D' and resid 123 through 131 Processing helix chain 'D' and resid 147 through 154 removed outlier: 4.144A pdb=" N ARG D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLY D 154 " --> pdb=" O VAL D 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 147 through 154' Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.908A pdb=" N VAL E 22 " --> pdb=" O GLY E 18 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TRP E 23 " --> pdb=" O LYS E 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 18 through 23' Processing helix chain 'E' and resid 28 through 36 removed outlier: 5.178A pdb=" N ASN E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 48 Processing helix chain 'E' and resid 60 through 73 Processing helix chain 'E' and resid 77 through 82 removed outlier: 3.710A pdb=" N ARG E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 77 through 82' Processing helix chain 'E' and resid 84 through 113 Proline residue: E 90 - end of helix removed outlier: 6.827A pdb=" N VAL E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 130 removed outlier: 3.685A pdb=" N VAL E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 157 Processing helix chain 'F' and resid 33 through 49 Processing helix chain 'F' and resid 98 through 114 Processing helix chain 'F' and resid 117 through 122 removed outlier: 5.662A pdb=" N HIS F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 4.881A pdb=" N PHE F 143 " --> pdb=" O TYR F 139 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU F 144 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 32 removed outlier: 4.512A pdb=" N TYR G 30 " --> pdb=" O HIS G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 removed outlier: 4.286A pdb=" N ILE G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LYS G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 92 through 97' Processing helix chain 'G' and resid 99 through 121 removed outlier: 3.891A pdb=" N GLN G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 26 removed outlier: 4.167A pdb=" N ASN H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY H 26 " --> pdb=" O PRO H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 72 through 88 Processing helix chain 'I' and resid 66 through 71 removed outlier: 5.400A pdb=" N LYS I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 127 removed outlier: 3.884A pdb=" N LEU I 125 " --> pdb=" O GLU I 121 " (cutoff:3.500A) Proline residue: I 127 - end of helix Processing helix chain 'I' and resid 128 through 133 Processing helix chain 'J' and resid 33 through 43 Processing helix chain 'J' and resid 45 through 50 removed outlier: 3.562A pdb=" N ILE J 49 " --> pdb=" O ASN J 45 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ALA J 50 " --> pdb=" O PRO J 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 45 through 50' Processing helix chain 'J' and resid 52 through 60 Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.644A pdb=" N ILE K 63 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLU K 64 " --> pdb=" O TYR K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 78 removed outlier: 3.734A pdb=" N LYS K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP K 78 " --> pdb=" O LYS K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 Processing helix chain 'K' and resid 131 through 140 removed outlier: 3.836A pdb=" N ASN K 137 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG K 138 " --> pdb=" O ASP K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 22 Processing helix chain 'L' and resid 23 through 32 removed outlier: 4.028A pdb=" N VAL L 29 " --> pdb=" O SER L 25 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 44 Processing helix chain 'L' and resid 100 through 105 removed outlier: 3.567A pdb=" N LEU L 104 " --> pdb=" O HIS L 100 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL L 105 " --> pdb=" O PRO L 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 100 through 105' Processing helix chain 'L' and resid 112 through 123 Processing helix chain 'M' and resid 58 through 67 removed outlier: 5.381A pdb=" N VAL M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS M 67 " --> pdb=" O ALA M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 81 removed outlier: 3.568A pdb=" N LEU M 80 " --> pdb=" O ASN M 76 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU M 81 " --> pdb=" O TYR M 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 76 through 81' Processing helix chain 'M' and resid 92 through 97 removed outlier: 5.472A pdb=" N SER M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 125 removed outlier: 3.596A pdb=" N VAL M 113 " --> pdb=" O GLU M 109 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLY M 125 " --> pdb=" O ARG M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'N' and resid 2 through 7 removed outlier: 4.161A pdb=" N THR N 6 " --> pdb=" O PRO N 2 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LYS N 7 " --> pdb=" O SER N 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2 through 7' Processing helix chain 'N' and resid 41 through 49 Processing helix chain 'N' and resid 64 through 69 removed outlier: 4.419A pdb=" N PHE N 68 " --> pdb=" O GLN N 64 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP N 69 " --> pdb=" O GLN N 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 64 through 69' Processing helix chain 'N' and resid 74 through 83 removed outlier: 4.577A pdb=" N TRP N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N THR N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU N 81 " --> pdb=" O LYS N 77 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Proline residue: N 83 - end of helix Processing helix chain 'N' and resid 86 through 94 removed outlier: 4.083A pdb=" N ALA N 94 " --> pdb=" O TYR N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 108 Processing helix chain 'N' and resid 131 through 142 Processing helix chain 'O' and resid 11 through 20 removed outlier: 4.576A pdb=" N ASN O 19 " --> pdb=" O LYS O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 59 removed outlier: 3.531A pdb=" N ASN O 42 " --> pdb=" O LYS O 38 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS O 45 " --> pdb=" O ARG O 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 26 through 37 Processing helix chain 'P' and resid 49 through 64 Processing helix chain 'P' and resid 73 through 82 removed outlier: 3.829A pdb=" N THR P 79 " --> pdb=" O ASN P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 104 removed outlier: 4.972A pdb=" N LEU P 104 " --> pdb=" O ILE P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 21 removed outlier: 3.857A pdb=" N ARG Q 19 " --> pdb=" O ASN Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 45 Processing helix chain 'Q' and resid 52 through 61 Processing helix chain 'R' and resid 21 through 26 removed outlier: 5.154A pdb=" N HIS R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 78 through 87 removed outlier: 3.853A pdb=" N THR R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU R 85 " --> pdb=" O ASP R 81 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR R 86 " --> pdb=" O LEU R 82 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N MET R 87 " --> pdb=" O GLU R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 4.186A pdb=" N VAL R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 45 removed outlier: 4.452A pdb=" N PHE S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR S 44 " --> pdb=" O ASP S 40 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 66 removed outlier: 3.621A pdb=" N TYR T 62 " --> pdb=" O ARG T 58 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA T 63 " --> pdb=" O PRO T 59 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR T 64 " --> pdb=" O ARG T 60 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER T 66 " --> pdb=" O TYR T 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 58 through 66' Processing helix chain 'T' and resid 81 through 113 removed outlier: 3.752A pdb=" N GLU T 110 " --> pdb=" O LYS T 106 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 12 removed outlier: 4.178A pdb=" N THR U 11 " --> pdb=" O TYR U 7 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS U 12 " --> pdb=" O GLU U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 38 removed outlier: 3.564A pdb=" N GLN U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU U 36 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER U 37 " --> pdb=" O VAL U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 71 removed outlier: 4.590A pdb=" N THR U 46 " --> pdb=" O PRO U 42 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 82 removed outlier: 5.175A pdb=" N ALA U 82 " --> pdb=" O LYS U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 91 Processing helix chain 'U' and resid 93 through 99 Processing helix chain 'U' and resid 101 through 111 Processing helix chain 'V' and resid 25 through 30 removed outlier: 4.459A pdb=" N LYS V 29 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS V 30 " --> pdb=" O ILE V 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 25 through 30' Processing helix chain 'V' and resid 34 through 49 Processing helix chain 'V' and resid 51 through 64 Processing helix chain 'V' and resid 65 through 77 Processing helix chain 'V' and resid 79 through 100 Processing helix chain 'W' and resid 4 through 11 removed outlier: 3.650A pdb=" N GLY W 9 " --> pdb=" O THR W 5 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS W 10 " --> pdb=" O PRO W 6 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG W 11 " --> pdb=" O SER W 7 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 58 Processing helix chain 'W' and resid 65 through 77 removed outlier: 5.840A pdb=" N HIS W 69 " --> pdb=" O ARG W 65 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL W 70 " --> pdb=" O TYR W 66 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N SER W 71 " --> pdb=" O LEU W 67 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG W 72 " --> pdb=" O LYS W 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 17 removed outlier: 3.795A pdb=" N ARG X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG X 17 " --> pdb=" O GLU X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 69 Processing helix chain 'Y' and resid 6 through 21 removed outlier: 5.317A pdb=" N ARG Y 21 " --> pdb=" O LYS Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 30 removed outlier: 4.498A pdb=" N ARG Y 28 " --> pdb=" O PRO Y 24 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG Y 30 " --> pdb=" O TRP Y 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 24 through 30' Processing helix chain 'Z' and resid 79 through 91 removed outlier: 3.873A pdb=" N TYR Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 48 Processing helix chain 'c' and resid 19 through 35 removed outlier: 3.578A pdb=" N GLN c 25 " --> pdb=" O SER c 21 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 92 removed outlier: 4.149A pdb=" N GLU c 91 " --> pdb=" O ARG c 87 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA c 92 " --> pdb=" O GLU c 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 25 removed outlier: 5.694A pdb=" N TRP d 8 " --> pdb=" O MET d 4 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 11 removed outlier: 4.394A pdb=" N GLY j 11 " --> pdb=" O ASN j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 39 removed outlier: 5.744A pdb=" N ARG j 37 " --> pdb=" O ASP j 33 " (cutoff:3.500A) Processing helix chain 'j' and resid 103 through 108 removed outlier: 4.097A pdb=" N VAL j 107 " --> pdb=" O PRO j 103 " (cutoff:3.500A) Proline residue: j 108 - end of helix No H-bonds generated for 'chain 'j' and resid 103 through 108' Processing helix chain 'j' and resid 181 through 193 removed outlier: 4.174A pdb=" N LEU j 191 " --> pdb=" O HIS j 187 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS j 192 " --> pdb=" O LYS j 188 " (cutoff:3.500A) Processing helix chain 'j' and resid 200 through 205 removed outlier: 3.826A pdb=" N MET j 204 " --> pdb=" O ARG j 200 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASN j 205 " --> pdb=" O GLY j 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 200 through 205' Processing helix chain 'j' and resid 173 through 178 removed outlier: 3.641A pdb=" N ASP j 176 " --> pdb=" O GLY j 173 " (cutoff:3.500A) Proline residue: j 178 - end of helix Processing helix chain 'k' and resid 111 through 120 removed outlier: 4.414A pdb=" N ARG k 117 " --> pdb=" O GLU k 113 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE k 118 " --> pdb=" O VAL k 114 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TYR k 119 " --> pdb=" O LYS k 115 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS k 120 " --> pdb=" O ARG k 116 " (cutoff:3.500A) Processing helix chain 'k' and resid 130 through 139 removed outlier: 3.972A pdb=" N ALA k 138 " --> pdb=" O SER k 134 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN k 139 " --> pdb=" O ALA k 135 " (cutoff:3.500A) Processing helix chain 'k' and resid 142 through 154 removed outlier: 4.412A pdb=" N ARG k 146 " --> pdb=" O ALA k 142 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU k 147 " --> pdb=" O GLY k 143 " (cutoff:3.500A) Processing helix chain 'k' and resid 165 through 170 removed outlier: 4.238A pdb=" N THR k 169 " --> pdb=" O GLN k 165 " (cutoff:3.500A) Proline residue: k 170 - end of helix No H-bonds generated for 'chain 'k' and resid 165 through 170' Processing helix chain 'k' and resid 187 through 199 Processing helix chain 'k' and resid 204 through 209 removed outlier: 4.181A pdb=" N VAL k 208 " --> pdb=" O ALA k 204 " (cutoff:3.500A) Processing helix chain 'k' and resid 228 through 233 Processing helix chain 'k' and resid 347 through 352 removed outlier: 6.411A pdb=" N LEU k 351 " --> pdb=" O SER k 347 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU k 352 " --> pdb=" O ARG k 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 347 through 352' Processing helix chain 'k' and resid 372 through 381 Processing helix chain 'l' and resid 31 through 46 removed outlier: 3.787A pdb=" N SER l 41 " --> pdb=" O THR l 37 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS l 44 " --> pdb=" O THR l 40 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN l 45 " --> pdb=" O SER l 41 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS l 46 " --> pdb=" O VAL l 42 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 131 removed outlier: 3.922A pdb=" N ALA l 130 " --> pdb=" O ILE l 126 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL l 131 " --> pdb=" O ALA l 127 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 139 Processing helix chain 'l' and resid 154 through 159 removed outlier: 4.896A pdb=" N SER l 158 " --> pdb=" O THR l 154 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE l 159 " --> pdb=" O ASP l 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 154 through 159' Processing helix chain 'l' and resid 161 through 173 Processing helix chain 'l' and resid 174 through 185 removed outlier: 4.235A pdb=" N LYS l 185 " --> pdb=" O VAL l 181 " (cutoff:3.500A) Processing helix chain 'l' and resid 191 through 196 removed outlier: 3.778A pdb=" N ARG l 195 " --> pdb=" O LYS l 191 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN l 196 " --> pdb=" O GLY l 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 191 through 196' Processing helix chain 'l' and resid 214 through 221 removed outlier: 4.755A pdb=" N ASN l 221 " --> pdb=" O LYS l 217 " (cutoff:3.500A) Processing helix chain 'l' and resid 234 through 240 Proline residue: l 240 - end of helix Processing helix chain 'l' and resid 251 through 262 removed outlier: 4.669A pdb=" N ASP l 259 " --> pdb=" O PHE l 255 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN l 260 " --> pdb=" O THR l 256 " (cutoff:3.500A) Processing helix chain 'l' and resid 285 through 292 Processing helix chain 'l' and resid 293 through 299 removed outlier: 3.687A pdb=" N ALA l 298 " --> pdb=" O GLU l 294 " (cutoff:3.500A) Processing helix chain 'l' and resid 320 through 328 Processing helix chain 'l' and resid 329 through 338 removed outlier: 4.449A pdb=" N VAL l 333 " --> pdb=" O PRO l 329 " (cutoff:3.500A) Processing helix chain 'l' and resid 352 through 361 Processing helix chain 'm' and resid 9 through 16 Processing helix chain 'm' and resid 20 through 26 Processing helix chain 'm' and resid 29 through 37 removed outlier: 3.682A pdb=" N ARG m 35 " --> pdb=" O TYR m 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 79 through 87 removed outlier: 4.613A pdb=" N LEU m 83 " --> pdb=" O TYR m 79 " (cutoff:3.500A) Proline residue: m 84 - end of helix Processing helix chain 'm' and resid 94 through 114 Processing helix chain 'm' and resid 115 through 120 removed outlier: 4.699A pdb=" N TYR m 119 " --> pdb=" O LEU m 115 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LYS m 120 " --> pdb=" O ASP m 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 115 through 120' Processing helix chain 'm' and resid 157 through 170 removed outlier: 3.763A pdb=" N GLY m 161 " --> pdb=" O ALA m 157 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY m 170 " --> pdb=" O ALA m 166 " (cutoff:3.500A) Processing helix chain 'm' and resid 191 through 201 removed outlier: 3.619A pdb=" N LEU m 195 " --> pdb=" O ASP m 191 " (cutoff:3.500A) Processing helix chain 'm' and resid 202 through 215 removed outlier: 3.708A pdb=" N TYR m 207 " --> pdb=" O HIS m 203 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP m 214 " --> pdb=" O GLU m 210 " (cutoff:3.500A) Processing helix chain 'm' and resid 216 through 223 removed outlier: 4.783A pdb=" N PHE m 223 " --> pdb=" O PHE m 219 " (cutoff:3.500A) Processing helix chain 'm' and resid 224 through 230 Processing helix chain 'm' and resid 234 through 250 removed outlier: 4.368A pdb=" N ASP m 238 " --> pdb=" O ASP m 234 " (cutoff:3.500A) Processing helix chain 'm' and resid 261 through 273 removed outlier: 3.767A pdb=" N GLU m 268 " --> pdb=" O GLN m 264 " (cutoff:3.500A) Processing helix chain 'm' and resid 278 through 294 Processing helix chain 'n' and resid 80 through 85 removed outlier: 3.994A pdb=" N VAL n 84 " --> pdb=" O ASN n 80 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE n 85 " --> pdb=" O ALA n 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 80 through 85' Processing helix chain 'n' and resid 102 through 107 removed outlier: 3.963A pdb=" N PHE n 106 " --> pdb=" O ASN n 102 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA n 107 " --> pdb=" O VAL n 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 102 through 107' Processing helix chain 'n' and resid 131 through 150 removed outlier: 3.875A pdb=" N LYS n 143 " --> pdb=" O LYS n 139 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA n 144 " --> pdb=" O VAL n 140 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA n 147 " --> pdb=" O LYS n 143 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU n 148 " --> pdb=" O ALA n 144 " (cutoff:3.500A) Processing helix chain 'n' and resid 154 through 162 removed outlier: 5.285A pdb=" N SER n 162 " --> pdb=" O TYR n 158 " (cutoff:3.500A) Processing helix chain 'o' and resid 27 through 73 Processing helix chain 'o' and resid 96 through 107 Processing helix chain 'o' and resid 120 through 131 removed outlier: 4.041A pdb=" N LEU o 126 " --> pdb=" O ALA o 122 " (cutoff:3.500A) Processing helix chain 'o' and resid 140 through 151 Processing helix chain 'o' and resid 165 through 173 removed outlier: 4.156A pdb=" N ILE o 169 " --> pdb=" O ASP o 165 " (cutoff:3.500A) Processing helix chain 'o' and resid 180 through 191 removed outlier: 4.171A pdb=" N VAL o 191 " --> pdb=" O GLU o 187 " (cutoff:3.500A) Processing helix chain 'o' and resid 194 through 203 removed outlier: 5.109A pdb=" N TRP o 203 " --> pdb=" O ASN o 199 " (cutoff:3.500A) Processing helix chain 'o' and resid 235 through 244 removed outlier: 3.632A pdb=" N LEU o 239 " --> pdb=" O PHE o 235 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 69 removed outlier: 4.222A pdb=" N LYS p 63 " --> pdb=" O GLN p 59 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE p 67 " --> pdb=" O LYS p 63 " (cutoff:3.500A) Processing helix chain 'p' and resid 72 through 80 removed outlier: 4.847A pdb=" N ALA p 76 " --> pdb=" O PRO p 72 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE p 78 " --> pdb=" O THR p 74 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLN p 79 " --> pdb=" O ILE p 75 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR p 80 " --> pdb=" O ALA p 76 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 98 removed outlier: 4.002A pdb=" N LYS p 96 " --> pdb=" O LYS p 92 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR p 97 " --> pdb=" O LEU p 93 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG p 98 " --> pdb=" O PHE p 94 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 119 Processing helix chain 'p' and resid 135 through 146 Processing helix chain 'p' and resid 159 through 174 removed outlier: 4.604A pdb=" N VAL p 163 " --> pdb=" O PRO p 159 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE p 165 " --> pdb=" O GLU p 161 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU p 166 " --> pdb=" O LEU p 162 " (cutoff:3.500A) Proline residue: p 167 - end of helix Processing helix chain 'p' and resid 182 through 191 Processing helix chain 'p' and resid 204 through 222 removed outlier: 3.675A pdb=" N GLU p 208 " --> pdb=" O ARG p 204 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA p 209 " --> pdb=" O ALA p 205 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA p 210 " --> pdb=" O GLU p 206 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR p 217 " --> pdb=" O LYS p 213 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA p 220 " --> pdb=" O SER p 216 " (cutoff:3.500A) Processing helix chain 'p' and resid 225 through 233 removed outlier: 4.682A pdb=" N LYS p 231 " --> pdb=" O ASP p 227 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS p 232 " --> pdb=" O GLU p 228 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TRP p 233 " --> pdb=" O VAL p 229 " (cutoff:3.500A) Processing helix chain 'p' and resid 239 through 255 removed outlier: 4.216A pdb=" N SER p 255 " --> pdb=" O LYS p 251 " (cutoff:3.500A) Processing helix chain 'q' and resid 61 through 84 removed outlier: 3.641A pdb=" N ARG q 69 " --> pdb=" O VAL q 65 " (cutoff:3.500A) Processing helix chain 'q' and resid 150 through 166 removed outlier: 4.143A pdb=" N CYS q 165 " --> pdb=" O LEU q 161 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG q 166 " --> pdb=" O GLN q 162 " (cutoff:3.500A) Processing helix chain 'q' and resid 171 through 176 removed outlier: 4.108A pdb=" N LEU q 176 " --> pdb=" O ILE q 172 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 10 removed outlier: 4.429A pdb=" N TYR r 9 " --> pdb=" O PRO r 5 " (cutoff:3.500A) Processing helix chain 'r' and resid 42 through 47 removed outlier: 4.412A pdb=" N PHE r 46 " --> pdb=" O THR r 42 " (cutoff:3.500A) Proline residue: r 47 - end of helix No H-bonds generated for 'chain 'r' and resid 42 through 47' Processing helix chain 'r' and resid 61 through 80 Processing helix chain 'r' and resid 107 through 112 removed outlier: 4.664A pdb=" N LEU r 111 " --> pdb=" O GLY r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 144 through 160 removed outlier: 3.558A pdb=" N GLU r 150 " --> pdb=" O ASP r 146 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR r 157 " --> pdb=" O ARG r 153 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS r 158 " --> pdb=" O ARG r 154 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE r 159 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 160 - end of helix Processing helix chain 'r' and resid 177 through 188 removed outlier: 4.306A pdb=" N ALA r 187 " --> pdb=" O LYS r 183 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLY r 188 " --> pdb=" O LYS r 184 " (cutoff:3.500A) Processing helix chain 'r' and resid 205 through 213 removed outlier: 4.577A pdb=" N PHE r 213 " --> pdb=" O ASN r 209 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 219 removed outlier: 4.577A pdb=" N ALA r 219 " --> pdb=" O GLU r 215 " (cutoff:3.500A) Processing helix chain 's' and resid 27 through 42 Processing helix chain 's' and resid 73 through 88 Processing helix chain 's' and resid 108 through 113 removed outlier: 4.450A pdb=" N LEU s 112 " --> pdb=" O GLU s 108 " (cutoff:3.500A) Processing helix chain 's' and resid 136 through 141 removed outlier: 3.837A pdb=" N ARG s 140 " --> pdb=" O ALA s 136 " (cutoff:3.500A) Processing helix chain 's' and resid 155 through 167 removed outlier: 4.922A pdb=" N TYR s 167 " --> pdb=" O PHE s 163 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 22 removed outlier: 4.153A pdb=" N ARG t 21 " --> pdb=" O HIS t 17 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL t 22 " --> pdb=" O TRP t 18 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 17 through 22' Processing helix chain 't' and resid 27 through 47 Processing helix chain 't' and resid 76 through 84 Processing helix chain 't' and resid 86 through 94 Processing helix chain 't' and resid 105 through 123 Processing helix chain 't' and resid 140 through 146 Proline residue: t 146 - end of helix Processing helix chain 't' and resid 165 through 180 removed outlier: 6.292A pdb=" N THR t 169 " --> pdb=" O SER t 165 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU t 170 " --> pdb=" O ALA t 166 " (cutoff:3.500A) Processing helix chain 't' and resid 181 through 193 Processing helix chain 'u' and resid 59 through 64 removed outlier: 4.075A pdb=" N VAL u 63 " --> pdb=" O ASN u 59 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VAL u 64 " --> pdb=" O LEU u 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 59 through 64' Processing helix chain 'u' and resid 77 through 89 Processing helix chain 'u' and resid 90 through 98 removed outlier: 3.837A pdb=" N SER u 97 " --> pdb=" O LYS u 93 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER u 98 " --> pdb=" O TRP u 94 " (cutoff:3.500A) Processing helix chain 'u' and resid 99 through 112 Processing helix chain 'u' and resid 113 through 138 removed outlier: 4.239A pdb=" N ALA u 136 " --> pdb=" O LYS u 132 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS u 137 " --> pdb=" O LYS u 133 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA u 138 " --> pdb=" O ALA u 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 21 removed outlier: 3.808A pdb=" N GLU a 16 " --> pdb=" O LEU a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 84 Processing helix chain 'a' and resid 153 through 160 removed outlier: 4.345A pdb=" N PHE a 157 " --> pdb=" O ASP a 153 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASN a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 161 through 175 removed outlier: 5.475A pdb=" N GLU a 175 " --> pdb=" O ASN a 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 177 through 206 removed outlier: 3.944A pdb=" N GLY a 206 " --> pdb=" O LEU a 202 " (cutoff:3.500A) Processing helix chain 'a' and resid 219 through 228 Processing helix chain 'a' and resid 232 through 244 Processing helix chain 'a' and resid 250 through 258 Processing helix chain 'a' and resid 259 through 278 Processing helix chain 'a' and resid 299 through 305 removed outlier: 4.250A pdb=" N ILE a 305 " --> pdb=" O ASP a 301 " (cutoff:3.500A) Processing helix chain 'a' and resid 317 through 324 removed outlier: 4.108A pdb=" N ASP a 322 " --> pdb=" O GLY a 318 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER a 323 " --> pdb=" O GLY a 319 " (cutoff:3.500A) Processing helix chain 'a' and resid 332 through 396 removed outlier: 6.631A pdb=" N THR a 336 " --> pdb=" O PRO a 332 " (cutoff:3.500A) Processing helix chain 'a' and resid 397 through 413 removed outlier: 3.570A pdb=" N GLN a 412 " --> pdb=" O GLY a 408 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN a 413 " --> pdb=" O LEU a 409 " (cutoff:3.500A) Processing helix chain 'a' and resid 415 through 430 Processing helix chain 'a' and resid 431 through 438 removed outlier: 4.138A pdb=" N LEU a 437 " --> pdb=" O ILE a 433 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASN a 438 " --> pdb=" O ALA a 434 " (cutoff:3.500A) Processing helix chain 'a' and resid 513 through 562 removed outlier: 3.591A pdb=" N GLN a 530 " --> pdb=" O LYS a 526 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS a 531 " --> pdb=" O THR a 527 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY a 540 " --> pdb=" O GLU a 536 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS a 541 " --> pdb=" O LYS a 537 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP a 551 " --> pdb=" O GLU a 547 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS a 556 " --> pdb=" O GLN a 552 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N HIS a 562 " --> pdb=" O LEU a 558 " (cutoff:3.500A) Processing helix chain 'a' and resid 593 through 604 Processing helix chain 'a' and resid 631 through 647 removed outlier: 4.240A pdb=" N GLU a 647 " --> pdb=" O MET a 643 " (cutoff:3.500A) Processing helix chain 'a' and resid 661 through 666 removed outlier: 3.585A pdb=" N VAL a 665 " --> pdb=" O PHE a 661 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER a 666 " --> pdb=" O ALA a 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 661 through 666' Processing helix chain 'a' and resid 839 through 850 removed outlier: 4.554A pdb=" N LYS a 843 " --> pdb=" O GLY a 839 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS a 846 " --> pdb=" O GLY a 842 " (cutoff:3.500A) Processing helix chain 'a' and resid 855 through 867 Processing helix chain 'a' and resid 868 through 910 removed outlier: 3.921A pdb=" N ARG a 886 " --> pdb=" O GLU a 882 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS a 906 " --> pdb=" O LEU a 902 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE a 907 " --> pdb=" O GLN a 903 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR a 908 " --> pdb=" O ALA a 904 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N LYS a 909 " --> pdb=" O LEU a 905 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS a 910 " --> pdb=" O LYS a 906 " (cutoff:3.500A) Processing helix chain 'a' and resid 916 through 924 removed outlier: 4.223A pdb=" N HIS a 920 " --> pdb=" O ASN a 916 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS a 921 " --> pdb=" O TYR a 917 " (cutoff:3.500A) Processing helix chain 'a' and resid 943 through 951 removed outlier: 4.690A pdb=" N LYS a 949 " --> pdb=" O PRO a 945 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR a 950 " --> pdb=" O ALA a 946 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LYS a 951 " --> pdb=" O LEU a 947 " (cutoff:3.500A) Processing helix chain 'a' and resid 962 through 977 removed outlier: 4.405A pdb=" N ARG a 977 " --> pdb=" O TYR a 973 " (cutoff:3.500A) Processing helix chain 'a' and resid 990 through 1001 removed outlier: 5.519A pdb=" N LYS a1001 " --> pdb=" O ILE a 997 " (cutoff:3.500A) Processing helix chain 'a' and resid 1002 through 1010 removed outlier: 3.884A pdb=" N LEU a1007 " --> pdb=" O GLN a1003 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU a1008 " --> pdb=" O ASP a1004 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N CYS a1010 " --> pdb=" O VAL a1006 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.617A pdb=" N GLN e 11 " --> pdb=" O ASN e 7 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR e 12 " --> pdb=" O THR e 8 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN e 13 " --> pdb=" O PHE e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 35 through 42 removed outlier: 3.621A pdb=" N LEU e 42 " --> pdb=" O LEU e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 removed outlier: 5.486A pdb=" N ARG e 57 " --> pdb=" O SER e 53 " (cutoff:3.500A) Processing helix chain 'e' and resid 58 through 76 removed outlier: 3.951A pdb=" N PHE e 76 " --> pdb=" O LEU e 72 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 84 removed outlier: 3.630A pdb=" N PHE e 83 " --> pdb=" O ASN e 79 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ASN e 84 " --> pdb=" O GLU e 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 79 through 84' Processing helix chain 'e' and resid 85 through 99 removed outlier: 3.518A pdb=" N ALA e 96 " --> pdb=" O SER e 92 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS e 97 " --> pdb=" O GLN e 93 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 122 Processing helix chain 'e' and resid 123 through 130 removed outlier: 6.216A pdb=" N LYS e 127 " --> pdb=" O LYS e 123 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N PHE e 128 " --> pdb=" O LYS e 124 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS e 130 " --> pdb=" O SER e 126 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 142 removed outlier: 4.220A pdb=" N LEU e 135 " --> pdb=" O ASP e 131 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU e 142 " --> pdb=" O LEU e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 144 through 160 Proline residue: e 150 - end of helix Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 175 through 186 Processing helix chain 'e' and resid 189 through 195 removed outlier: 4.480A pdb=" N ASP e 195 " --> pdb=" O ASP e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 200 through 227 removed outlier: 3.717A pdb=" N SER e 204 " --> pdb=" O SER e 200 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N PHE e 206 " --> pdb=" O GLU e 202 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS e 227 " --> pdb=" O PHE e 223 " (cutoff:3.500A) Processing helix chain 'e' and resid 228 through 234 Processing helix chain 'e' and resid 235 through 243 Processing helix chain 'e' and resid 244 through 251 removed outlier: 3.751A pdb=" N LEU e 249 " --> pdb=" O SER e 245 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU e 250 " --> pdb=" O ILE e 246 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ASN e 251 " --> pdb=" O TRP e 247 " (cutoff:3.500A) Processing helix chain 'e' and resid 257 through 275 removed outlier: 4.620A pdb=" N TYR e 261 " --> pdb=" O ASN e 257 " (cutoff:3.500A) Processing helix chain 'e' and resid 276 through 281 removed outlier: 4.148A pdb=" N LYS e 281 " --> pdb=" O MET e 277 " (cutoff:3.500A) Processing helix chain 'e' and resid 282 through 298 removed outlier: 3.628A pdb=" N THR e 296 " --> pdb=" O LEU e 292 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE e 298 " --> pdb=" O SER e 294 " (cutoff:3.500A) Processing helix chain 'e' and resid 302 through 311 Proline residue: e 308 - end of helix Proline residue: e 311 - end of helix Processing helix chain 'e' and resid 312 through 325 removed outlier: 3.646A pdb=" N TYR e 323 " --> pdb=" O THR e 319 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU e 324 " --> pdb=" O LEU e 320 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP e 325 " --> pdb=" O ASP e 321 " (cutoff:3.500A) Processing helix chain 'e' and resid 326 through 333 removed outlier: 3.566A pdb=" N SER e 330 " --> pdb=" O GLY e 326 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP e 332 " --> pdb=" O ILE e 328 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS e 333 " --> pdb=" O TRP e 329 " (cutoff:3.500A) Processing helix chain 'e' and resid 334 through 350 removed outlier: 3.972A pdb=" N THR e 348 " --> pdb=" O SER e 344 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER e 349 " --> pdb=" O VAL e 345 " (cutoff:3.500A) Proline residue: e 350 - end of helix Processing helix chain 'e' and resid 353 through 369 removed outlier: 4.497A pdb=" N ARG e 367 " --> pdb=" O SER e 363 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N HIS e 368 " --> pdb=" O SER e 364 " (cutoff:3.500A) Processing helix chain 'e' and resid 375 through 392 Proline residue: e 379 - end of helix removed outlier: 3.609A pdb=" N GLY e 392 " --> pdb=" O LEU e 388 " (cutoff:3.500A) Processing helix chain 'e' and resid 397 through 417 removed outlier: 3.631A pdb=" N ASP e 415 " --> pdb=" O LYS e 411 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER e 416 " --> pdb=" O PHE e 412 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER e 417 " --> pdb=" O ALA e 413 " (cutoff:3.500A) Processing helix chain 'e' and resid 418 through 436 Processing helix chain 'e' and resid 438 through 443 removed outlier: 4.877A pdb=" N THR e 443 " --> pdb=" O LEU e 439 " (cutoff:3.500A) Processing helix chain 'e' and resid 444 through 450 removed outlier: 3.571A pdb=" N SER e 450 " --> pdb=" O ASN e 446 " (cutoff:3.500A) Processing helix chain 'e' and resid 454 through 468 removed outlier: 3.608A pdb=" N TRP e 458 " --> pdb=" O PRO e 454 " (cutoff:3.500A) Processing helix chain 'e' and resid 469 through 477 removed outlier: 5.140A pdb=" N VAL e 477 " --> pdb=" O ARG e 473 " (cutoff:3.500A) Processing helix chain 'e' and resid 478 through 490 Processing helix chain 'e' and resid 493 through 512 Proline residue: e 512 - end of helix Processing helix chain 'e' and resid 514 through 520 removed outlier: 3.676A pdb=" N TYR e 519 " --> pdb=" O VAL e 515 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP e 520 " --> pdb=" O PHE e 516 " (cutoff:3.500A) Processing helix chain 'e' and resid 521 through 533 removed outlier: 4.835A pdb=" N ASP e 533 " --> pdb=" O PHE e 529 " (cutoff:3.500A) Processing helix chain 'e' and resid 534 through 552 removed outlier: 4.502A pdb=" N GLY e 539 " --> pdb=" O ILE e 535 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LYS e 540 " --> pdb=" O PHE e 536 " (cutoff:3.500A) Proline residue: e 549 - end of helix Processing helix chain 'e' and resid 556 through 571 removed outlier: 3.718A pdb=" N ILE e 563 " --> pdb=" O ASN e 559 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS e 571 " --> pdb=" O TYR e 567 " (cutoff:3.500A) Processing helix chain 'e' and resid 572 through 577 removed outlier: 5.365A pdb=" N THR e 577 " --> pdb=" O PHE e 573 " (cutoff:3.500A) Processing helix chain 'e' and resid 578 through 594 removed outlier: 4.978A pdb=" N ASN e 594 " --> pdb=" O ALA e 590 " (cutoff:3.500A) Processing helix chain 'e' and resid 596 through 608 removed outlier: 5.285A pdb=" N ASP e 608 " --> pdb=" O MET e 604 " (cutoff:3.500A) Processing helix chain 'e' and resid 609 through 619 removed outlier: 5.366A pdb=" N ASP e 619 " --> pdb=" O LEU e 615 " (cutoff:3.500A) Processing helix chain 'e' and resid 622 through 634 Processing helix chain 'e' and resid 640 through 646 removed outlier: 4.438A pdb=" N ASN e 646 " --> pdb=" O ILE e 642 " (cutoff:3.500A) Processing helix chain 'e' and resid 651 through 666 Processing helix chain 'e' and resid 667 through 679 removed outlier: 4.834A pdb=" N ASP e 679 " --> pdb=" O LEU e 675 " (cutoff:3.500A) Processing helix chain 'e' and resid 680 through 690 Processing helix chain 'e' and resid 691 through 698 removed outlier: 5.336A pdb=" N TYR e 698 " --> pdb=" O SER e 694 " (cutoff:3.500A) Processing helix chain 'e' and resid 701 through 720 removed outlier: 4.386A pdb=" N SER e 720 " --> pdb=" O ALA e 716 " (cutoff:3.500A) Processing helix chain 'e' and resid 721 through 737 Processing helix chain 'e' and resid 742 through 758 removed outlier: 4.317A pdb=" N TYR e 746 " --> pdb=" O ALA e 742 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU e 752 " --> pdb=" O THR e 748 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU e 753 " --> pdb=" O HIS e 749 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN e 758 " --> pdb=" O ILE e 754 " (cutoff:3.500A) Processing helix chain 'e' and resid 759 through 765 removed outlier: 3.907A pdb=" N ILE e 763 " --> pdb=" O ASP e 759 " (cutoff:3.500A) Processing helix chain 'e' and resid 768 through 777 removed outlier: 3.982A pdb=" N VAL e 772 " --> pdb=" O ASN e 768 " (cutoff:3.500A) Processing helix chain 'e' and resid 781 through 788 removed outlier: 4.185A pdb=" N SER e 785 " --> pdb=" O ASP e 781 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU e 786 " --> pdb=" O TYR e 782 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL e 787 " --> pdb=" O ARG e 783 " (cutoff:3.500A) Processing helix chain 'e' and resid 792 through 798 removed outlier: 4.581A pdb=" N LEU e 796 " --> pdb=" O THR e 792 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU e 797 " --> pdb=" O ASN e 793 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU e 798 " --> pdb=" O THR e 794 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 792 through 798' Processing helix chain 'e' and resid 805 through 827 Proline residue: e 827 - end of helix Processing helix chain 'e' and resid 831 through 852 Processing helix chain 'e' and resid 856 through 861 removed outlier: 4.284A pdb=" N TYR e 860 " --> pdb=" O ASN e 856 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP e 861 " --> pdb=" O ASP e 857 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 856 through 861' Processing helix chain 'e' and resid 875 through 886 Proline residue: e 886 - end of helix Processing helix chain 'e' and resid 895 through 903 removed outlier: 3.558A pdb=" N SER e 901 " --> pdb=" O ASP e 897 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASN e 902 " --> pdb=" O ILE e 898 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N SER e 903 " --> pdb=" O ALA e 899 " (cutoff:3.500A) Processing helix chain 'e' and resid 904 through 921 Processing helix chain 'e' and resid 927 through 947 removed outlier: 3.638A pdb=" N SER e 935 " --> pdb=" O GLY e 931 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLN e 947 " --> pdb=" O THR e 943 " (cutoff:3.500A) Processing helix chain 'e' and resid 950 through 965 Processing helix chain 'e' and resid 970 through 986 removed outlier: 3.834A pdb=" N THR e 974 " --> pdb=" O LYS e 970 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY e 986 " --> pdb=" O SER e 982 " (cutoff:3.500A) Processing helix chain 'e' and resid 988 through 995 Processing helix chain 'e' and resid 996 through 1008 Processing helix chain 'e' and resid 1020 through 1037 Processing helix chain 'e' and resid 1044 through 1063 removed outlier: 4.387A pdb=" N VAL e1048 " --> pdb=" O SER e1044 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE e1062 " --> pdb=" O LYS e1058 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLU e1063 " --> pdb=" O LEU e1059 " (cutoff:3.500A) Processing helix chain 'e' and resid 1064 through 1069 removed outlier: 3.790A pdb=" N GLY e1069 " --> pdb=" O VAL e1065 " (cutoff:3.500A) Processing helix chain 'e' and resid 1070 through 1090 removed outlier: 3.515A pdb=" N LEU e1075 " --> pdb=" O THR e1071 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP e1090 " --> pdb=" O MET e1086 " (cutoff:3.500A) Processing helix chain 'e' and resid 1094 through 1111 Processing helix chain 'e' and resid 1123 through 1137 removed outlier: 3.702A pdb=" N MET e1135 " --> pdb=" O LEU e1131 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE e1136 " --> pdb=" O ILE e1132 " (cutoff:3.500A) Processing helix chain 'e' and resid 1145 through 1163 removed outlier: 3.651A pdb=" N THR e1149 " --> pdb=" O ASN e1145 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N GLU e1163 " --> pdb=" O ILE e1159 " (cutoff:3.500A) Processing helix chain 'e' and resid 1164 through 1172 removed outlier: 3.587A pdb=" N SER e1169 " --> pdb=" O LYS e1165 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN e1170 " --> pdb=" O LYS e1166 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LYS e1172 " --> pdb=" O GLU e1168 " (cutoff:3.500A) Processing helix chain 'e' and resid 1173 through 1181 removed outlier: 4.571A pdb=" N ASP e1181 " --> pdb=" O VAL e1177 " (cutoff:3.500A) Processing helix chain 'e' and resid 1182 through 1188 removed outlier: 4.688A pdb=" N ASN e1187 " --> pdb=" O ASP e1183 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE e1188 " --> pdb=" O ILE e1184 " (cutoff:3.500A) Processing helix chain 'e' and resid 1189 through 1217 removed outlier: 3.628A pdb=" N ASP e1208 " --> pdb=" O LYS e1204 " (cutoff:3.500A) Processing helix chain 'e' and resid 1235 through 1240 removed outlier: 3.728A pdb=" N LYS e1239 " --> pdb=" O ASN e1235 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU e1240 " --> pdb=" O SER e1236 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 1235 through 1240' Processing helix chain 'e' and resid 1241 through 1251 Processing helix chain 'e' and resid 1261 through 1281 removed outlier: 3.543A pdb=" N TYR e1278 " --> pdb=" O LEU e1274 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE e1279 " --> pdb=" O ILE e1275 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP e1281 " --> pdb=" O MET e1277 " (cutoff:3.500A) Processing helix chain 'e' and resid 1283 through 1298 removed outlier: 3.505A pdb=" N ILE e1289 " --> pdb=" O ASN e1285 " (cutoff:3.500A) Processing helix chain 'e' and resid 1299 through 1312 removed outlier: 5.363A pdb=" N ASP e1312 " --> pdb=" O THR e1308 " (cutoff:3.500A) Processing helix chain 'e' and resid 1315 through 1323 removed outlier: 3.984A pdb=" N TRP e1319 " --> pdb=" O ASP e1315 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASP e1323 " --> pdb=" O TRP e1319 " (cutoff:3.500A) Processing helix chain 'e' and resid 1324 through 1329 Processing helix chain 'e' and resid 1341 through 1363 Processing helix chain 'e' and resid 1364 through 1374 removed outlier: 4.948A pdb=" N SER e1368 " --> pdb=" O GLY e1364 " (cutoff:3.500A) Processing helix chain 'e' and resid 1376 through 1390 Processing helix chain 'e' and resid 1391 through 1411 removed outlier: 4.599A pdb=" N ASP e1408 " --> pdb=" O ASN e1404 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ARG e1409 " --> pdb=" O SER e1405 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU e1410 " --> pdb=" O LYS e1406 " (cutoff:3.500A) Processing helix chain 'e' and resid 1465 through 1481 Processing helix chain 'e' and resid 1486 through 1503 Processing helix chain 'e' and resid 1535 through 1547 removed outlier: 4.303A pdb=" N GLY e1547 " --> pdb=" O PHE e1543 " (cutoff:3.500A) Processing helix chain 'g' and resid 12 through 17 removed outlier: 4.234A pdb=" N PHE g 16 " --> pdb=" O GLU g 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 42 removed outlier: 3.829A pdb=" N PHE g 38 " --> pdb=" O PHE g 34 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 63 removed outlier: 4.797A pdb=" N MET g 62 " --> pdb=" O ILE g 58 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 88 Processing helix chain 'g' and resid 103 through 108 Processing helix chain 'g' and resid 122 through 133 Processing helix chain 'g' and resid 147 through 152 Processing helix chain 'g' and resid 166 through 178 Processing helix chain 'g' and resid 192 through 197 Processing helix chain 'g' and resid 211 through 223 Processing helix chain 'v' and resid 22 through 27 removed outlier: 5.217A pdb=" N ARG v 27 " --> pdb=" O CYS v 23 " (cutoff:3.500A) Processing helix chain 'v' and resid 118 through 131 Processing helix chain 'w' and resid 5 through 21 Processing helix chain 'w' and resid 70 through 81 removed outlier: 3.729A pdb=" N SER w 79 " --> pdb=" O ASP w 75 " (cutoff:3.500A) Processing helix chain 'w' and resid 86 through 94 removed outlier: 3.660A pdb=" N ASN w 94 " --> pdb=" O LEU w 90 " (cutoff:3.500A) Processing helix chain 'w' and resid 96 through 108 removed outlier: 4.878A pdb=" N ASN w 108 " --> pdb=" O SER w 104 " (cutoff:3.500A) Processing helix chain 'w' and resid 113 through 124 removed outlier: 4.556A pdb=" N LYS w 118 " --> pdb=" O GLU w 114 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN w 119 " --> pdb=" O VAL w 115 " (cutoff:3.500A) Proline residue: w 121 - end of helix Processing helix chain 'w' and resid 126 through 132 Processing helix chain 'w' and resid 143 through 154 Processing helix chain 'w' and resid 175 through 195 removed outlier: 5.072A pdb=" N LYS w 195 " --> pdb=" O VAL w 191 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 37 Proline residue: z 34 - end of helix Processing helix chain 'z' and resid 39 through 52 Processing helix chain 'z' and resid 77 through 87 removed outlier: 5.034A pdb=" N GLU z 87 " --> pdb=" O THR z 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 106 through 118 Processing helix chain 'z' and resid 125 through 138 removed outlier: 4.663A pdb=" N SER z 138 " --> pdb=" O GLY z 134 " (cutoff:3.500A) Processing helix chain 'z' and resid 151 through 156 removed outlier: 5.015A pdb=" N ASN z 156 " --> pdb=" O ILE z 152 " (cutoff:3.500A) Processing helix chain 'z' and resid 158 through 163 Proline residue: z 163 - end of helix Processing helix chain '0' and resid 3 through 23 removed outlier: 4.981A pdb=" N LYS 0 23 " --> pdb=" O LEU 0 19 " (cutoff:3.500A) Processing helix chain '0' and resid 34 through 46 Processing helix chain '0' and resid 55 through 71 removed outlier: 4.923A pdb=" N SER 0 68 " --> pdb=" O ARG 0 64 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP 0 69 " --> pdb=" O GLY 0 65 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU 0 70 " --> pdb=" O PHE 0 66 " (cutoff:3.500A) Proline residue: 0 71 - end of helix Processing helix chain '0' and resid 72 through 81 removed outlier: 4.428A pdb=" N LEU 0 76 " --> pdb=" O ASP 0 72 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU 0 77 " --> pdb=" O PHE 0 73 " (cutoff:3.500A) Proline residue: 0 78 - end of helix removed outlier: 4.205A pdb=" N LYS 0 81 " --> pdb=" O LEU 0 77 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 72 through 81' Processing helix chain '0' and resid 93 through 103 Processing sheet with id= 1, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.466A pdb=" N VAL A 35 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 61 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY A 58 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A 133 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 117 through 121 removed outlier: 3.635A pdb=" N ASN A 117 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR A 129 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 6 through 10 Processing sheet with id= 4, first strand: chain 'C' and resid 16 through 20 Processing sheet with id= 5, first strand: chain 'C' and resid 57 through 60 removed outlier: 5.436A pdb=" N LYS C 80 " --> pdb=" O PHE C 60 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 124 through 131 No H-bonds generated for sheet with id= 6 Processing sheet with id= 7, first strand: chain 'D' and resid 119 through 122 removed outlier: 4.878A pdb=" N THR D 100 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'F' and resid 24 through 31 removed outlier: 6.707A pdb=" N ILE F 10 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 87 through 96 removed outlier: 5.102A pdb=" N ASN F 74 " --> pdb=" O ILE F 129 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 6 through 10 removed outlier: 4.567A pdb=" N GLU F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 38 through 43 removed outlier: 4.577A pdb=" N ASP G 38 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS G 60 " --> pdb=" O ILE G 42 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 54 through 58 removed outlier: 6.172A pdb=" N ASN H 101 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 79 through 82 removed outlier: 3.921A pdb=" N ALA I 82 " --> pdb=" O ASP I 97 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP I 97 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN I 98 " --> pdb=" O ILE I 22 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA I 21 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET I 59 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP I 56 " --> pdb=" O VAL I 78 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 84 through 87 removed outlier: 4.506A pdb=" N VAL I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'I' and resid 75 through 78 Processing sheet with id= 16, first strand: chain 'J' and resid 3 through 6 removed outlier: 6.440A pdb=" N GLU J 4 " --> pdb=" O LYS J 12 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS J 12 " --> pdb=" O GLU J 4 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP J 6 " --> pdb=" O GLY J 10 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 18 through 22 Processing sheet with id= 18, first strand: chain 'K' and resid 81 through 86 removed outlier: 3.734A pdb=" N LYS K 120 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR K 119 " --> pdb=" O ARG K 115 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 56 through 59 removed outlier: 4.092A pdb=" N GLN L 66 " --> pdb=" O VAL L 58 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'L' and resid 72 through 75 Processing sheet with id= 21, first strand: chain 'L' and resid 86 through 89 removed outlier: 4.344A pdb=" N ALA L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 8 through 13 removed outlier: 4.145A pdb=" N LYS M 9 " --> pdb=" O ILE M 25 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS M 21 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 27 through 30 removed outlier: 4.643A pdb=" N LYS M 27 " --> pdb=" O LEU M 42 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'N' and resid 99 through 102 Processing sheet with id= 25, first strand: chain 'P' and resid 22 through 25 removed outlier: 6.372A pdb=" N LYS P 22 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU P 41 " --> pdb=" O ILE P 92 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS P 66 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Q' and resid 48 through 51 removed outlier: 4.934A pdb=" N ASP Q 48 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL Q 8 " --> pdb=" O ARG Q 77 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR Q 9 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 71 through 77 Processing sheet with id= 28, first strand: chain 'S' and resid 11 through 15 removed outlier: 6.754A pdb=" N LEU S 29 " --> pdb=" O LEU S 14 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG S 82 " --> pdb=" O THR S 72 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS S 63 " --> pdb=" O ALA S 55 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS S 47 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG S 48 " --> pdb=" O PHE S 101 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'S' and resid 8 through 14 removed outlier: 4.046A pdb=" N ALA S 96 " --> pdb=" O HIS S 13 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'T' and resid 19 through 24 removed outlier: 4.587A pdb=" N LYS T 19 " --> pdb=" O VAL T 35 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'X' and resid 2 through 5 removed outlier: 4.535A pdb=" N VAL X 55 " --> pdb=" O ILE X 5 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR X 22 " --> pdb=" O ARG X 46 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Z' and resid 100 through 103 removed outlier: 4.137A pdb=" N ALA Z 101 " --> pdb=" O CYS Z 96 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS Z 93 " --> pdb=" O LYS Z 124 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLN Z 120 " --> pdb=" O ARG Z 97 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'b' and resid 7 through 10 removed outlier: 4.478A pdb=" N VAL b 68 " --> pdb=" O LEU b 85 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR b 79 " --> pdb=" O CYS b 74 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'c' and resid 47 through 50 removed outlier: 6.881A pdb=" N ILE c 54 " --> pdb=" O GLY c 50 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY c 53 " --> pdb=" O GLY c 66 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS c 62 " --> pdb=" O CYS c 57 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'j' and resid 47 through 50 removed outlier: 3.921A pdb=" N GLN j 47 " --> pdb=" O LYS j 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS j 60 " --> pdb=" O LYS j 46 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN j 86 " --> pdb=" O VAL j 45 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'j' and resid 111 through 114 removed outlier: 4.418A pdb=" N THR j 111 " --> pdb=" O ILE j 136 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG j 147 " --> pdb=" O ILE j 137 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'j' and resid 58 through 64 Processing sheet with id= 38, first strand: chain 'j' and resid 145 through 150 removed outlier: 4.406A pdb=" N ALA j 154 " --> pdb=" O LEU j 150 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'k' and resid 41 through 44 removed outlier: 4.889A pdb=" N ALA k 42 " --> pdb=" O ASN k 184 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLN k 182 " --> pdb=" O THR k 44 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N HIS k 177 " --> pdb=" O THR k 164 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU k 161 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS k 201 " --> pdb=" O VAL k 86 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'k' and resid 53 through 59 removed outlier: 6.661A pdb=" N VAL k 78 " --> pdb=" O ALA k 51 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG k 334 " --> pdb=" O LYS k 50 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE k 335 " --> pdb=" O VAL k 220 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL k 220 " --> pdb=" O ILE k 335 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS k 273 " --> pdb=" O THR k 221 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'k' and resid 98 through 101 Processing sheet with id= 42, first strand: chain 'k' and resid 284 through 288 removed outlier: 3.741A pdb=" N GLY k 288 " --> pdb=" O ASN k 319 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN k 319 " --> pdb=" O GLY k 288 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'k' and resid 76 through 80 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'k' and resid 88 through 93 removed outlier: 3.745A pdb=" N GLY k 88 " --> pdb=" O LEU k 161 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'k' and resid 213 through 216 removed outlier: 4.189A pdb=" N GLU k 213 " --> pdb=" O ILE k 282 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'l' and resid 75 through 78 removed outlier: 4.383A pdb=" N GLN l 87 " --> pdb=" O VAL l 77 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'l' and resid 205 through 208 Processing sheet with id= 48, first strand: chain 'm' and resid 72 through 75 removed outlier: 6.834A pdb=" N ILE m 64 " --> pdb=" O LEU m 75 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'n' and resid 37 through 42 removed outlier: 3.956A pdb=" N THR n 38 " --> pdb=" O TYR n 54 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS n 50 " --> pdb=" O LEU n 42 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'o' and resid 133 through 138 removed outlier: 7.864A pdb=" N TYR o 133 " --> pdb=" O ILE o 89 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LYS o 82 " --> pdb=" O VAL o 119 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER o 113 " --> pdb=" O ARG o 88 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASN o 112 " --> pdb=" O LEU o 207 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'o' and resid 152 through 155 removed outlier: 8.623A pdb=" N GLY o 152 " --> pdb=" O LEU o 163 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'p' and resid 176 through 181 Processing sheet with id= 53, first strand: chain 'q' and resid 5 through 12 removed outlier: 4.944A pdb=" N GLN q 51 " --> pdb=" O VAL q 12 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU q 52 " --> pdb=" O VAL q 48 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'q' and resid 17 through 20 removed outlier: 5.995A pdb=" N ARG q 23 " --> pdb=" O LEU q 38 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 132 through 137 removed outlier: 4.963A pdb=" N GLU q 143 " --> pdb=" O SER q 137 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP q 142 " --> pdb=" O TYR q 92 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'q' and resid 86 through 90 Processing sheet with id= 57, first strand: chain 'r' and resid 34 through 37 removed outlier: 6.337A pdb=" N TYR r 34 " --> pdb=" O VAL r 89 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU r 52 " --> pdb=" O ILE r 135 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN r 133 " --> pdb=" O SER r 54 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'r' and resid 56 through 59 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'r' and resid 189 through 193 removed outlier: 7.658A pdb=" N GLU r 189 " --> pdb=" O LEU r 200 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE r 196 " --> pdb=" O ASP r 193 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'r' and resid 49 through 55 removed outlier: 5.069A pdb=" N CYS r 49 " --> pdb=" O SER r 168 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN r 162 " --> pdb=" O ASN r 55 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 's' and resid 45 through 49 removed outlier: 5.683A pdb=" N SER s 22 " --> pdb=" O GLY s 124 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLY s 124 " --> pdb=" O SER s 22 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 's' and resid 52 through 55 removed outlier: 7.191A pdb=" N TYR s 52 " --> pdb=" O ARG s 61 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG s 61 " --> pdb=" O TYR s 52 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 's' and resid 89 through 92 removed outlier: 3.628A pdb=" N ASP s 170 " --> pdb=" O TYR s 89 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU s 91 " --> pdb=" O ASP s 170 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 't' and resid 56 through 59 Processing sheet with id= 65, first strand: chain 'u' and resid 19 through 24 removed outlier: 4.472A pdb=" N ARG u 19 " --> pdb=" O ILE u 35 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS u 31 " --> pdb=" O ILE u 23 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'u' and resid 36 through 39 removed outlier: 6.764A pdb=" N LYS u 43 " --> pdb=" O ILE u 39 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'a' and resid 24 through 27 removed outlier: 4.391A pdb=" N TYR a 24 " --> pdb=" O LEU a 89 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYS a 87 " --> pdb=" O LEU a 26 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'a' and resid 28 through 32 removed outlier: 3.592A pdb=" N ASN a 28 " --> pdb=" O LYS a 42 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N GLN a 38 " --> pdb=" O ILE a 32 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'a' and resid 91 through 94 removed outlier: 6.887A pdb=" N ARG a 99 " --> pdb=" O PHE a 116 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASN a 121 " --> pdb=" O GLU a 115 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'a' and resid 306 through 310 No H-bonds generated for sheet with id= 70 Processing sheet with id= 71, first strand: chain 'a' and resid 446 through 454 removed outlier: 8.826A pdb=" N ASN a 446 " --> pdb=" O LEU a 510 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLU a 502 " --> pdb=" O LEU a 454 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'a' and resid 577 through 581 removed outlier: 4.044A pdb=" N LEU a 587 " --> pdb=" O LYS a 623 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY a 591 " --> pdb=" O HIS a 619 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N HIS a 619 " --> pdb=" O GLY a 591 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'a' and resid 656 through 660 Processing sheet with id= 74, first strand: chain 'a' and resid 939 through 942 removed outlier: 4.719A pdb=" N TYR a 952 " --> pdb=" O PHE a 703 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY a 959 " --> pdb=" O LYS a1013 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS a1013 " --> pdb=" O GLY a 959 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'e' and resid 1417 through 1423 removed outlier: 5.632A pdb=" N ASN e1426 " --> pdb=" O LEU e1445 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLU e1440 " --> pdb=" O VAL e1459 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'g' and resid 23 through 27 Processing sheet with id= 77, first strand: chain 'g' and resid 69 through 73 Processing sheet with id= 78, first strand: chain 'g' and resid 114 through 117 Processing sheet with id= 79, first strand: chain 'g' and resid 158 through 161 Processing sheet with id= 80, first strand: chain 'v' and resid 18 through 21 removed outlier: 3.677A pdb=" N SER v 149 " --> pdb=" O THR v 137 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'v' and resid 30 through 33 removed outlier: 4.741A pdb=" N GLY v 30 " --> pdb=" O ILE v 41 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL v 60 " --> pdb=" O VAL v 42 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'v' and resid 101 through 104 removed outlier: 3.654A pdb=" N ASP v 108 " --> pdb=" O ASN v 104 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'v' and resid 57 through 63 removed outlier: 4.295A pdb=" N LYS v 68 " --> pdb=" O ASP v 63 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'w' and resid 49 through 53 removed outlier: 7.222A pdb=" N PHE w 49 " --> pdb=" O LEU w 159 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'w' and resid 65 through 68 Processing sheet with id= 86, first strand: chain 'w' and resid 163 through 169 removed outlier: 6.356A pdb=" N LEU w 163 " --> pdb=" O LEU w 38 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL w 32 " --> pdb=" O VAL w 169 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU w 204 " --> pdb=" O LEU w 216 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'z' and resid 11 through 17 removed outlier: 3.527A pdb=" N LYS z 11 " --> pdb=" O GLN z 65 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL z 60 " --> pdb=" O PRO z 75 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain '0' and resid 49 through 53 removed outlier: 3.837A pdb=" N SER 0 24 " --> pdb=" O THR 0 89 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL 0 27 " --> pdb=" O VAL 0 188 " (cutoff:3.500A) 3349 hydrogen bonds defined for protein. 9954 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2919 hydrogen bonds 4662 hydrogen bond angles 0 basepair planarities 1185 basepair parallelities 2012 stacking parallelities Total time for adding SS restraints: 248.59 Time building geometry restraints manager: 65.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 29733 1.33 - 1.46: 64944 1.46 - 1.60: 63280 1.60 - 1.73: 3656 1.73 - 1.86: 280 Bond restraints: 161893 Sorted by residual: bond pdb=" OP1 I x 34 " pdb=" P I x 34 " ideal model delta sigma weight residual 1.510 1.860 -0.350 2.00e-02 2.50e+03 3.06e+02 bond pdb=" C6 I x 34 " pdb=" O6 I x 34 " ideal model delta sigma weight residual 1.185 1.383 -0.198 2.00e-02 2.50e+03 9.81e+01 bond pdb=" C2 I y 34 " pdb=" N3 I y 34 " ideal model delta sigma weight residual 1.462 1.306 0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C4 I x 34 " pdb=" N3 I x 34 " ideal model delta sigma weight residual 1.492 1.348 0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C4 I y 34 " pdb=" N3 I y 34 " ideal model delta sigma weight residual 1.492 1.357 0.135 2.00e-02 2.50e+03 4.54e+01 ... (remaining 161888 not shown) Histogram of bond angle deviations from ideal: 76.12 - 89.90: 2 89.90 - 103.68: 10329 103.68 - 117.46: 131900 117.46 - 131.23: 93054 131.23 - 145.01: 1196 Bond angle restraints: 236481 Sorted by residual: angle pdb=" O5' I x 34 " pdb=" P I x 34 " pdb=" OP2 I x 34 " ideal model delta sigma weight residual 108.00 145.01 -37.01 3.00e+00 1.11e-01 1.52e+02 angle pdb=" N GLY e1364 " pdb=" CA GLY e1364 " pdb=" C GLY e1364 " ideal model delta sigma weight residual 112.49 127.31 -14.82 1.21e+00 6.83e-01 1.50e+02 angle pdb=" O3' U x 33 " pdb=" P I x 34 " pdb=" OP1 I x 34 " ideal model delta sigma weight residual 108.00 76.12 31.88 3.00e+00 1.11e-01 1.13e+02 angle pdb=" N SER e1460 " pdb=" CA SER e1460 " pdb=" C SER e1460 " ideal model delta sigma weight residual 111.36 122.31 -10.95 1.09e+00 8.42e-01 1.01e+02 angle pdb=" N ASP e1181 " pdb=" CA ASP e1181 " pdb=" C ASP e1181 " ideal model delta sigma weight residual 111.28 120.90 -9.62 1.09e+00 8.42e-01 7.80e+01 ... (remaining 236476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 93065 35.99 - 71.99: 8354 71.99 - 107.98: 869 107.98 - 143.98: 21 143.98 - 179.97: 58 Dihedral angle restraints: 102367 sinusoidal: 74912 harmonic: 27455 Sorted by residual: dihedral pdb=" CA GLY e 392 " pdb=" C GLY e 392 " pdb=" N PHE e 393 " pdb=" CA PHE e 393 " ideal model delta harmonic sigma weight residual -180.00 -47.08 -132.92 0 5.00e+00 4.00e-02 7.07e+02 dihedral pdb=" CA THR p 30 " pdb=" C THR p 30 " pdb=" N PRO p 31 " pdb=" CA PRO p 31 " ideal model delta harmonic sigma weight residual -180.00 -124.96 -55.04 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA LYS U 83 " pdb=" C LYS U 83 " pdb=" N LYS U 84 " pdb=" CA LYS U 84 " ideal model delta harmonic sigma weight residual 180.00 -133.03 -46.97 0 5.00e+00 4.00e-02 8.83e+01 ... (remaining 102364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 28916 0.149 - 0.298: 547 0.298 - 0.447: 53 0.447 - 0.597: 2 0.597 - 0.746: 1 Chirality restraints: 29519 Sorted by residual: chirality pdb=" CB ILE U 118 " pdb=" CA ILE U 118 " pdb=" CG1 ILE U 118 " pdb=" CG2 ILE U 118 " both_signs ideal model delta sigma weight residual False 2.64 1.90 0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CA ASP p 158 " pdb=" N ASP p 158 " pdb=" C ASP p 158 " pdb=" CB ASP p 158 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" C3' G f 282 " pdb=" C4' G f 282 " pdb=" O3' G f 282 " pdb=" C2' G f 282 " both_signs ideal model delta sigma weight residual False -2.48 -2.01 -0.47 2.00e-01 2.50e+01 5.48e+00 ... (remaining 29516 not shown) Planarity restraints: 16484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' I y 34 " 0.195 2.00e-02 2.50e+03 5.59e-01 7.04e+03 pdb=" C2' I y 34 " -0.211 2.00e-02 2.50e+03 pdb=" C3' I y 34 " -0.550 2.00e-02 2.50e+03 pdb=" C4' I y 34 " 0.462 2.00e-02 2.50e+03 pdb=" C5' I y 34 " 0.003 2.00e-02 2.50e+03 pdb=" N9 I y 34 " -0.887 2.00e-02 2.50e+03 pdb=" O2' I y 34 " 0.819 2.00e-02 2.50e+03 pdb=" O3' I y 34 " -0.525 2.00e-02 2.50e+03 pdb=" O4' I y 34 " 0.695 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' I x 34 " -0.236 2.00e-02 2.50e+03 4.80e-01 5.17e+03 pdb=" C2' I x 34 " 0.287 2.00e-02 2.50e+03 pdb=" C3' I x 34 " 0.561 2.00e-02 2.50e+03 pdb=" C4' I x 34 " -0.408 2.00e-02 2.50e+03 pdb=" C5' I x 34 " 0.048 2.00e-02 2.50e+03 pdb=" N9 I x 34 " 0.676 2.00e-02 2.50e+03 pdb=" O2' I x 34 " -0.745 2.00e-02 2.50e+03 pdb=" O3' I x 34 " 0.366 2.00e-02 2.50e+03 pdb=" O4' I x 34 " -0.550 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP m 95 " -0.034 2.00e-02 2.50e+03 3.46e-02 2.99e+01 pdb=" CG TRP m 95 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 TRP m 95 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP m 95 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP m 95 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP m 95 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP m 95 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 95 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 95 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP m 95 " -0.008 2.00e-02 2.50e+03 ... (remaining 16481 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 19 2.12 - 2.81: 40531 2.81 - 3.51: 199647 3.51 - 4.20: 467143 4.20 - 4.90: 650556 Nonbonded interactions: 1357896 Sorted by model distance: nonbonded pdb=" O3' A x 76 " pdb=" C UNK 1 58 " model vdw 1.419 3.270 nonbonded pdb=" OP1 U f1258 " pdb=" NH1 ARG 0 46 " model vdw 1.522 2.520 nonbonded pdb=" CB GLU e 324 " pdb=" OG1 THR e 327 " model vdw 1.547 3.440 nonbonded pdb=" O ASN e 882 " pdb=" O GLN e 885 " model vdw 1.687 3.040 nonbonded pdb=" NE2 GLN e1477 " pdb=" OG1 THR e1481 " model vdw 1.841 2.520 ... (remaining 1357891 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'x' and (resid 1 through 17 or resid 21 through 76)) selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 23.140 Check model and map are aligned: 1.670 Set scattering table: 1.060 Process input model: 625.090 Find NCS groups from input model: 3.480 Set up NCS constraints: 0.520 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:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 671.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.350 161893 Z= 0.388 Angle : 0.916 37.012 236481 Z= 0.504 Chirality : 0.054 0.746 29519 Planarity : 0.009 0.559 16484 Dihedral : 21.657 179.972 84603 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.79 % Favored : 96.10 % Rotamer: Outliers : 1.14 % Allowed : 1.52 % Favored : 97.34 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.08), residues: 9312 helix: 0.70 (0.08), residues: 3867 sheet: -0.03 (0.14), residues: 1220 loop : -1.18 (0.08), residues: 4225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP m 95 HIS 0.017 0.002 HIS r 123 PHE 0.046 0.002 PHE o 229 TYR 0.067 0.002 TYR N 60 ARG 0.025 0.001 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1324 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1238 time to evaluate : 8.575 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: E 148 ASP cc_start: 0.8877 (t70) cc_final: 0.8421 (t0) REVERT: H 25 ASN cc_start: 0.9002 (m-40) cc_final: 0.8776 (m-40) REVERT: H 104 ARG cc_start: 0.8744 (ttp80) cc_final: 0.8440 (ttp80) REVERT: M 103 GLN cc_start: 0.7683 (tp40) cc_final: 0.7462 (mm-40) REVERT: M 109 GLU cc_start: 0.8332 (tp30) cc_final: 0.7971 (tp30) REVERT: P 27 TYR cc_start: 0.8562 (t80) cc_final: 0.8179 (t80) REVERT: X 5 ILE cc_start: 0.9063 (tp) cc_final: 0.8527 (tp) REVERT: j 33 ASP cc_start: 0.7946 (p0) cc_final: 0.7635 (p0) REVERT: k 214 MET cc_start: 0.8255 (mmm) cc_final: 0.7993 (mmm) REVERT: m 90 HIS cc_start: 0.8016 (m-70) cc_final: 0.7679 (m-70) REVERT: m 206 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7678 (tm-30) REVERT: n 99 GLU cc_start: 0.8042 (pm20) cc_final: 0.7778 (pp20) REVERT: n 102 ASN cc_start: 0.8751 (p0) cc_final: 0.7966 (p0) REVERT: o 64 GLN cc_start: 0.8385 (tp40) cc_final: 0.8088 (mm110) REVERT: q 160 ASP cc_start: 0.7475 (m-30) cc_final: 0.7250 (m-30) REVERT: r 73 ASN cc_start: 0.8756 (t0) cc_final: 0.8536 (t0) REVERT: r 112 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7930 (mm-40) REVERT: s 48 SER cc_start: 0.9279 (m) cc_final: 0.8931 (p) REVERT: s 170 ASP cc_start: 0.7529 (p0) cc_final: 0.7066 (p0) REVERT: s 172 LEU cc_start: 0.9093 (tp) cc_final: 0.8742 (tp) REVERT: u 11 ASN cc_start: 0.8408 (p0) cc_final: 0.8140 (p0) REVERT: a 351 LEU cc_start: 0.8856 (mt) cc_final: 0.8641 (pp) REVERT: a 365 ASP cc_start: 0.9502 (m-30) cc_final: 0.9112 (p0) REVERT: a 699 MET cc_start: 0.8998 (mmp) cc_final: 0.8692 (mmm) REVERT: a 884 MET cc_start: 0.8561 (tmm) cc_final: 0.8265 (OUTLIER) REVERT: e 323 TYR cc_start: 0.8181 (t80) cc_final: 0.7930 (t80) REVERT: e 709 PHE cc_start: 0.9509 (t80) cc_final: 0.9305 (t80) REVERT: e 733 HIS cc_start: 0.8902 (OUTLIER) cc_final: 0.8516 (t-90) REVERT: e 799 THR cc_start: 0.5888 (OUTLIER) cc_final: 0.5453 (t) REVERT: e 826 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7597 (tt) REVERT: e 853 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7101 (mm-30) REVERT: e 1028 PHE cc_start: 0.8995 (m-10) cc_final: 0.8558 (m-80) REVERT: e 1145 ASN cc_start: 0.5970 (m-40) cc_final: 0.5539 (m-40) REVERT: e 1179 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.6676 (mt) REVERT: e 1246 GLN cc_start: 0.7666 (mt0) cc_final: 0.7387 (pp30) REVERT: e 1261 ASN cc_start: 0.6335 (m-40) cc_final: 0.5777 (p0) REVERT: e 1281 ASP cc_start: 0.8109 (m-30) cc_final: 0.7204 (p0) REVERT: e 1329 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7493 (mp0) REVERT: e 1410 LEU cc_start: 0.8794 (tp) cc_final: 0.8356 (tp) REVERT: e 1421 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7317 (mp) REVERT: g 18 LYS cc_start: 0.8144 (tppt) cc_final: 0.7624 (tppt) REVERT: g 67 ARG cc_start: 0.9228 (ptm-80) cc_final: 0.8740 (ptm-80) REVERT: g 140 GLN cc_start: 0.8519 (tp40) cc_final: 0.8200 (tp-100) REVERT: g 162 HIS cc_start: 0.6984 (t70) cc_final: 0.6775 (t70) REVERT: v 18 THR cc_start: 0.9195 (p) cc_final: 0.8991 (t) REVERT: v 99 PHE cc_start: 0.8886 (m-80) cc_final: 0.8335 (m-10) REVERT: v 125 GLN cc_start: 0.9602 (tp-100) cc_final: 0.9288 (tp-100) REVERT: v 136 VAL cc_start: 0.8325 (t) cc_final: 0.7843 (p) REVERT: v 138 ILE cc_start: 0.9421 (pt) cc_final: 0.9221 (pp) REVERT: w 12 HIS cc_start: 0.9496 (m90) cc_final: 0.9114 (m90) REVERT: w 49 PHE cc_start: 0.9197 (p90) cc_final: 0.8916 (p90) REVERT: w 60 ARG cc_start: 0.9269 (mtm-85) cc_final: 0.8975 (mtm-85) REVERT: w 182 GLN cc_start: 0.8542 (mt0) cc_final: 0.8312 (mm-40) REVERT: 0 20 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8796 (mt-10) REVERT: 0 37 GLN cc_start: 0.7669 (mt0) cc_final: 0.7078 (mt0) REVERT: 0 52 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8834 (tm) REVERT: 0 60 ARG cc_start: 0.8764 (mtt180) cc_final: 0.8468 (mtt-85) REVERT: 0 71 PRO cc_start: 0.9332 (Cg_endo) cc_final: 0.8310 (Cg_exo) REVERT: 0 78 PRO cc_start: 0.9481 (Cg_exo) cc_final: 0.8878 (Cg_endo) REVERT: 0 83 ASN cc_start: 0.5662 (t0) cc_final: 0.5246 (t0) REVERT: 0 191 TYR cc_start: 0.8811 (t80) cc_final: 0.8301 (t80) outliers start: 86 outliers final: 12 residues processed: 1303 average time/residue: 2.0704 time to fit residues: 3972.9583 Evaluate side-chains 909 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 890 time to evaluate : 8.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain q residue 120 ASP Chi-restraints excluded: chain r residue 112 GLN Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 309 VAL Chi-restraints excluded: chain e residue 394 SER Chi-restraints excluded: chain e residue 733 HIS Chi-restraints excluded: chain e residue 799 THR Chi-restraints excluded: chain e residue 826 LEU Chi-restraints excluded: chain e residue 853 GLU Chi-restraints excluded: chain e residue 867 PHE Chi-restraints excluded: chain e residue 951 ASP Chi-restraints excluded: chain e residue 1059 LEU Chi-restraints excluded: chain e residue 1179 LEU Chi-restraints excluded: chain e residue 1363 VAL Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1421 LEU Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain 0 residue 52 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1083 optimal weight: 20.0000 chunk 972 optimal weight: 5.9990 chunk 539 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 655 optimal weight: 10.0000 chunk 519 optimal weight: 10.0000 chunk 1005 optimal weight: 5.9990 chunk 389 optimal weight: 10.0000 chunk 611 optimal weight: 10.0000 chunk 748 optimal weight: 7.9990 chunk 1165 optimal weight: 3.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN A G 131 GLN I 4 ASN ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 103 GLN P 75 ASN S 42 GLN T 3 GLN X 40 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 32 ASN b 22 GLN j 24 GLN k 293 ASN m 39 GLN p 59 GLN p 77 GLN r 51 HIS r 100 ASN r 123 HIS s 47 GLN t 114 GLN a 141 HIS ** a 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 189 ASN e 226 ASN ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 795 HIS e 805 ASN e 810 GLN ** e 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1141 GLN ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e1457 ASN e1477 GLN g 50 HIS g 83 HIS ** g 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 36 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.131 161893 Z= 0.465 Angle : 0.698 18.658 236481 Z= 0.370 Chirality : 0.044 0.327 29519 Planarity : 0.006 0.109 16484 Dihedral : 22.679 179.972 66865 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.96 % Favored : 95.98 % Rotamer: Outliers : 2.59 % Allowed : 10.38 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.08), residues: 9312 helix: 1.01 (0.08), residues: 3907 sheet: -0.16 (0.15), residues: 1187 loop : -0.98 (0.09), residues: 4218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP n 9 HIS 0.009 0.001 HIS r 123 PHE 0.048 0.002 PHE 0 88 TYR 0.033 0.002 TYR N 60 ARG 0.012 0.001 ARG w 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 915 time to evaluate : 8.673 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: A 104 GLU cc_start: 0.7694 (tt0) cc_final: 0.7494 (tt0) REVERT: E 148 ASP cc_start: 0.8907 (t70) cc_final: 0.8427 (t0) REVERT: H 49 ASN cc_start: 0.8059 (t0) cc_final: 0.7696 (t0) REVERT: L 74 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.8357 (m-80) REVERT: M 88 ASP cc_start: 0.8151 (t0) cc_final: 0.7718 (p0) REVERT: M 108 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7938 (mm-30) REVERT: M 109 GLU cc_start: 0.8382 (tp30) cc_final: 0.7971 (tp30) REVERT: P 59 TYR cc_start: 0.9230 (m-80) cc_final: 0.9011 (m-80) REVERT: X 5 ILE cc_start: 0.9056 (tp) cc_final: 0.8436 (tp) REVERT: X 10 GLN cc_start: 0.8349 (tt0) cc_final: 0.8128 (tt0) REVERT: X 67 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: Z 120 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8246 (mt0) REVERT: j 33 ASP cc_start: 0.8324 (p0) cc_final: 0.8097 (p0) REVERT: j 74 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8017 (mm-30) REVERT: m 206 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7701 (tm-30) REVERT: o 225 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: s 48 SER cc_start: 0.8712 (m) cc_final: 0.8057 (p) REVERT: s 77 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7489 (tm-30) REVERT: s 90 GLN cc_start: 0.8519 (mm110) cc_final: 0.8283 (mm110) REVERT: s 93 ASP cc_start: 0.9007 (t70) cc_final: 0.8572 (t0) REVERT: s 107 ASP cc_start: 0.8473 (t0) cc_final: 0.8215 (t0) REVERT: s 167 TYR cc_start: 0.7792 (m-80) cc_final: 0.7323 (m-80) REVERT: a 351 LEU cc_start: 0.8934 (mt) cc_final: 0.8626 (tm) REVERT: a 365 ASP cc_start: 0.9521 (m-30) cc_final: 0.9140 (p0) REVERT: a 590 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7730 (ttp) REVERT: e 271 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8945 (mm) REVERT: e 378 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8085 (mt) REVERT: e 777 MET cc_start: 0.6857 (tpp) cc_final: 0.6576 (tpp) REVERT: e 798 LEU cc_start: 0.8714 (tp) cc_final: 0.8511 (tp) REVERT: e 799 THR cc_start: 0.6314 (OUTLIER) cc_final: 0.5713 (t) REVERT: e 858 LEU cc_start: 0.8711 (tp) cc_final: 0.8404 (tp) REVERT: e 1068 MET cc_start: 0.7685 (mtm) cc_final: 0.7404 (ptt) REVERT: e 1281 ASP cc_start: 0.8276 (m-30) cc_final: 0.7199 (p0) REVERT: e 1303 MET cc_start: 0.7408 (tpp) cc_final: 0.7168 (tpt) REVERT: e 1474 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7610 (mtp) REVERT: g 18 LYS cc_start: 0.8206 (tppt) cc_final: 0.7848 (tppt) REVERT: g 67 ARG cc_start: 0.9108 (ptm-80) cc_final: 0.8847 (ptm160) REVERT: g 123 ARG cc_start: 0.8731 (ttp80) cc_final: 0.8512 (ttp80) REVERT: g 140 GLN cc_start: 0.8622 (tp40) cc_final: 0.8208 (tp-100) REVERT: v 27 ARG cc_start: 0.7695 (mtp-110) cc_final: 0.7479 (mmm-85) REVERT: w 8 GLN cc_start: 0.9159 (mt0) cc_final: 0.8873 (pt0) REVERT: w 11 GLU cc_start: 0.9424 (OUTLIER) cc_final: 0.9171 (pp20) REVERT: w 12 HIS cc_start: 0.9396 (m90) cc_final: 0.8831 (m-70) REVERT: w 60 ARG cc_start: 0.9335 (mtm-85) cc_final: 0.9069 (mtt90) REVERT: w 65 ILE cc_start: 0.8983 (mp) cc_final: 0.8573 (mp) REVERT: w 110 PHE cc_start: 0.9089 (m-10) cc_final: 0.8616 (m-80) REVERT: w 174 MET cc_start: 0.7282 (mpt) cc_final: 0.6847 (mpt) REVERT: w 182 GLN cc_start: 0.8553 (mt0) cc_final: 0.8193 (mm-40) REVERT: 0 6 GLU cc_start: 0.8418 (pp20) cc_final: 0.8167 (pp20) REVERT: 0 10 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8512 (mp0) REVERT: 0 37 GLN cc_start: 0.6933 (mt0) cc_final: 0.6574 (mt0) REVERT: 0 40 GLU cc_start: 0.8304 (pp20) cc_final: 0.8006 (pp20) REVERT: 0 64 ARG cc_start: 0.8931 (mtm110) cc_final: 0.8594 (mtm-85) REVERT: 0 78 PRO cc_start: 0.9432 (Cg_exo) cc_final: 0.9144 (Cg_endo) REVERT: 0 191 TYR cc_start: 0.8833 (t80) cc_final: 0.8552 (t80) outliers start: 196 outliers final: 89 residues processed: 1018 average time/residue: 2.0925 time to fit residues: 3170.9569 Evaluate side-chains 937 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 837 time to evaluate : 8.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 16 THR Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain J residue 41 LYS Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 14 ILE Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain U residue 71 LYS Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 27 ILE Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 67 GLN Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Z residue 88 LYS Chi-restraints excluded: chain Z residue 120 GLN Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain b residue 99 GLN Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain j residue 74 GLU Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 225 GLN Chi-restraints excluded: chain p residue 66 SER Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 203 VAL Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 112 LEU Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain u residue 5 SER Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 151 MET Chi-restraints excluded: chain a residue 192 TYR Chi-restraints excluded: chain a residue 261 LEU Chi-restraints excluded: chain a residue 439 LEU Chi-restraints excluded: chain a residue 581 ILE Chi-restraints excluded: chain a residue 590 MET Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 948 LEU Chi-restraints excluded: chain a residue 1017 THR Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain e residue 271 LEU Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 378 LEU Chi-restraints excluded: chain e residue 799 THR Chi-restraints excluded: chain e residue 801 ASP Chi-restraints excluded: chain e residue 812 LEU Chi-restraints excluded: chain e residue 852 SER Chi-restraints excluded: chain e residue 857 ASP Chi-restraints excluded: chain e residue 867 PHE Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1051 LEU Chi-restraints excluded: chain e residue 1057 THR Chi-restraints excluded: chain e residue 1079 LEU Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1421 LEU Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1474 MET Chi-restraints excluded: chain e residue 1488 LEU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 146 ILE Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain w residue 11 GLU Chi-restraints excluded: chain w residue 66 CYS Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 69 ASP Chi-restraints excluded: chain 0 residue 88 PHE Chi-restraints excluded: chain 0 residue 186 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 647 optimal weight: 10.0000 chunk 361 optimal weight: 7.9990 chunk 969 optimal weight: 30.0000 chunk 793 optimal weight: 8.9990 chunk 321 optimal weight: 6.9990 chunk 1167 optimal weight: 3.9990 chunk 1260 optimal weight: 50.0000 chunk 1039 optimal weight: 0.9990 chunk 1157 optimal weight: 0.9980 chunk 397 optimal weight: 10.0000 chunk 936 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 138 GLN G 112 ASN G 131 GLN M 106 GLN O 19 ASN T 3 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 32 ASN j 24 GLN j 132 ASN n 97 ASN p 59 GLN p 77 GLN ** p 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 157 ASN s 47 GLN s 90 GLN t 114 GLN u 27 GLN ** a 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 810 GLN ** e 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 52 HIS v 88 ASN 0 39 HIS ** 0 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 161893 Z= 0.296 Angle : 0.608 15.191 236481 Z= 0.323 Chirality : 0.039 0.280 29519 Planarity : 0.005 0.114 16484 Dihedral : 22.629 179.521 66837 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.07 % Favored : 95.89 % Rotamer: Outliers : 2.55 % Allowed : 12.32 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: 0.20 (0.08), residues: 9312 helix: 1.29 (0.08), residues: 3881 sheet: -0.06 (0.15), residues: 1178 loop : -0.88 (0.09), residues: 4253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 92 HIS 0.009 0.001 HIS e1273 PHE 0.029 0.002 PHE e 939 TYR 0.024 0.002 TYR p 80 ARG 0.012 0.001 ARG a 889 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 888 time to evaluate : 8.772 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: C 120 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8296 (p0) REVERT: E 148 ASP cc_start: 0.8889 (t70) cc_final: 0.8487 (t0) REVERT: G 127 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8270 (tp40) REVERT: H 49 ASN cc_start: 0.8118 (t0) cc_final: 0.7611 (t0) REVERT: L 74 TYR cc_start: 0.8793 (OUTLIER) cc_final: 0.8321 (m-80) REVERT: M 108 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7813 (mm-30) REVERT: M 109 GLU cc_start: 0.8342 (tp30) cc_final: 0.7927 (tp30) REVERT: P 27 TYR cc_start: 0.8432 (t80) cc_final: 0.8150 (t80) REVERT: P 59 TYR cc_start: 0.9225 (m-80) cc_final: 0.9017 (m-80) REVERT: X 5 ILE cc_start: 0.8913 (tp) cc_final: 0.8561 (tp) REVERT: X 10 GLN cc_start: 0.8299 (tt0) cc_final: 0.8084 (tt0) REVERT: j 33 ASP cc_start: 0.8121 (p0) cc_final: 0.7893 (p0) REVERT: j 74 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7976 (mm-30) REVERT: k 214 MET cc_start: 0.8272 (mmm) cc_final: 0.7765 (mmm) REVERT: m 206 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7874 (tm-30) REVERT: r 123 HIS cc_start: 0.8209 (OUTLIER) cc_final: 0.7671 (p90) REVERT: s 48 SER cc_start: 0.8749 (m) cc_final: 0.8034 (p) REVERT: s 77 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7532 (tm-30) REVERT: s 81 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8023 (mm-30) REVERT: s 93 ASP cc_start: 0.9039 (t70) cc_final: 0.8653 (t0) REVERT: s 107 ASP cc_start: 0.8540 (t0) cc_final: 0.8247 (t0) REVERT: s 167 TYR cc_start: 0.7611 (m-80) cc_final: 0.7365 (m-80) REVERT: u 12 TRP cc_start: 0.7605 (OUTLIER) cc_final: 0.6585 (p90) REVERT: a 351 LEU cc_start: 0.8879 (mt) cc_final: 0.8587 (tm) REVERT: a 365 ASP cc_start: 0.9514 (m-30) cc_final: 0.9126 (p0) REVERT: e 277 MET cc_start: 0.8340 (mtm) cc_final: 0.8123 (mtm) REVERT: e 284 MET cc_start: 0.8031 (ttp) cc_final: 0.7774 (ttp) REVERT: e 777 MET cc_start: 0.6905 (tpp) cc_final: 0.6698 (tpp) REVERT: e 858 LEU cc_start: 0.8617 (tp) cc_final: 0.8276 (tp) REVERT: e 1041 TYR cc_start: 0.7886 (m-80) cc_final: 0.7633 (m-10) REVERT: e 1163 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8162 (pt0) REVERT: e 1474 MET cc_start: 0.8206 (mtp) cc_final: 0.7826 (mtp) REVERT: g 18 LYS cc_start: 0.8277 (tppt) cc_final: 0.7882 (tppt) REVERT: g 67 ARG cc_start: 0.9116 (ptm-80) cc_final: 0.8842 (ptm-80) REVERT: g 140 GLN cc_start: 0.8589 (tp40) cc_final: 0.8148 (tp-100) REVERT: g 157 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8713 (mm-40) REVERT: v 18 THR cc_start: 0.9008 (p) cc_final: 0.8710 (t) REVERT: v 21 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6981 (tmm) REVERT: v 27 ARG cc_start: 0.7892 (mtp-110) cc_final: 0.7590 (mtp180) REVERT: v 88 ASN cc_start: 0.9287 (m-40) cc_final: 0.9064 (m-40) REVERT: v 125 GLN cc_start: 0.9559 (tp-100) cc_final: 0.9285 (tp-100) REVERT: w 11 GLU cc_start: 0.9461 (OUTLIER) cc_final: 0.9171 (pp20) REVERT: w 12 HIS cc_start: 0.9361 (m90) cc_final: 0.8767 (m90) REVERT: w 60 ARG cc_start: 0.9378 (mtm-85) cc_final: 0.9122 (mtt90) REVERT: w 110 PHE cc_start: 0.8986 (m-10) cc_final: 0.8735 (m-80) REVERT: w 174 MET cc_start: 0.7305 (mpt) cc_final: 0.6821 (mpt) REVERT: 0 37 GLN cc_start: 0.7055 (mt0) cc_final: 0.6719 (mt0) REVERT: 0 66 PHE cc_start: 0.8997 (m-80) cc_final: 0.8666 (m-80) REVERT: 0 69 ASP cc_start: 0.9458 (OUTLIER) cc_final: 0.8792 (p0) REVERT: 0 78 PRO cc_start: 0.9487 (Cg_exo) cc_final: 0.9237 (Cg_endo) REVERT: 0 97 LYS cc_start: 0.6624 (pttt) cc_final: 0.6384 (pttt) REVERT: 0 191 TYR cc_start: 0.8787 (t80) cc_final: 0.8582 (t80) outliers start: 193 outliers final: 86 residues processed: 989 average time/residue: 2.1379 time to fit residues: 3145.6157 Evaluate side-chains 928 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 834 time to evaluate : 8.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain U residue 71 LYS Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain Z residue 88 LYS Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain d residue 4 MET Chi-restraints excluded: chain j residue 74 GLU Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 143 THR Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 160 ILE Chi-restraints excluded: chain p residue 203 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 39 GLN Chi-restraints excluded: chain s residue 41 SER Chi-restraints excluded: chain s residue 112 LEU Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain u residue 3 THR Chi-restraints excluded: chain u residue 5 SER Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 192 TYR Chi-restraints excluded: chain a residue 362 LYS Chi-restraints excluded: chain a residue 439 LEU Chi-restraints excluded: chain a residue 581 ILE Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 1005 LEU Chi-restraints excluded: chain a residue 1017 THR Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain e residue 309 VAL Chi-restraints excluded: chain e residue 801 ASP Chi-restraints excluded: chain e residue 852 SER Chi-restraints excluded: chain e residue 857 ASP Chi-restraints excluded: chain e residue 867 PHE Chi-restraints excluded: chain e residue 951 ASP Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1037 SER Chi-restraints excluded: chain e residue 1079 LEU Chi-restraints excluded: chain e residue 1202 VAL Chi-restraints excluded: chain e residue 1365 CYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1421 LEU Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1488 LEU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 146 ILE Chi-restraints excluded: chain v residue 21 MET Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain w residue 11 GLU Chi-restraints excluded: chain w residue 66 CYS Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 69 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1153 optimal weight: 3.9990 chunk 877 optimal weight: 1.9990 chunk 605 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 557 optimal weight: 40.0000 chunk 783 optimal weight: 0.0370 chunk 1171 optimal weight: 10.0000 chunk 1240 optimal weight: 8.9990 chunk 612 optimal weight: 10.0000 chunk 1110 optimal weight: 0.9990 chunk 334 optimal weight: 10.0000 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 138 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 GLN Y 32 ASN j 24 GLN j 97 ASN p 59 GLN p 77 GLN ** p 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 100 ASN r 113 GLN s 47 GLN s 90 GLN t 114 GLN u 27 GLN a 31 ASN ** a 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 810 GLN ** e 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1455 GLN ** g 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 52 HIS v 104 ASN ** w 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 161893 Z= 0.239 Angle : 0.577 15.124 236481 Z= 0.307 Chirality : 0.037 0.292 29519 Planarity : 0.004 0.112 16484 Dihedral : 22.565 179.751 66836 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 3.09 % Allowed : 13.47 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.35 (0.09), residues: 9312 helix: 1.43 (0.08), residues: 3895 sheet: -0.05 (0.15), residues: 1168 loop : -0.80 (0.09), residues: 4249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP n 9 HIS 0.007 0.001 HIS e1273 PHE 0.030 0.001 PHE 0 88 TYR 0.021 0.001 TYR P 68 ARG 0.007 0.000 ARG g 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 873 time to evaluate : 8.744 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: A 104 GLU cc_start: 0.7644 (tt0) cc_final: 0.7428 (tt0) REVERT: B 34 VAL cc_start: 0.9276 (OUTLIER) cc_final: 0.9044 (m) REVERT: C 120 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8130 (p0) REVERT: E 148 ASP cc_start: 0.8852 (t70) cc_final: 0.8424 (t0) REVERT: H 49 ASN cc_start: 0.8122 (t0) cc_final: 0.7890 (t0) REVERT: H 92 TRP cc_start: 0.7697 (m-10) cc_final: 0.7368 (m-10) REVERT: L 74 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8257 (m-80) REVERT: M 108 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7807 (mm-30) REVERT: N 120 ASN cc_start: 0.8669 (t0) cc_final: 0.8424 (t0) REVERT: P 59 TYR cc_start: 0.9217 (m-80) cc_final: 0.8954 (m-80) REVERT: R 19 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8645 (ttp-170) REVERT: X 5 ILE cc_start: 0.8742 (tp) cc_final: 0.8343 (tp) REVERT: X 10 GLN cc_start: 0.8312 (tt0) cc_final: 0.8084 (tt0) REVERT: j 33 ASP cc_start: 0.7959 (p0) cc_final: 0.7751 (p0) REVERT: j 74 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7970 (mm-30) REVERT: k 214 MET cc_start: 0.8270 (mmm) cc_final: 0.7836 (mmm) REVERT: m 206 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7914 (tm-30) REVERT: n 136 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: o 110 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.8216 (ttm170) REVERT: q 143 GLU cc_start: 0.8273 (tt0) cc_final: 0.7488 (tt0) REVERT: r 123 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7803 (p90) REVERT: s 48 SER cc_start: 0.8770 (m) cc_final: 0.8028 (p) REVERT: s 77 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7608 (tm-30) REVERT: s 81 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8156 (mm-30) REVERT: s 93 ASP cc_start: 0.9045 (t70) cc_final: 0.8642 (t0) REVERT: s 107 ASP cc_start: 0.8489 (t0) cc_final: 0.8215 (t0) REVERT: u 12 TRP cc_start: 0.7715 (OUTLIER) cc_final: 0.6516 (p90) REVERT: a 351 LEU cc_start: 0.8863 (mt) cc_final: 0.8573 (tm) REVERT: a 365 ASP cc_start: 0.9477 (m-30) cc_final: 0.9083 (p0) REVERT: a 884 MET cc_start: 0.8673 (tmm) cc_final: 0.8437 (tmm) REVERT: a 1002 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: a 1004 ASP cc_start: 0.9291 (OUTLIER) cc_final: 0.8944 (p0) REVERT: e 858 LEU cc_start: 0.8664 (tp) cc_final: 0.8320 (tp) REVERT: e 1041 TYR cc_start: 0.7917 (m-80) cc_final: 0.7673 (m-10) REVERT: g 18 LYS cc_start: 0.8271 (tppt) cc_final: 0.7872 (tppt) REVERT: g 67 ARG cc_start: 0.9138 (ptm-80) cc_final: 0.8917 (ptm-80) REVERT: g 140 GLN cc_start: 0.8583 (tp40) cc_final: 0.8113 (tp-100) REVERT: v 18 THR cc_start: 0.9021 (p) cc_final: 0.8770 (t) REVERT: v 27 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7619 (mmm-85) REVERT: v 88 ASN cc_start: 0.9299 (m-40) cc_final: 0.9098 (m-40) REVERT: v 125 GLN cc_start: 0.9621 (tp-100) cc_final: 0.9325 (tp-100) REVERT: w 110 PHE cc_start: 0.8929 (m-10) cc_final: 0.8671 (m-10) REVERT: w 174 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6702 (mpt) REVERT: w 210 MET cc_start: 0.4674 (mmp) cc_final: 0.4385 (mmp) REVERT: 0 16 ARG cc_start: 0.9465 (tpp80) cc_final: 0.8862 (tpp80) REVERT: 0 37 GLN cc_start: 0.7005 (mt0) cc_final: 0.6673 (mt0) REVERT: 0 69 ASP cc_start: 0.9462 (OUTLIER) cc_final: 0.8822 (p0) REVERT: 0 78 PRO cc_start: 0.9515 (Cg_exo) cc_final: 0.9208 (Cg_endo) outliers start: 234 outliers final: 96 residues processed: 1013 average time/residue: 2.0217 time to fit residues: 3060.8817 Evaluate side-chains 939 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 829 time to evaluate : 8.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain U residue 71 LYS Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 27 ILE Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Z residue 88 LYS Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain d residue 4 MET Chi-restraints excluded: chain j residue 74 GLU Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 136 GLU Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 110 ARG Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 203 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 41 SER Chi-restraints excluded: chain s residue 112 LEU Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain u residue 5 SER Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 56 CYS Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 192 TYR Chi-restraints excluded: chain a residue 362 LYS Chi-restraints excluded: chain a residue 368 ARG Chi-restraints excluded: chain a residue 439 LEU Chi-restraints excluded: chain a residue 696 GLN Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 1002 GLU Chi-restraints excluded: chain a residue 1004 ASP Chi-restraints excluded: chain a residue 1005 LEU Chi-restraints excluded: chain a residue 1017 THR Chi-restraints excluded: chain e residue 229 VAL Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 309 VAL Chi-restraints excluded: chain e residue 801 ASP Chi-restraints excluded: chain e residue 857 ASP Chi-restraints excluded: chain e residue 867 PHE Chi-restraints excluded: chain e residue 951 ASP Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1202 VAL Chi-restraints excluded: chain e residue 1365 CYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1488 LEU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 146 ILE Chi-restraints excluded: chain g residue 206 THR Chi-restraints excluded: chain v residue 23 CYS Chi-restraints excluded: chain v residue 27 ARG Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 104 ASN Chi-restraints excluded: chain v residue 110 LYS Chi-restraints excluded: chain w residue 66 CYS Chi-restraints excluded: chain w residue 174 MET Chi-restraints excluded: chain 0 residue 69 ASP Chi-restraints excluded: chain 0 residue 186 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1032 optimal weight: 10.0000 chunk 703 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 923 optimal weight: 1.9990 chunk 511 optimal weight: 10.0000 chunk 1058 optimal weight: 20.0000 chunk 857 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 633 optimal weight: 10.0000 chunk 1113 optimal weight: 0.5980 chunk 312 optimal weight: 10.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 GLN F 138 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN G 131 GLN M 106 GLN ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 GLN Y 32 ASN j 24 GLN p 77 GLN ** p 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 100 ASN s 6 GLN s 47 GLN s 90 GLN t 114 GLN ** a 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 894 ASN a 920 HIS ** a 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1003 GLN ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 810 GLN ** e 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 162 HIS v 52 HIS v 104 ASN ** 0 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 161893 Z= 0.294 Angle : 0.595 15.074 236481 Z= 0.315 Chirality : 0.038 0.296 29519 Planarity : 0.005 0.113 16484 Dihedral : 22.521 179.717 66834 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 2.91 % Allowed : 15.05 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: 0.38 (0.09), residues: 9312 helix: 1.47 (0.08), residues: 3898 sheet: -0.06 (0.15), residues: 1172 loop : -0.78 (0.09), residues: 4242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP n 9 HIS 0.009 0.001 HIS e1273 PHE 0.035 0.002 PHE z 53 TYR 0.026 0.001 TYR 0 191 ARG 0.011 0.000 ARG v 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 846 time to evaluate : 8.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.7662 (tt0) cc_final: 0.7452 (tt0) REVERT: B 34 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.9046 (m) REVERT: C 120 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8222 (p0) REVERT: E 148 ASP cc_start: 0.8890 (t70) cc_final: 0.8462 (t0) REVERT: G 127 GLN cc_start: 0.8234 (mm-40) cc_final: 0.8018 (tp40) REVERT: H 23 THR cc_start: 0.9503 (OUTLIER) cc_final: 0.9279 (t) REVERT: H 49 ASN cc_start: 0.8218 (t0) cc_final: 0.7863 (t0) REVERT: L 74 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: M 108 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7782 (mm-30) REVERT: P 27 TYR cc_start: 0.8375 (t80) cc_final: 0.8119 (t80) REVERT: P 59 TYR cc_start: 0.9221 (m-80) cc_final: 0.8965 (m-80) REVERT: R 19 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8568 (ttp-170) REVERT: X 5 ILE cc_start: 0.8800 (tp) cc_final: 0.8516 (tp) REVERT: j 33 ASP cc_start: 0.8037 (p0) cc_final: 0.7836 (p0) REVERT: j 74 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7968 (mm-30) REVERT: k 214 MET cc_start: 0.8245 (mmm) cc_final: 0.7924 (mmm) REVERT: m 206 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7839 (tm-30) REVERT: s 48 SER cc_start: 0.8701 (m) cc_final: 0.8001 (p) REVERT: s 77 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7690 (tm-30) REVERT: s 81 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8331 (mm-30) REVERT: s 93 ASP cc_start: 0.9085 (t70) cc_final: 0.8698 (t0) REVERT: s 107 ASP cc_start: 0.8479 (t0) cc_final: 0.8215 (t0) REVERT: u 12 TRP cc_start: 0.7852 (OUTLIER) cc_final: 0.6615 (p90) REVERT: a 351 LEU cc_start: 0.8861 (mt) cc_final: 0.8562 (tm) REVERT: a 362 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8096 (pttm) REVERT: a 365 ASP cc_start: 0.9472 (m-30) cc_final: 0.9029 (p0) REVERT: a 884 MET cc_start: 0.8643 (tmm) cc_final: 0.8384 (tmm) REVERT: a 1002 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: a 1004 ASP cc_start: 0.9297 (OUTLIER) cc_final: 0.8921 (p0) REVERT: e 59 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: e 1041 TYR cc_start: 0.7881 (m-80) cc_final: 0.7665 (m-10) REVERT: e 1474 MET cc_start: 0.8356 (ttm) cc_final: 0.7261 (ttm) REVERT: g 18 LYS cc_start: 0.8296 (tppt) cc_final: 0.8005 (tppt) REVERT: g 95 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8700 (tp-100) REVERT: g 140 GLN cc_start: 0.8590 (tp40) cc_final: 0.8119 (tp-100) REVERT: v 18 THR cc_start: 0.9022 (p) cc_final: 0.8809 (t) REVERT: v 21 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7309 (tmm) REVERT: v 27 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7550 (mmm-85) REVERT: v 88 ASN cc_start: 0.9372 (m-40) cc_final: 0.9146 (m-40) REVERT: v 125 GLN cc_start: 0.9635 (tp-100) cc_final: 0.9358 (tp-100) REVERT: w 35 GLN cc_start: 0.8129 (OUTLIER) cc_final: 0.7870 (pp30) REVERT: w 60 ARG cc_start: 0.8833 (mtt90) cc_final: 0.8357 (mmt90) REVERT: w 110 PHE cc_start: 0.8925 (m-10) cc_final: 0.8678 (m-80) REVERT: w 174 MET cc_start: 0.7331 (mpt) cc_final: 0.6870 (mpt) REVERT: w 210 MET cc_start: 0.4750 (mmp) cc_final: 0.4435 (mmt) REVERT: 0 22 TYR cc_start: 0.9194 (m-10) cc_final: 0.8525 (m-80) REVERT: 0 37 GLN cc_start: 0.6911 (mt0) cc_final: 0.6613 (mt0) REVERT: 0 66 PHE cc_start: 0.9072 (m-80) cc_final: 0.8778 (m-80) REVERT: 0 69 ASP cc_start: 0.9489 (OUTLIER) cc_final: 0.8871 (p0) outliers start: 220 outliers final: 113 residues processed: 979 average time/residue: 2.0653 time to fit residues: 3023.2425 Evaluate side-chains 953 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 825 time to evaluate : 7.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 92 LYS Chi-restraints excluded: chain U residue 71 LYS Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Z residue 88 LYS Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 56 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 4 MET Chi-restraints excluded: chain j residue 74 GLU Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 203 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 41 SER Chi-restraints excluded: chain s residue 112 LEU Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain u residue 5 SER Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain a residue 51 ASN Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 56 CYS Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 82 LYS Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 192 TYR Chi-restraints excluded: chain a residue 362 LYS Chi-restraints excluded: chain a residue 368 ARG Chi-restraints excluded: chain a residue 439 LEU Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 1002 GLU Chi-restraints excluded: chain a residue 1004 ASP Chi-restraints excluded: chain a residue 1017 THR Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 229 VAL Chi-restraints excluded: chain e residue 309 VAL Chi-restraints excluded: chain e residue 801 ASP Chi-restraints excluded: chain e residue 804 ILE Chi-restraints excluded: chain e residue 857 ASP Chi-restraints excluded: chain e residue 867 PHE Chi-restraints excluded: chain e residue 924 VAL Chi-restraints excluded: chain e residue 951 ASP Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1037 SER Chi-restraints excluded: chain e residue 1051 LEU Chi-restraints excluded: chain e residue 1079 LEU Chi-restraints excluded: chain e residue 1365 CYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1488 LEU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 146 ILE Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain g residue 206 THR Chi-restraints excluded: chain v residue 21 MET Chi-restraints excluded: chain v residue 23 CYS Chi-restraints excluded: chain v residue 27 ARG Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 42 VAL Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 110 LYS Chi-restraints excluded: chain w residue 35 GLN Chi-restraints excluded: chain w residue 66 CYS Chi-restraints excluded: chain 0 residue 69 ASP Chi-restraints excluded: chain 0 residue 188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 417 optimal weight: 10.0000 chunk 1116 optimal weight: 0.9990 chunk 245 optimal weight: 0.9990 chunk 728 optimal weight: 8.9990 chunk 306 optimal weight: 0.0060 chunk 1241 optimal weight: 6.9990 chunk 1030 optimal weight: 40.0000 chunk 574 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 410 optimal weight: 10.0000 chunk 651 optimal weight: 10.0000 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 GLN F 138 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 ASN T 3 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 24 GLN p 77 GLN ** p 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 100 ASN r 113 GLN s 6 GLN s 47 GLN s 90 GLN t 114 GLN a 599 GLN ** a 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 810 GLN ** e 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1130 ASN ** g 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 162 HIS v 52 HIS ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 161893 Z= 0.203 Angle : 0.566 14.983 236481 Z= 0.300 Chirality : 0.036 0.292 29519 Planarity : 0.004 0.112 16484 Dihedral : 22.520 179.785 66834 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 2.82 % Allowed : 15.70 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.47 (0.09), residues: 9312 helix: 1.57 (0.08), residues: 3889 sheet: -0.03 (0.15), residues: 1181 loop : -0.75 (0.09), residues: 4242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 92 HIS 0.008 0.001 HIS e1273 PHE 0.053 0.001 PHE e1028 TYR 0.019 0.001 TYR P 68 ARG 0.009 0.000 ARG I 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 858 time to evaluate : 8.725 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: A 104 GLU cc_start: 0.7665 (tt0) cc_final: 0.7455 (tt0) REVERT: B 34 VAL cc_start: 0.9260 (OUTLIER) cc_final: 0.9038 (m) REVERT: C 120 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8101 (p0) REVERT: E 86 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7675 (tp30) REVERT: E 92 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: E 148 ASP cc_start: 0.8899 (t70) cc_final: 0.8414 (t0) REVERT: H 23 THR cc_start: 0.9490 (OUTLIER) cc_final: 0.9260 (t) REVERT: H 49 ASN cc_start: 0.8260 (t0) cc_final: 0.8043 (t0) REVERT: H 92 TRP cc_start: 0.7675 (m-10) cc_final: 0.7470 (m-10) REVERT: J 4 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8352 (mm-30) REVERT: L 74 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: M 108 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7815 (mm-30) REVERT: P 59 TYR cc_start: 0.9209 (m-80) cc_final: 0.8939 (m-80) REVERT: R 19 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8636 (ttp-170) REVERT: X 10 GLN cc_start: 0.8408 (tt0) cc_final: 0.8197 (tt0) REVERT: j 74 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7974 (mm-30) REVERT: k 214 MET cc_start: 0.8211 (mmm) cc_final: 0.7931 (mmm) REVERT: m 206 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7877 (tm-30) REVERT: m 218 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7874 (mtt180) REVERT: n 142 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7605 (m-30) REVERT: p 246 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8321 (ttp) REVERT: s 48 SER cc_start: 0.8641 (m) cc_final: 0.7957 (p) REVERT: s 77 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7654 (tm-30) REVERT: s 81 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8173 (mm-30) REVERT: s 93 ASP cc_start: 0.9078 (t70) cc_final: 0.8701 (t0) REVERT: u 12 TRP cc_start: 0.7825 (OUTLIER) cc_final: 0.6611 (p90) REVERT: a 351 LEU cc_start: 0.8847 (mt) cc_final: 0.8557 (tm) REVERT: a 362 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8079 (pttm) REVERT: a 365 ASP cc_start: 0.9465 (m-30) cc_final: 0.9021 (p0) REVERT: a 884 MET cc_start: 0.8657 (tmm) cc_final: 0.8432 (tmm) REVERT: a 1002 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7774 (mt-10) REVERT: a 1004 ASP cc_start: 0.9285 (OUTLIER) cc_final: 0.8956 (p0) REVERT: e 59 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7664 (tm-30) REVERT: g 1 MET cc_start: 0.6990 (tmm) cc_final: 0.6469 (tmt) REVERT: g 18 LYS cc_start: 0.8257 (tppt) cc_final: 0.7852 (tppt) REVERT: g 140 GLN cc_start: 0.8582 (tp40) cc_final: 0.8097 (tp-100) REVERT: g 197 MET cc_start: 0.8391 (ptm) cc_final: 0.8051 (ppp) REVERT: v 18 THR cc_start: 0.8996 (p) cc_final: 0.8682 (t) REVERT: v 21 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7309 (tmm) REVERT: v 27 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7694 (mmm-85) REVERT: v 125 GLN cc_start: 0.9621 (tp-100) cc_final: 0.9333 (tp-100) REVERT: w 110 PHE cc_start: 0.8921 (m-10) cc_final: 0.8632 (m-10) REVERT: w 152 ARG cc_start: 0.9216 (ttt90) cc_final: 0.8761 (ttt90) REVERT: w 174 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6671 (mpt) REVERT: w 210 MET cc_start: 0.4607 (mmp) cc_final: 0.4292 (mmt) REVERT: w 214 PHE cc_start: 0.8720 (m-80) cc_final: 0.8464 (m-80) REVERT: 0 10 GLU cc_start: 0.8421 (pp20) cc_final: 0.8217 (pp20) REVERT: 0 22 TYR cc_start: 0.9201 (m-10) cc_final: 0.8409 (m-80) REVERT: 0 66 PHE cc_start: 0.9044 (m-80) cc_final: 0.8793 (m-80) REVERT: 0 69 ASP cc_start: 0.9499 (OUTLIER) cc_final: 0.8889 (p0) REVERT: 0 88 PHE cc_start: 0.8334 (m-10) cc_final: 0.8124 (m-10) outliers start: 213 outliers final: 110 residues processed: 986 average time/residue: 2.0000 time to fit residues: 2947.5162 Evaluate side-chains 955 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 827 time to evaluate : 8.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain I residue 74 MET Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 92 LYS Chi-restraints excluded: chain U residue 71 LYS Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Z residue 88 LYS Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain d residue 4 MET Chi-restraints excluded: chain j residue 74 GLU Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 142 ASP Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 203 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain p residue 208 GLU Chi-restraints excluded: chain p residue 246 MET Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 41 SER Chi-restraints excluded: chain s residue 112 LEU Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain u residue 5 SER Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain a residue 51 ASN Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 56 CYS Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 82 LYS Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 192 TYR Chi-restraints excluded: chain a residue 362 LYS Chi-restraints excluded: chain a residue 368 ARG Chi-restraints excluded: chain a residue 439 LEU Chi-restraints excluded: chain a residue 506 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 1002 GLU Chi-restraints excluded: chain a residue 1004 ASP Chi-restraints excluded: chain a residue 1017 THR Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 229 VAL Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 309 VAL Chi-restraints excluded: chain e residue 801 ASP Chi-restraints excluded: chain e residue 804 ILE Chi-restraints excluded: chain e residue 857 ASP Chi-restraints excluded: chain e residue 867 PHE Chi-restraints excluded: chain e residue 924 VAL Chi-restraints excluded: chain e residue 951 ASP Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1051 LEU Chi-restraints excluded: chain e residue 1079 LEU Chi-restraints excluded: chain e residue 1351 LEU Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1488 LEU Chi-restraints excluded: chain g residue 62 MET Chi-restraints excluded: chain g residue 110 CYS Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 146 ILE Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain g residue 201 ASP Chi-restraints excluded: chain g residue 206 THR Chi-restraints excluded: chain v residue 21 MET Chi-restraints excluded: chain v residue 23 CYS Chi-restraints excluded: chain v residue 27 ARG Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 110 LYS Chi-restraints excluded: chain w residue 66 CYS Chi-restraints excluded: chain w residue 174 MET Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 69 ASP Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 188 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1196 optimal weight: 10.0000 chunk 139 optimal weight: 0.4980 chunk 707 optimal weight: 0.6980 chunk 906 optimal weight: 6.9990 chunk 702 optimal weight: 0.5980 chunk 1044 optimal weight: 5.9990 chunk 693 optimal weight: 0.4980 chunk 1236 optimal weight: 6.9990 chunk 773 optimal weight: 3.9990 chunk 753 optimal weight: 10.0000 chunk 570 optimal weight: 10.0000 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 ASN F 138 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN N 120 ASN T 3 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 24 GLN l 116 ASN ** p 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 6 GLN s 90 GLN t 114 GLN ** a 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 810 GLN e 831 ASN ** e 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1130 ASN ** g 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 162 HIS g 225 GLN ** w 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 161893 Z= 0.147 Angle : 0.548 14.893 236481 Z= 0.289 Chirality : 0.034 0.285 29519 Planarity : 0.004 0.111 16484 Dihedral : 22.476 179.652 66834 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 2.37 % Allowed : 16.77 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: 0.60 (0.09), residues: 9312 helix: 1.66 (0.08), residues: 3897 sheet: 0.13 (0.15), residues: 1189 loop : -0.70 (0.09), residues: 4226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 92 HIS 0.007 0.001 HIS e1273 PHE 0.033 0.001 PHE e1028 TYR 0.026 0.001 TYR P 27 ARG 0.013 0.000 ARG E 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 888 time to evaluate : 8.598 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: B 34 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.9034 (m) REVERT: E 148 ASP cc_start: 0.8918 (t70) cc_final: 0.8445 (t0) REVERT: H 23 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.9239 (t) REVERT: H 49 ASN cc_start: 0.8292 (t0) cc_final: 0.7880 (t0) REVERT: J 4 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8333 (mm-30) REVERT: L 74 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: P 55 GLU cc_start: 0.8084 (tt0) cc_final: 0.7859 (tt0) REVERT: P 59 TYR cc_start: 0.9188 (m-80) cc_final: 0.8962 (m-80) REVERT: R 19 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8624 (ttp-170) REVERT: k 214 MET cc_start: 0.8220 (mmm) cc_final: 0.7848 (mmm) REVERT: m 206 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7837 (tm-30) REVERT: n 142 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: r 113 GLN cc_start: 0.6936 (mm110) cc_final: 0.6682 (mm110) REVERT: s 48 SER cc_start: 0.8602 (m) cc_final: 0.7954 (p) REVERT: s 77 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7353 (tm-30) REVERT: s 81 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8089 (tp30) REVERT: s 93 ASP cc_start: 0.9071 (t70) cc_final: 0.8692 (t0) REVERT: u 12 TRP cc_start: 0.7798 (OUTLIER) cc_final: 0.6539 (p90) REVERT: a 351 LEU cc_start: 0.8908 (mt) cc_final: 0.8610 (tm) REVERT: a 362 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8035 (pttm) REVERT: a 365 ASP cc_start: 0.9479 (m-30) cc_final: 0.9036 (p0) REVERT: a 1004 ASP cc_start: 0.9234 (OUTLIER) cc_final: 0.8904 (p0) REVERT: e 777 MET cc_start: 0.6751 (mmm) cc_final: 0.6299 (mmm) REVERT: g 18 LYS cc_start: 0.8201 (tppt) cc_final: 0.7795 (tppt) REVERT: g 140 GLN cc_start: 0.8565 (tp40) cc_final: 0.8090 (tp-100) REVERT: g 197 MET cc_start: 0.8336 (ptm) cc_final: 0.8133 (ppp) REVERT: v 21 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7275 (tmm) REVERT: v 49 THR cc_start: 0.8485 (p) cc_final: 0.8245 (p) REVERT: v 125 GLN cc_start: 0.9630 (tp-100) cc_final: 0.9345 (tp-100) REVERT: w 152 ARG cc_start: 0.9202 (ttt90) cc_final: 0.8765 (ttt90) REVERT: w 174 MET cc_start: 0.7155 (OUTLIER) cc_final: 0.6652 (mpt) REVERT: w 210 MET cc_start: 0.4412 (mmp) cc_final: 0.4111 (mmt) REVERT: w 214 PHE cc_start: 0.8738 (m-80) cc_final: 0.8425 (m-80) REVERT: 0 10 GLU cc_start: 0.8459 (pp20) cc_final: 0.8256 (pp20) REVERT: 0 22 TYR cc_start: 0.9170 (m-10) cc_final: 0.8397 (m-80) REVERT: 0 66 PHE cc_start: 0.9022 (m-80) cc_final: 0.8748 (m-80) REVERT: 0 69 ASP cc_start: 0.9499 (OUTLIER) cc_final: 0.8928 (p0) REVERT: 0 189 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7767 (tm-30) outliers start: 179 outliers final: 95 residues processed: 996 average time/residue: 2.0834 time to fit residues: 3120.2124 Evaluate side-chains 947 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 841 time to evaluate : 7.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain U residue 71 LYS Chi-restraints excluded: chain X residue 67 GLN Chi-restraints excluded: chain Z residue 88 LYS Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 142 ASP Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 164 SER Chi-restraints excluded: chain o residue 143 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 203 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain p residue 208 GLU Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 108 GLU Chi-restraints excluded: chain s residue 112 LEU Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain u residue 5 SER Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 56 CYS Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 192 TYR Chi-restraints excluded: chain a residue 362 LYS Chi-restraints excluded: chain a residue 368 ARG Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 1004 ASP Chi-restraints excluded: chain a residue 1017 THR Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 229 VAL Chi-restraints excluded: chain e residue 284 MET Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 804 ILE Chi-restraints excluded: chain e residue 857 ASP Chi-restraints excluded: chain e residue 867 PHE Chi-restraints excluded: chain e residue 924 VAL Chi-restraints excluded: chain e residue 951 ASP Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1079 LEU Chi-restraints excluded: chain e residue 1267 LYS Chi-restraints excluded: chain e residue 1351 LEU Chi-restraints excluded: chain e residue 1365 CYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1486 SER Chi-restraints excluded: chain e residue 1488 LEU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 110 CYS Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain v residue 21 MET Chi-restraints excluded: chain v residue 23 CYS Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain w residue 66 CYS Chi-restraints excluded: chain w residue 174 MET Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 69 ASP Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 188 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 765 optimal weight: 7.9990 chunk 493 optimal weight: 10.0000 chunk 738 optimal weight: 0.9990 chunk 372 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 786 optimal weight: 9.9990 chunk 842 optimal weight: 5.9990 chunk 611 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 972 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN C 137 ASN F 138 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN H 52 ASN M 106 GLN ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 ASN P 75 ASN T 3 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 99 GLN j 24 GLN l 116 ASN l 361 HIS s 6 GLN ** a 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1130 ASN ** g 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 162 HIS g 225 GLN w 171 ASN ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 161893 Z= 0.337 Angle : 0.614 14.940 236481 Z= 0.323 Chirality : 0.039 0.325 29519 Planarity : 0.005 0.113 16484 Dihedral : 22.429 179.956 66834 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.32 % Favored : 95.64 % Rotamer: Outliers : 2.52 % Allowed : 17.06 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: 0.48 (0.09), residues: 9312 helix: 1.55 (0.08), residues: 3891 sheet: -0.02 (0.15), residues: 1152 loop : -0.72 (0.09), residues: 4269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 92 HIS 0.009 0.001 HIS e1273 PHE 0.034 0.002 PHE e1028 TYR 0.024 0.002 TYR P 27 ARG 0.014 0.001 ARG g 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1018 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 827 time to evaluate : 7.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 148 ASP cc_start: 0.8946 (t70) cc_final: 0.8500 (t0) REVERT: H 23 THR cc_start: 0.9497 (OUTLIER) cc_final: 0.9270 (t) REVERT: H 49 ASN cc_start: 0.8296 (t0) cc_final: 0.8062 (t0) REVERT: J 4 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8305 (mt-10) REVERT: L 74 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8335 (m-80) REVERT: P 59 TYR cc_start: 0.9210 (m-80) cc_final: 0.9005 (m-80) REVERT: R 19 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8534 (ttp-170) REVERT: X 10 GLN cc_start: 0.8358 (tt0) cc_final: 0.8087 (tt0) REVERT: j 74 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8017 (mm-30) REVERT: j 118 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: m 206 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7816 (tm-30) REVERT: n 142 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7490 (m-30) REVERT: r 113 GLN cc_start: 0.7011 (mm110) cc_final: 0.6720 (mm110) REVERT: s 48 SER cc_start: 0.8707 (m) cc_final: 0.8032 (p) REVERT: s 77 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7517 (tm-30) REVERT: s 81 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8108 (tp30) REVERT: s 93 ASP cc_start: 0.9092 (t70) cc_final: 0.8702 (t0) REVERT: u 12 TRP cc_start: 0.7951 (OUTLIER) cc_final: 0.6619 (p90) REVERT: a 351 LEU cc_start: 0.8829 (mt) cc_final: 0.8505 (tm) REVERT: a 365 ASP cc_start: 0.9468 (m-30) cc_final: 0.8972 (p0) REVERT: a 1002 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: a 1004 ASP cc_start: 0.9303 (OUTLIER) cc_final: 0.8970 (p0) REVERT: e 277 MET cc_start: 0.8821 (tpp) cc_final: 0.8545 (tpp) REVERT: e 777 MET cc_start: 0.6976 (mmm) cc_final: 0.6576 (mmm) REVERT: g 1 MET cc_start: 0.7102 (tmm) cc_final: 0.6594 (tmt) REVERT: g 18 LYS cc_start: 0.8270 (tppt) cc_final: 0.7970 (tppt) REVERT: g 67 ARG cc_start: 0.9190 (ptm-80) cc_final: 0.8908 (ptm-80) REVERT: g 140 GLN cc_start: 0.8600 (tp40) cc_final: 0.8104 (tp-100) REVERT: v 21 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7410 (tmm) REVERT: v 125 GLN cc_start: 0.9634 (tp-100) cc_final: 0.9353 (tp-100) REVERT: w 33 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6243 (pm20) REVERT: w 66 CYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6884 (p) REVERT: w 152 ARG cc_start: 0.9195 (ttt90) cc_final: 0.8741 (ttt90) REVERT: w 174 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6601 (mpt) REVERT: w 210 MET cc_start: 0.4567 (mmp) cc_final: 0.4284 (mmt) REVERT: w 214 PHE cc_start: 0.8713 (m-80) cc_final: 0.8322 (m-80) REVERT: 0 22 TYR cc_start: 0.8894 (m-10) cc_final: 0.8270 (m-80) REVERT: 0 69 ASP cc_start: 0.9467 (OUTLIER) cc_final: 0.8895 (p0) REVERT: 0 189 GLN cc_start: 0.8481 (mm-40) cc_final: 0.7868 (tm-30) outliers start: 191 outliers final: 118 residues processed: 952 average time/residue: 2.0498 time to fit residues: 2905.0901 Evaluate side-chains 941 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 809 time to evaluate : 8.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 133 LEU Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain U residue 71 LYS Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain X residue 67 GLN Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Z residue 88 LYS Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain j residue 74 GLU Chi-restraints excluded: chain j residue 118 GLU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 142 ASP Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 164 SER Chi-restraints excluded: chain o residue 143 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain p residue 208 GLU Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 108 GLU Chi-restraints excluded: chain s residue 111 ASP Chi-restraints excluded: chain s residue 112 LEU Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain u residue 5 SER Chi-restraints excluded: chain u residue 6 ILE Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain a residue 51 ASN Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 82 LYS Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 192 TYR Chi-restraints excluded: chain a residue 362 LYS Chi-restraints excluded: chain a residue 696 GLN Chi-restraints excluded: chain a residue 918 ASP Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 1002 GLU Chi-restraints excluded: chain a residue 1004 ASP Chi-restraints excluded: chain a residue 1017 THR Chi-restraints excluded: chain a residue 1018 ILE Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 229 VAL Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 309 VAL Chi-restraints excluded: chain e residue 320 LEU Chi-restraints excluded: chain e residue 384 SER Chi-restraints excluded: chain e residue 801 ASP Chi-restraints excluded: chain e residue 804 ILE Chi-restraints excluded: chain e residue 857 ASP Chi-restraints excluded: chain e residue 924 VAL Chi-restraints excluded: chain e residue 951 ASP Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1198 LEU Chi-restraints excluded: chain e residue 1239 LYS Chi-restraints excluded: chain e residue 1275 ILE Chi-restraints excluded: chain e residue 1365 CYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1486 SER Chi-restraints excluded: chain e residue 1488 LEU Chi-restraints excluded: chain e residue 1500 LEU Chi-restraints excluded: chain g residue 110 CYS Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 146 ILE Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain g residue 206 THR Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 21 MET Chi-restraints excluded: chain v residue 23 CYS Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain w residue 33 GLU Chi-restraints excluded: chain w residue 66 CYS Chi-restraints excluded: chain w residue 174 MET Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 69 ASP Chi-restraints excluded: chain 0 residue 188 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 1124 optimal weight: 3.9990 chunk 1184 optimal weight: 5.9990 chunk 1080 optimal weight: 8.9990 chunk 1152 optimal weight: 1.9990 chunk 693 optimal weight: 0.6980 chunk 502 optimal weight: 10.0000 chunk 904 optimal weight: 4.9990 chunk 353 optimal weight: 10.0000 chunk 1041 optimal weight: 0.9990 chunk 1089 optimal weight: 8.9990 chunk 1148 optimal weight: 20.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN F 138 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN G 131 GLN ** I 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 ASN T 3 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 99 GLN j 24 GLN ** p 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 6 GLN t 114 GLN ** a 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1130 ASN ** g 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 162 HIS ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 161893 Z= 0.211 Angle : 0.589 16.804 236481 Z= 0.311 Chirality : 0.036 0.311 29519 Planarity : 0.004 0.112 16484 Dihedral : 22.471 179.870 66832 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.20 % Favored : 95.76 % Rotamer: Outliers : 2.22 % Allowed : 17.68 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: 0.52 (0.09), residues: 9312 helix: 1.57 (0.08), residues: 3889 sheet: 0.03 (0.15), residues: 1163 loop : -0.69 (0.09), residues: 4260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP H 92 HIS 0.007 0.001 HIS e1273 PHE 0.033 0.001 PHE v 150 TYR 0.024 0.001 TYR P 27 ARG 0.014 0.000 ARG v 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 834 time to evaluate : 7.835 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: B 34 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.9046 (m) REVERT: C 120 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8134 (p0) REVERT: E 148 ASP cc_start: 0.8949 (t70) cc_final: 0.8485 (t0) REVERT: G 104 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7679 (tm-30) REVERT: H 23 THR cc_start: 0.9485 (OUTLIER) cc_final: 0.9254 (t) REVERT: H 49 ASN cc_start: 0.8290 (t0) cc_final: 0.8056 (t0) REVERT: J 4 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8337 (mt-10) REVERT: L 74 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: P 59 TYR cc_start: 0.9190 (m-80) cc_final: 0.8972 (m-80) REVERT: R 19 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8562 (ttp-170) REVERT: X 10 GLN cc_start: 0.8431 (tt0) cc_final: 0.8215 (tt0) REVERT: j 74 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8006 (mm-30) REVERT: k 59 ASP cc_start: 0.6517 (OUTLIER) cc_final: 0.5593 (t0) REVERT: k 214 MET cc_start: 0.8304 (mmm) cc_final: 0.7816 (mmm) REVERT: m 206 GLN cc_start: 0.8263 (tm-30) cc_final: 0.7779 (tm-30) REVERT: n 142 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: q 143 GLU cc_start: 0.8262 (tt0) cc_final: 0.7930 (tt0) REVERT: r 113 GLN cc_start: 0.6989 (mm110) cc_final: 0.6701 (mm110) REVERT: s 6 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7366 (mm-40) REVERT: s 48 SER cc_start: 0.8642 (m) cc_final: 0.7956 (p) REVERT: s 77 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7229 (tm-30) REVERT: s 81 GLU cc_start: 0.8519 (mm-30) cc_final: 0.7875 (tp30) REVERT: s 93 ASP cc_start: 0.9078 (t70) cc_final: 0.8682 (t0) REVERT: s 108 GLU cc_start: 0.8544 (pp20) cc_final: 0.6462 (pp20) REVERT: s 111 ASP cc_start: 0.8907 (t0) cc_final: 0.8678 (p0) REVERT: u 12 TRP cc_start: 0.7937 (OUTLIER) cc_final: 0.6608 (p90) REVERT: a 351 LEU cc_start: 0.8836 (mt) cc_final: 0.8539 (tm) REVERT: a 365 ASP cc_start: 0.9414 (m-30) cc_final: 0.8962 (p0) REVERT: a 1002 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: a 1004 ASP cc_start: 0.9282 (OUTLIER) cc_final: 0.8926 (p0) REVERT: e 277 MET cc_start: 0.8855 (tpp) cc_final: 0.8638 (tpp) REVERT: e 777 MET cc_start: 0.6959 (mmm) cc_final: 0.6512 (mmm) REVERT: g 1 MET cc_start: 0.6978 (tmm) cc_final: 0.6329 (tmt) REVERT: g 18 LYS cc_start: 0.8271 (tppt) cc_final: 0.7908 (tppt) REVERT: g 67 ARG cc_start: 0.9169 (ptm-80) cc_final: 0.8945 (ptm-80) REVERT: g 140 GLN cc_start: 0.8584 (tp40) cc_final: 0.8083 (tp-100) REVERT: g 197 MET cc_start: 0.8261 (ptm) cc_final: 0.7932 (ppp) REVERT: g 223 ARG cc_start: 0.7813 (tpt170) cc_final: 0.6553 (tpt170) REVERT: v 21 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7413 (tmm) REVERT: v 27 ARG cc_start: 0.7610 (mmt90) cc_final: 0.7356 (mmm160) REVERT: v 81 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7872 (tp30) REVERT: v 125 GLN cc_start: 0.9629 (tp-100) cc_final: 0.9343 (tp-100) REVERT: w 33 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6427 (pm20) REVERT: w 66 CYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6798 (p) REVERT: w 152 ARG cc_start: 0.9210 (ttt90) cc_final: 0.8764 (ttt90) REVERT: w 174 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6466 (mpt) REVERT: w 210 MET cc_start: 0.4460 (mmp) cc_final: 0.4188 (mmt) REVERT: w 214 PHE cc_start: 0.8680 (m-80) cc_final: 0.8301 (m-80) REVERT: 0 16 ARG cc_start: 0.9480 (tpp80) cc_final: 0.8937 (tpp80) REVERT: 0 22 TYR cc_start: 0.8952 (m-10) cc_final: 0.8302 (m-80) REVERT: 0 69 ASP cc_start: 0.9460 (OUTLIER) cc_final: 0.8914 (p0) REVERT: 0 189 GLN cc_start: 0.8472 (mm-40) cc_final: 0.7892 (tm-30) outliers start: 168 outliers final: 103 residues processed: 947 average time/residue: 2.0687 time to fit residues: 2917.7623 Evaluate side-chains 943 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 822 time to evaluate : 8.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain U residue 71 LYS Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Z residue 88 LYS Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain j residue 74 GLU Chi-restraints excluded: chain j residue 142 ASP Chi-restraints excluded: chain k residue 59 ASP Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 142 ASP Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 164 SER Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain p residue 208 GLU Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 6 GLN Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain u residue 6 ILE Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain a residue 51 ASN Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 192 TYR Chi-restraints excluded: chain a residue 362 LYS Chi-restraints excluded: chain a residue 506 VAL Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 1002 GLU Chi-restraints excluded: chain a residue 1004 ASP Chi-restraints excluded: chain a residue 1017 THR Chi-restraints excluded: chain a residue 1018 ILE Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 229 VAL Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 309 VAL Chi-restraints excluded: chain e residue 320 LEU Chi-restraints excluded: chain e residue 801 ASP Chi-restraints excluded: chain e residue 804 ILE Chi-restraints excluded: chain e residue 857 ASP Chi-restraints excluded: chain e residue 924 VAL Chi-restraints excluded: chain e residue 951 ASP Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1079 LEU Chi-restraints excluded: chain e residue 1198 LEU Chi-restraints excluded: chain e residue 1275 ILE Chi-restraints excluded: chain e residue 1365 CYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1486 SER Chi-restraints excluded: chain e residue 1488 LEU Chi-restraints excluded: chain e residue 1500 LEU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 110 CYS Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 21 MET Chi-restraints excluded: chain v residue 23 CYS Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 81 GLU Chi-restraints excluded: chain w residue 33 GLU Chi-restraints excluded: chain w residue 66 CYS Chi-restraints excluded: chain w residue 174 MET Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 69 ASP Chi-restraints excluded: chain 0 residue 188 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 756 optimal weight: 6.9990 chunk 1218 optimal weight: 6.9990 chunk 743 optimal weight: 7.9990 chunk 578 optimal weight: 10.0000 chunk 847 optimal weight: 4.9990 chunk 1278 optimal weight: 8.9990 chunk 1176 optimal weight: 20.0000 chunk 1017 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 786 optimal weight: 0.5980 chunk 624 optimal weight: 10.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 138 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN ** I 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 ASN T 3 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 99 GLN j 24 GLN o 194 HIS s 6 GLN t 114 GLN ** a 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 831 ASN ** e 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1130 ASN ** g 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 162 HIS ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 161893 Z= 0.359 Angle : 0.641 18.276 236481 Z= 0.337 Chirality : 0.040 0.329 29519 Planarity : 0.005 0.114 16484 Dihedral : 22.452 179.643 66832 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.50 % Rotamer: Outliers : 2.04 % Allowed : 17.91 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: 0.39 (0.09), residues: 9312 helix: 1.46 (0.08), residues: 3897 sheet: -0.06 (0.15), residues: 1167 loop : -0.76 (0.09), residues: 4248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 92 HIS 0.010 0.001 HIS e1273 PHE 0.039 0.002 PHE 0 197 TYR 0.023 0.002 TYR H 36 ARG 0.017 0.001 ARG V 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 816 time to evaluate : 8.618 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: E 148 ASP cc_start: 0.9005 (t70) cc_final: 0.8547 (t0) REVERT: H 23 THR cc_start: 0.9494 (OUTLIER) cc_final: 0.9265 (t) REVERT: H 49 ASN cc_start: 0.8320 (t0) cc_final: 0.8021 (t0) REVERT: J 4 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8297 (mt-10) REVERT: L 74 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.8314 (m-80) REVERT: P 59 TYR cc_start: 0.9225 (m-80) cc_final: 0.9014 (m-80) REVERT: R 19 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8500 (ttp-170) REVERT: j 74 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8039 (mm-30) REVERT: k 59 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.5757 (t0) REVERT: m 206 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7801 (tm-30) REVERT: n 142 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7511 (m-30) REVERT: q 143 GLU cc_start: 0.8328 (tt0) cc_final: 0.7538 (tt0) REVERT: s 48 SER cc_start: 0.8706 (m) cc_final: 0.8011 (p) REVERT: s 77 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7259 (tm-30) REVERT: s 81 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7813 (tp30) REVERT: s 93 ASP cc_start: 0.9083 (t70) cc_final: 0.8715 (t0) REVERT: u 12 TRP cc_start: 0.8118 (OUTLIER) cc_final: 0.6869 (p90) REVERT: a 351 LEU cc_start: 0.8835 (mt) cc_final: 0.8526 (tm) REVERT: a 365 ASP cc_start: 0.9415 (m-30) cc_final: 0.8959 (p0) REVERT: a 1002 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: a 1004 ASP cc_start: 0.9294 (OUTLIER) cc_final: 0.8965 (p0) REVERT: e 777 MET cc_start: 0.7057 (mmm) cc_final: 0.6650 (mmm) REVERT: g 18 LYS cc_start: 0.8271 (tppt) cc_final: 0.7956 (tppt) REVERT: g 140 GLN cc_start: 0.8617 (tp40) cc_final: 0.8128 (tp-100) REVERT: g 197 MET cc_start: 0.8480 (ptm) cc_final: 0.8167 (ppp) REVERT: v 21 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7463 (tmm) REVERT: v 81 GLU cc_start: 0.8214 (tp30) cc_final: 0.7914 (tp30) REVERT: v 125 GLN cc_start: 0.9630 (tp-100) cc_final: 0.9348 (tp-100) REVERT: w 12 HIS cc_start: 0.9224 (m90) cc_final: 0.8558 (m90) REVERT: w 33 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.6498 (pm20) REVERT: w 66 CYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6260 (p) REVERT: w 110 PHE cc_start: 0.8837 (m-10) cc_final: 0.8130 (m-10) REVERT: w 152 ARG cc_start: 0.9206 (ttt90) cc_final: 0.8754 (ttt90) REVERT: w 174 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6596 (mpt) REVERT: w 210 MET cc_start: 0.4501 (mmp) cc_final: 0.4246 (mmt) REVERT: w 214 PHE cc_start: 0.8711 (m-80) cc_final: 0.8255 (m-80) REVERT: 0 22 TYR cc_start: 0.8963 (m-10) cc_final: 0.8253 (m-80) REVERT: 0 69 ASP cc_start: 0.9474 (OUTLIER) cc_final: 0.8893 (p0) outliers start: 154 outliers final: 111 residues processed: 919 average time/residue: 2.0902 time to fit residues: 2853.3042 Evaluate side-chains 929 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 804 time to evaluate : 7.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 VAL Chi-restraints excluded: chain R residue 3 SER Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain U residue 71 LYS Chi-restraints excluded: chain V residue 46 GLU Chi-restraints excluded: chain X residue 67 GLN Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain j residue 74 GLU Chi-restraints excluded: chain k residue 59 ASP Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 38 THR Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain n residue 142 ASP Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain n residue 164 SER Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain p residue 208 GLU Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 107 ASP Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain s residue 7 ASN Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 84 LEU Chi-restraints excluded: chain s residue 111 ASP Chi-restraints excluded: chain s residue 161 SER Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 69 VAL Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain a residue 51 ASN Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 192 TYR Chi-restraints excluded: chain a residue 362 LYS Chi-restraints excluded: chain a residue 696 GLN Chi-restraints excluded: chain a residue 918 ASP Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain a residue 1002 GLU Chi-restraints excluded: chain a residue 1004 ASP Chi-restraints excluded: chain a residue 1017 THR Chi-restraints excluded: chain a residue 1018 ILE Chi-restraints excluded: chain e residue 116 MET Chi-restraints excluded: chain e residue 223 PHE Chi-restraints excluded: chain e residue 229 VAL Chi-restraints excluded: chain e residue 296 THR Chi-restraints excluded: chain e residue 309 VAL Chi-restraints excluded: chain e residue 320 LEU Chi-restraints excluded: chain e residue 801 ASP Chi-restraints excluded: chain e residue 804 ILE Chi-restraints excluded: chain e residue 924 VAL Chi-restraints excluded: chain e residue 951 ASP Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1079 LEU Chi-restraints excluded: chain e residue 1198 LEU Chi-restraints excluded: chain e residue 1239 LYS Chi-restraints excluded: chain e residue 1275 ILE Chi-restraints excluded: chain e residue 1365 CYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1454 ILE Chi-restraints excluded: chain e residue 1486 SER Chi-restraints excluded: chain e residue 1488 LEU Chi-restraints excluded: chain e residue 1500 LEU Chi-restraints excluded: chain g residue 94 ILE Chi-restraints excluded: chain g residue 110 CYS Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 21 MET Chi-restraints excluded: chain v residue 23 CYS Chi-restraints excluded: chain w residue 33 GLU Chi-restraints excluded: chain w residue 66 CYS Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain w residue 174 MET Chi-restraints excluded: chain 0 residue 69 ASP Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 0 residue 188 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1283 random chunks: chunk 808 optimal weight: 3.9990 chunk 1084 optimal weight: 30.0000 chunk 311 optimal weight: 0.1980 chunk 938 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 282 optimal weight: 3.9990 chunk 1019 optimal weight: 9.9990 chunk 426 optimal weight: 10.0000 chunk 1046 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 187 optimal weight: 0.0980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 138 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN ** I 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 GLN N 120 ASN T 3 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 99 GLN j 24 GLN l 116 ASN s 90 GLN t 114 GLN a 395 ASN ** a 438 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 831 ASN ** e 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 885 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e1130 ASN ** g 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 162 HIS ** v 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.073030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.057466 restraints weight = 511221.999| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.45 r_work: 0.2825 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 161893 Z= 0.156 Angle : 0.583 20.833 236481 Z= 0.306 Chirality : 0.035 0.300 29519 Planarity : 0.004 0.111 16484 Dihedral : 22.484 179.753 66832 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 1.65 % Allowed : 18.50 % Favored : 79.84 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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: 0.57 (0.09), residues: 9312 helix: 1.62 (0.08), residues: 3866 sheet: 0.04 (0.15), residues: 1176 loop : -0.66 (0.09), residues: 4270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 92 HIS 0.011 0.001 HIS s 109 PHE 0.033 0.001 PHE v 150 TYR 0.017 0.001 TYR P 68 ARG 0.015 0.000 ARG v 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 48436.82 seconds wall clock time: 842 minutes 50.80 seconds (50570.80 seconds total)