Starting phenix.real_space_refine on Tue Mar 26 05:25:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agx_15427/03_2024/8agx_15427_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agx_15427/03_2024/8agx_15427.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agx_15427/03_2024/8agx_15427_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agx_15427/03_2024/8agx_15427_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agx_15427/03_2024/8agx_15427_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agx_15427/03_2024/8agx_15427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agx_15427/03_2024/8agx_15427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agx_15427/03_2024/8agx_15427_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agx_15427/03_2024/8agx_15427_updated.pdb" } resolution = 2.4 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= 0.020 sd= 0.132 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 3642 5.49 5 Mg 13 5.21 5 S 170 5.16 5 C 80300 2.51 5 N 27325 2.21 5 O 38249 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 PHE 412": "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 "e PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 1078": "NH1" <-> "NH2" Residue "e ARG 1099": "NH1" <-> "NH2" Residue "e ARG 1192": "NH1" <-> "NH2" Residue "e ARG 1377": "NH1" <-> "NH2" Residue "v GLU 71": "OE1" <-> "OE2" Residue "0 ARG 61": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149706 Number of models: 1 Model: "" Number of chains: 68 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: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 812 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 2, 'TRANS': 99} 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: 68782 Number of conformers: 1 Conformer: "" 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 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: 6579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6579 Classifications: {'peptide': 848} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 29, 'TRANS': 818} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 161 Chain: "e" Number of atoms: 11508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1527, 11508 Classifications: {'peptide': 1527} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 271} Link IDs: {'CIS': 1, 'PTRANS': 38, 'TRANS': 1487} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 982 Unresolved non-hydrogen angles: 1253 Unresolved non-hydrogen dihedrals: 815 Unresolved non-hydrogen chiralities: 81 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: "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': 7, 'rna3p': 1, 'rna3p_pur': 27, 'rna3p_pyr': 31} Link IDs: {'rna2p': 15, 'rna3p': 58} 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: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 728 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 182 Chain: "0" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "1" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "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 20917 SG CYS T 44 120.424 169.153 212.409 1.00 54.16 S ATOM 20935 SG CYS T 47 122.513 166.501 211.315 1.00 59.61 S ATOM 21207 SG CYS T 84 123.703 168.968 214.148 1.00 57.91 S ATOM 23318 SG CYS W 19 85.228 187.024 170.070 1.00 40.18 S ATOM 23343 SG CYS W 22 83.488 187.119 166.784 1.00 41.00 S ATOM 23443 SG CYS W 34 87.219 187.113 166.839 1.00 38.42 S ATOM 23461 SG CYS W 37 85.259 190.203 168.004 1.00 40.17 S ATOM 25018 SG CYS Z 96 133.710 138.570 76.350 1.00 54.37 S ATOM 25044 SG CYS Z 99 131.078 136.883 78.346 1.00 53.18 S ATOM 25131 SG CYS Z 110 130.960 136.369 74.664 1.00 52.08 S ATOM 25177 SG CYS Z 115 129.905 139.590 75.918 1.00 52.77 S ATOM 25375 SG CYS b 12 132.848 245.923 110.443 1.00 63.95 S ATOM 25410 SG CYS b 17 134.140 249.461 109.562 1.00 72.10 S ATOM 25874 SG CYS b 74 136.340 246.929 111.687 1.00 60.93 S ATOM 25896 SG CYS b 77 133.243 248.772 112.864 1.00 66.15 S ATOM 26419 SG CYS c 39 139.082 166.642 205.614 1.00 58.71 S ATOM 26442 SG CYS c 42 138.452 163.654 207.694 1.00 62.48 S ATOM 26551 SG CYS c 57 136.245 164.188 204.698 1.00 55.64 S ATOM 26569 SG CYS c 60 135.823 166.644 207.462 1.00 57.82 S ATOM A0W6W SG CYS e1527 42.807 134.808 183.242 1.00285.10 S ATOM A0W7G SG CYS e1530 39.249 133.033 182.243 1.00279.23 S ATOM A0WC8 SG CYS e1551 41.637 135.379 180.036 1.00286.27 S ATOM A0WCT SG CYS e1554 39.642 136.891 182.198 1.00284.05 S ATOM A0W2U SG CYS e1508 45.832 129.138 172.559 1.00285.58 S ATOM A0W3D SG CYS e1511 46.182 127.534 169.029 1.00284.14 S ATOM A0W96 SG CYS e1538 48.545 130.171 170.192 1.00281.30 S Residues with excluded nonbonded symmetry interactions: 197 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 185 not shown) Time building chain proxies: 57.14, per 1000 atoms: 0.38 Number of scatterers: 149706 At special positions: 0 Unit cell: (232.98, 281.694, 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 170 16.00 P 3642 15.00 Mg 13 11.99 O 38249 8.00 N 27325 7.00 C 80300 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: 59.97 Conformation dependent library (CDL) restraints added in 10.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 47 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 84 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 44 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 22 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 19 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 34 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 37 " pdb=" ZN Z 201 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 99 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 110 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 115 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 96 " pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 12 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 17 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 39 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 57 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 42 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 60 " pdb=" ZN e2001 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1527 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1530 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1554 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1551 " 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 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17354 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: 355 helices and 84 sheets defined 49.0% alpha, 13.0% beta 1185 base pairs and 2011 stacking pairs defined. Time for finding SS restraints: 86.24 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: 4.137A pdb=" N LYS A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 4.988A 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: 3.690A 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: 5.055A 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: 3.688A 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: 4.022A 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: 3.926A 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: 3.728A 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: 3.639A 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: 4.065A pdb=" N GLU C 75 " --> pdb=" O GLN C 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 40 Processing helix chain 'D' and resid 42 through 54 removed outlier: 3.961A pdb=" N LYS D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Proline residue: D 60 - end of helix Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.813A 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: 3.909A pdb=" N VAL E 22 " --> pdb=" O GLY E 18 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TRP E 23 " --> pdb=" O LYS E 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 18 through 23' Processing helix chain 'E' and resid 28 through 36 removed outlier: 5.178A pdb=" N ASN E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 48 Processing helix chain 'E' and resid 60 through 73 Processing helix chain 'E' and resid 77 through 82 removed outlier: 3.710A pdb=" N ARG E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LYS E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 77 through 82' Processing helix chain 'E' and resid 84 through 113 Proline residue: E 90 - end of helix removed outlier: 6.827A pdb=" N VAL E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 130 removed outlier: 3.684A 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: 3.960A 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: 4.168A 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: 5.401A pdb=" N LYS I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 127 removed outlier: 3.885A 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: 3.837A 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: 4.375A 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: 4.945A 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: 5.302A 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: 5.473A 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: 4.160A pdb=" N THR N 6 " --> pdb=" O PRO N 2 " (cutoff:3.500A) removed outlier: 5.942A 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: 4.409A pdb=" N LEU N 81 " --> pdb=" O LYS N 77 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Proline residue: N 83 - end of helix Processing helix chain 'N' and resid 86 through 94 removed outlier: 4.083A pdb=" N ALA N 94 " --> pdb=" O TYR N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 108 Processing helix chain 'N' and resid 131 through 142 Processing helix chain 'O' and resid 11 through 20 removed outlier: 4.643A pdb=" N ASN O 19 " --> pdb=" O LYS O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 59 removed outlier: 3.531A pdb=" N ASN O 42 " --> pdb=" O LYS O 38 " (cutoff:3.500A) removed outlier: 3.943A 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: 5.155A pdb=" N HIS R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 78 through 87 removed outlier: 3.852A pdb=" N THR R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 4.676A 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: 4.187A pdb=" N VAL R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 45 removed outlier: 4.451A 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: 4.494A pdb=" N ALA T 63 " --> pdb=" O PRO T 59 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR T 64 " --> pdb=" O ARG T 60 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) removed outlier: 5.746A 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: 4.618A pdb=" N LYS U 12 " --> pdb=" O GLU U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 38 removed outlier: 3.564A pdb=" N GLN U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU U 36 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER U 37 " --> pdb=" O VAL U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 71 removed outlier: 4.591A pdb=" N THR U 46 " --> pdb=" O PRO U 42 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 82 removed outlier: 5.174A 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: 3.651A 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: 5.841A pdb=" N HIS W 69 " --> pdb=" O ARG W 65 " (cutoff:3.500A) removed outlier: 4.019A 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: 4.973A pdb=" N ARG W 72 " --> pdb=" O LYS W 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 17 removed outlier: 3.795A pdb=" N ARG X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG X 17 " --> pdb=" O GLU X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 69 Processing helix chain 'Y' and resid 6 through 21 removed outlier: 5.318A pdb=" N ARG Y 21 " --> pdb=" O LYS Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 30 removed outlier: 4.498A pdb=" N ARG Y 28 " --> pdb=" O PRO Y 24 " (cutoff:3.500A) removed outlier: 4.618A 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: 3.872A pdb=" N TYR Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 48 Processing helix chain 'c' and resid 19 through 35 removed outlier: 3.577A pdb=" N GLN c 25 " --> pdb=" O SER c 21 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 92 removed outlier: 4.149A pdb=" N GLU c 91 " --> pdb=" O ARG c 87 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA c 92 " --> pdb=" O GLU c 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 25 removed outlier: 5.695A pdb=" N TRP d 8 " --> pdb=" O MET d 4 " (cutoff:3.500A) removed outlier: 3.682A 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: 3.640A pdb=" N ASP j 176 " --> pdb=" O GLY j 173 " (cutoff:3.500A) Proline residue: j 178 - end of helix Processing helix chain 'k' and resid 111 through 120 removed outlier: 4.414A pdb=" N ARG k 117 " --> pdb=" O GLU k 113 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE k 118 " --> pdb=" O VAL k 114 " (cutoff:3.500A) removed outlier: 4.587A 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: 3.973A pdb=" N ALA k 138 " --> pdb=" O SER k 134 " (cutoff:3.500A) removed outlier: 5.254A 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: 4.301A 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: 4.792A pdb=" N LYS l 46 " --> pdb=" O VAL l 42 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 131 removed outlier: 3.923A pdb=" N ALA l 130 " --> pdb=" O ILE l 126 " (cutoff:3.500A) removed outlier: 4.670A 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: 4.897A 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: 3.777A pdb=" N ARG l 195 " --> pdb=" O LYS l 191 " (cutoff:3.500A) removed outlier: 4.004A 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: 4.213A 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: 4.668A 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: 3.707A pdb=" N TYR m 207 " --> pdb=" O HIS m 203 " (cutoff:3.500A) removed outlier: 4.799A 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: 4.367A 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: 3.868A 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: 4.157A 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: 5.108A 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: 4.399A 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: 4.003A 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: 4.311A 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: 3.674A pdb=" N GLU p 208 " --> pdb=" O ARG p 204 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ALA p 209 " --> pdb=" O ALA p 205 " (cutoff:3.500A) removed outlier: 5.917A 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: 3.804A pdb=" N ALA p 220 " --> pdb=" O SER p 216 " (cutoff:3.500A) Processing helix chain 'p' and resid 225 through 233 removed outlier: 4.681A pdb=" N LYS p 231 " --> pdb=" O ASP p 227 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS p 232 " --> pdb=" O GLU p 228 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TRP p 233 " --> pdb=" O VAL p 229 " (cutoff:3.500A) Processing helix chain 'p' and resid 239 through 255 removed outlier: 4.214A 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: 4.553A pdb=" N ARG q 166 " --> pdb=" O GLN q 162 " (cutoff:3.500A) Processing helix chain 'q' and resid 171 through 176 removed outlier: 4.107A pdb=" N LEU q 176 " --> pdb=" O ILE q 172 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 10 removed outlier: 4.430A pdb=" N TYR r 9 " --> pdb=" O PRO r 5 " (cutoff:3.500A) Processing helix chain 'r' and resid 42 through 47 removed outlier: 4.413A 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: 3.559A pdb=" N GLU r 150 " --> pdb=" O ASP r 146 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR r 157 " --> pdb=" O ARG r 153 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS r 158 " --> pdb=" O ARG r 154 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE r 159 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 160 - end of helix Processing helix chain 'r' and resid 177 through 188 removed outlier: 4.306A pdb=" N ALA r 187 " --> pdb=" O LYS r 183 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY r 188 " --> pdb=" O LYS r 184 " (cutoff:3.500A) Processing helix chain 'r' and resid 205 through 213 removed outlier: 4.578A 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: 4.449A 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: 6.291A 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: 4.074A 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: 5.600A pdb=" N SER u 98 " --> pdb=" O TRP u 94 " (cutoff:3.500A) Processing helix chain 'u' and resid 99 through 112 Processing helix chain 'u' and resid 113 through 138 removed outlier: 4.240A 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: 3.807A 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: 5.476A 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: 4.107A 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: 3.571A 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: 4.139A 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: 3.515A 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: 3.708A 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: 5.024A 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: 5.006A 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: 3.754A 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: 4.543A 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 Processing helix chain 'e' and resid 35 through 42 Processing helix chain 'e' and resid 44 through 57 removed outlier: 5.360A pdb=" N ARG e 57 " --> pdb=" O SER e 53 " (cutoff:3.500A) Processing helix chain 'e' and resid 58 through 76 removed outlier: 4.197A pdb=" N PHE e 76 " --> pdb=" O LEU e 72 " (cutoff:3.500A) Processing helix chain 'e' and resid 77 through 83 removed outlier: 4.577A pdb=" N TYR e 81 " --> pdb=" O ASN e 77 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 99 removed outlier: 3.864A 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 127 through 141 removed outlier: 4.356A pdb=" N ASP e 131 " --> pdb=" O LYS e 127 " (cutoff:3.500A) Proline residue: e 134 - end of helix 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: 4.728A pdb=" N ASP e 195 " --> pdb=" O ASP e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 200 through 226 removed outlier: 3.615A pdb=" N SER e 204 " --> pdb=" O SER e 200 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N PHE e 206 " --> pdb=" O GLU e 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 228 through 234 Processing helix chain 'e' and resid 235 through 244 removed outlier: 5.102A pdb=" N GLU e 244 " --> pdb=" O ILE e 240 " (cutoff:3.500A) Processing helix chain 'e' and resid 245 through 251 removed outlier: 4.161A pdb=" N ASN e 251 " --> pdb=" O TRP e 247 " (cutoff:3.500A) Processing helix chain 'e' and resid 257 through 275 removed outlier: 4.295A pdb=" N TYR e 261 " --> pdb=" O ASN e 257 " (cutoff:3.500A) Processing helix chain 'e' and resid 276 through 281 Processing helix chain 'e' and resid 282 through 299 removed outlier: 5.301A pdb=" N THR e 299 " --> pdb=" O LEU e 295 " (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: 5.201A pdb=" N GLU e 324 " --> pdb=" O LEU e 320 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP e 325 " --> pdb=" O ASP e 321 " (cutoff:3.500A) Processing helix chain 'e' and resid 326 through 333 removed outlier: 3.663A pdb=" N SER e 330 " --> pdb=" O GLY e 326 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS e 333 " --> pdb=" O TRP e 329 " (cutoff:3.500A) Processing helix chain 'e' and resid 334 through 350 removed outlier: 3.650A 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: 4.123A pdb=" N HIS e 368 " --> pdb=" O SER e 364 " (cutoff:3.500A) Processing helix chain 'e' and resid 375 through 392 Proline residue: e 379 - end of helix Processing helix chain 'e' and resid 397 through 417 removed outlier: 3.977A pdb=" N SER e 416 " --> pdb=" O PHE e 412 " (cutoff:3.500A) Processing helix chain 'e' and resid 418 through 436 Processing helix chain 'e' and resid 437 through 443 removed outlier: 5.178A pdb=" N THR e 443 " --> pdb=" O LEU e 439 " (cutoff:3.500A) Processing helix chain 'e' and resid 444 through 451 removed outlier: 4.282A pdb=" N GLY e 451 " --> pdb=" O GLN e 447 " (cutoff:3.500A) Processing helix chain 'e' and resid 454 through 469 removed outlier: 4.871A pdb=" N ASP e 469 " --> pdb=" O TYR e 465 " (cutoff:3.500A) Processing helix chain 'e' and resid 470 through 477 removed outlier: 4.896A 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 494 through 511 removed outlier: 3.525A pdb=" N LEU e 507 " --> pdb=" O PHE e 503 " (cutoff:3.500A) Processing helix chain 'e' and resid 512 through 519 Processing helix chain 'e' and resid 520 through 533 removed outlier: 4.708A pdb=" N ASP e 533 " --> pdb=" O PHE e 529 " (cutoff:3.500A) Processing helix chain 'e' and resid 537 through 551 Proline residue: e 549 - end of helix Processing helix chain 'e' and resid 555 through 568 removed outlier: 4.187A pdb=" N ASN e 559 " --> pdb=" O SER e 555 " (cutoff:3.500A) Processing helix chain 'e' and resid 570 through 577 removed outlier: 4.050A pdb=" N LYS e 574 " --> pdb=" O SER e 570 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR e 577 " --> pdb=" O PHE e 573 " (cutoff:3.500A) Processing helix chain 'e' and resid 578 through 594 removed outlier: 4.816A pdb=" N ASN e 594 " --> pdb=" O ALA e 590 " (cutoff:3.500A) Processing helix chain 'e' and resid 596 through 608 removed outlier: 4.468A pdb=" N ASP e 608 " --> pdb=" O MET e 604 " (cutoff:3.500A) Processing helix chain 'e' and resid 609 through 619 removed outlier: 5.244A 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: 4.414A 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: 4.418A pdb=" N ASP e 679 " --> pdb=" O LEU e 675 " (cutoff:3.500A) Processing helix chain 'e' and resid 680 through 691 removed outlier: 4.847A pdb=" N ASP e 691 " --> pdb=" O LEU e 687 " (cutoff:3.500A) Processing helix chain 'e' and resid 692 through 699 removed outlier: 5.535A pdb=" N TYR e 698 " --> pdb=" O SER e 694 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU e 699 " --> pdb=" O CYS e 695 " (cutoff:3.500A) Processing helix chain 'e' and resid 701 through 717 Processing helix chain 'e' and resid 719 through 737 Processing helix chain 'e' and resid 741 through 755 removed outlier: 4.489A pdb=" N LYS e 745 " --> pdb=" O GLY e 741 " (cutoff:3.500A) Processing helix chain 'e' and resid 757 through 766 Proline residue: e 766 - end of helix Processing helix chain 'e' and resid 768 through 777 Processing helix chain 'e' and resid 781 through 786 removed outlier: 3.713A pdb=" N SER e 785 " --> pdb=" O ASP e 781 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU e 786 " --> pdb=" O TYR e 782 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 781 through 786' Processing helix chain 'e' and resid 791 through 798 removed outlier: 6.235A pdb=" N HIS e 795 " --> pdb=" O SER e 791 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU e 798 " --> pdb=" O THR e 794 " (cutoff:3.500A) Processing helix chain 'e' and resid 805 through 827 removed outlier: 3.668A pdb=" N MET e 809 " --> pdb=" O ASN e 805 " (cutoff:3.500A) Proline residue: e 827 - end of helix Processing helix chain 'e' and resid 831 through 852 removed outlier: 3.894A pdb=" N ASP e 847 " --> pdb=" O GLU e 843 " (cutoff:3.500A) Processing helix chain 'e' and resid 856 through 861 removed outlier: 4.044A pdb=" N TYR e 860 " --> pdb=" O ASN e 856 " (cutoff:3.500A) removed outlier: 4.122A 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 removed outlier: 3.537A pdb=" N ILE e 879 " --> pdb=" O ASN e 875 " (cutoff:3.500A) Proline residue: e 886 - end of helix Processing helix chain 'e' and resid 895 through 903 removed outlier: 4.377A pdb=" N ALA e 899 " --> pdb=" O THR e 895 " (cutoff:3.500A) removed outlier: 4.571A 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 925 through 947 removed outlier: 5.001A pdb=" N GLN e 947 " --> pdb=" O THR e 943 " (cutoff:3.500A) Processing helix chain 'e' and resid 950 through 965 removed outlier: 3.563A pdb=" N CYS e 957 " --> pdb=" O ASP e 953 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE e 959 " --> pdb=" O LEU e 955 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU e 960 " --> pdb=" O LEU e 956 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU e 962 " --> pdb=" O ALA e 958 " (cutoff:3.500A) Processing helix chain 'e' and resid 970 through 987 removed outlier: 3.632A pdb=" N THR e 974 " --> pdb=" O LYS e 970 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLY e 986 " --> pdb=" O SER e 982 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE e 987 " --> pdb=" O GLN e 983 " (cutoff:3.500A) Processing helix chain 'e' and resid 988 through 994 Processing helix chain 'e' and resid 995 through 1008 removed outlier: 3.833A pdb=" N SER e 999 " --> pdb=" O GLN e 995 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA e1001 " --> pdb=" O PHE e 997 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU e1002 " --> pdb=" O LYS e 998 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU e1006 " --> pdb=" O LEU e1002 " (cutoff:3.500A) Processing helix chain 'e' and resid 1020 through 1038 removed outlier: 4.263A pdb=" N ASP e1038 " --> pdb=" O TRP e1034 " (cutoff:3.500A) Processing helix chain 'e' and resid 1044 through 1063 removed outlier: 3.934A pdb=" N VAL e1048 " --> pdb=" O SER e1044 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU e1063 " --> pdb=" O LEU e1059 " (cutoff:3.500A) Processing helix chain 'e' and resid 1064 through 1069 Processing helix chain 'e' and resid 1070 through 1090 removed outlier: 3.743A pdb=" N ARG e1078 " --> pdb=" O GLU e1074 " (cutoff:3.500A) removed outlier: 4.906A 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: 6.194A pdb=" N ILE e1127 " --> pdb=" O TYR e1123 " (cutoff:3.500A) Processing helix chain 'e' and resid 1145 through 1163 removed outlier: 4.938A pdb=" N GLU e1163 " --> pdb=" O ILE e1159 " (cutoff:3.500A) Processing helix chain 'e' and resid 1164 through 1171 Processing helix chain 'e' and resid 1172 through 1181 removed outlier: 5.061A pdb=" N ASP e1181 " --> pdb=" O VAL e1177 " (cutoff:3.500A) Processing helix chain 'e' and resid 1182 through 1188 removed outlier: 3.792A pdb=" N ILE e1188 " --> pdb=" O ILE e1184 " (cutoff:3.500A) Processing helix chain 'e' and resid 1189 through 1217 removed outlier: 3.854A pdb=" N ILE e1211 " --> pdb=" O GLN e1207 " (cutoff:3.500A) Processing helix chain 'e' and resid 1235 through 1240 removed outlier: 4.880A pdb=" N LEU e1240 " --> pdb=" O SER e1236 " (cutoff:3.500A) Processing helix chain 'e' and resid 1241 through 1252 removed outlier: 4.834A pdb=" N VAL e1252 " --> pdb=" O VAL e1248 " (cutoff:3.500A) Processing helix chain 'e' and resid 1261 through 1281 removed outlier: 3.587A pdb=" N TYR e1278 " --> pdb=" O LEU e1274 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE e1279 " --> pdb=" O ILE e1275 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP e1281 " --> pdb=" O MET e1277 " (cutoff:3.500A) Processing helix chain 'e' and resid 1283 through 1298 Processing helix chain 'e' and resid 1299 through 1312 removed outlier: 5.538A pdb=" N ASP e1312 " --> pdb=" O THR e1308 " (cutoff:3.500A) Processing helix chain 'e' and resid 1315 through 1323 removed outlier: 3.547A pdb=" N TRP e1319 " --> pdb=" O ASP e1315 " (cutoff:3.500A) removed outlier: 5.474A 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: 5.076A 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: 3.501A pdb=" N LEU e1395 " --> pdb=" O ILE e1391 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP e1408 " --> pdb=" O ASN e1404 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG e1409 " --> pdb=" O SER e1405 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU e1410 " --> pdb=" O LYS e1406 " (cutoff:3.500A) Processing helix chain 'e' and resid 1448 through 1453 removed outlier: 4.214A pdb=" N ASN e1453 " --> pdb=" O TYR e1449 " (cutoff:3.500A) Processing helix chain 'e' and resid 1465 through 1481 removed outlier: 3.644A pdb=" N ILE e1480 " --> pdb=" O THR e1476 " (cutoff:3.500A) Processing helix chain 'e' and resid 1486 through 1503 Processing helix chain 'e' and resid 1535 through 1546 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: 3.728A pdb=" N SER w 79 " --> pdb=" O ASP w 75 " (cutoff:3.500A) Processing helix chain 'w' and resid 86 through 94 removed outlier: 3.659A 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: 4.555A 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: 5.071A 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 55 removed outlier: 4.296A pdb=" N PHE z 53 " --> pdb=" O ALA z 49 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS z 54 " --> pdb=" O THR z 50 " (cutoff:3.500A) Processing helix chain 'z' and resid 77 through 87 removed outlier: 5.036A 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: 4.662A 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: 4.429A pdb=" N LEU 0 76 " --> pdb=" O ASP 0 72 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU 0 77 " --> pdb=" O PHE 0 73 " (cutoff:3.500A) Proline residue: 0 78 - end of helix removed outlier: 4.206A 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: 6.467A pdb=" N VAL A 35 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE A 61 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY A 58 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 6.781A 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: 3.634A 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: 5.435A 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) removed outlier: 8.192A pdb=" N TRP H 92 " --> pdb=" O TYR H 108 " (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: 6.089A pdb=" N ASP I 97 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ASN I 98 " --> pdb=" O ILE I 22 " (cutoff:3.500A) removed outlier: 4.217A 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: 4.359A 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: 4.345A 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: 4.144A pdb=" N LYS M 9 " --> pdb=" O ILE M 25 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS M 21 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 27 through 30 removed outlier: 4.643A pdb=" N LYS M 27 " --> pdb=" O LEU M 42 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'N' and resid 99 through 102 Processing sheet with id= 25, first strand: chain 'P' and resid 22 through 25 removed outlier: 6.372A 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: 5.026A 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: 6.989A pdb=" N THR Q 9 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 71 through 77 Processing sheet with id= 28, first strand: chain 'S' and resid 11 through 15 removed outlier: 6.753A pdb=" N LEU S 29 " --> pdb=" O LEU S 14 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG S 82 " --> pdb=" O THR S 72 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS S 63 " --> pdb=" O ALA S 55 " (cutoff:3.500A) removed outlier: 4.491A 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: 4.536A 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: 4.139A 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: 4.477A 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: 4.643A pdb=" N GLY c 53 " --> pdb=" O GLY c 66 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS c 62 " --> pdb=" O CYS c 57 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'j' and resid 47 through 50 removed outlier: 3.921A pdb=" N GLN j 47 " --> pdb=" O LYS j 60 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS j 60 " --> pdb=" O LYS j 46 " (cutoff:3.500A) removed outlier: 4.447A 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: 6.428A pdb=" N ARG j 147 " --> pdb=" O ILE j 137 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'j' and resid 58 through 64 Processing sheet with id= 38, first strand: chain 'j' and resid 145 through 150 removed outlier: 4.406A 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: 4.890A 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: 4.561A pdb=" N LEU k 161 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 3.964A 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: 4.192A 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: 4.554A 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: 3.740A pdb=" N GLY k 288 " --> pdb=" O ASN k 319 " (cutoff:3.500A) removed outlier: 5.357A 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: 3.744A 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: 4.188A 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: 4.384A 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: 7.863A pdb=" N TYR o 133 " --> pdb=" O ILE o 89 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS o 82 " --> pdb=" O VAL o 119 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER o 113 " --> pdb=" O ARG o 88 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASN o 112 " --> pdb=" O LEU o 207 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'o' and resid 152 through 155 removed outlier: 8.624A pdb=" N GLY o 152 " --> pdb=" O LEU o 163 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'p' and resid 176 through 181 Processing sheet with id= 53, first strand: chain 'q' and resid 5 through 12 removed outlier: 4.943A pdb=" N GLN q 51 " --> pdb=" O VAL q 12 " (cutoff:3.500A) removed outlier: 6.650A 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: 5.994A 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: 6.338A 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: 4.255A 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: 7.657A 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: 5.068A 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: 5.682A pdb=" N SER s 22 " --> pdb=" O GLY s 124 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N GLY s 124 " --> pdb=" O SER s 22 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 's' and resid 52 through 55 removed outlier: 7.191A pdb=" N TYR s 52 " --> pdb=" O ARG s 61 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG s 61 " --> pdb=" O TYR s 52 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 's' and resid 89 through 92 removed outlier: 3.627A pdb=" N ASP s 170 " --> pdb=" O TYR s 89 " (cutoff:3.500A) removed outlier: 3.895A 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: 4.225A 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: 4.400A 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: 5.236A 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: 6.888A 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: 7.661A 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: 4.045A 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: 6.539A 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: 5.030A pdb=" N LYS a1013 " --> pdb=" O GLY a 959 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'e' and resid 1416 through 1423 removed outlier: 4.310A pdb=" N ALA e1416 " --> pdb=" O LEU e1433 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU e1433 " --> pdb=" O ALA e1416 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASN e1426 " --> pdb=" O LEU e1445 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'v' and resid 18 through 21 removed outlier: 3.678A pdb=" N SER v 149 " --> pdb=" O THR v 137 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'v' and resid 30 through 33 removed outlier: 4.742A 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= 78, 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= 79, first strand: chain 'v' and resid 57 through 63 removed outlier: 4.294A pdb=" N LYS v 68 " --> pdb=" O ASP v 63 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'w' and resid 49 through 53 removed outlier: 7.221A pdb=" N PHE w 49 " --> pdb=" O LEU w 159 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'w' and resid 65 through 68 Processing sheet with id= 82, first strand: chain 'w' and resid 163 through 169 removed outlier: 6.356A pdb=" N LEU w 163 " --> pdb=" O LEU w 38 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL w 32 " --> pdb=" O VAL w 169 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU w 204 " --> pdb=" O LEU w 216 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'z' and resid 11 through 17 removed outlier: 3.527A pdb=" N LYS z 11 " --> pdb=" O GLN z 65 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL z 60 " --> pdb=" O PRO z 75 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain '0' and resid 49 through 53 removed outlier: 3.838A pdb=" N SER 0 24 " --> pdb=" O THR 0 89 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL 0 27 " --> pdb=" O VAL 0 188 " (cutoff:3.500A) 3311 hydrogen bonds defined for protein. 9840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2919 hydrogen bonds 4656 hydrogen bond angles 0 basepair planarities 1185 basepair parallelities 2011 stacking parallelities Total time for adding SS restraints: 277.36 Time building geometry restraints manager: 65.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 17692 1.32 - 1.45: 65874 1.45 - 1.58: 69095 1.58 - 1.71: 7267 1.71 - 1.84: 269 Bond restraints: 160197 Sorted by residual: bond pdb=" N UNK 1 58 " pdb=" CA UNK 1 58 " ideal model delta sigma weight residual 1.458 1.666 -0.208 1.90e-02 2.77e+03 1.19e+02 bond pdb=" C2 I y 34 " pdb=" N3 I y 34 " ideal model delta sigma weight residual 1.462 1.305 0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" C2 I x 34 " pdb=" N3 I x 34 " ideal model delta sigma weight residual 1.462 1.307 0.155 2.00e-02 2.50e+03 5.97e+01 bond pdb=" CA THR C 129 " pdb=" C THR C 129 " ideal model delta sigma weight residual 1.522 1.440 0.082 1.20e-02 6.94e+03 4.63e+01 bond pdb=" C4 I x 34 " pdb=" N3 I x 34 " ideal model delta sigma weight residual 1.492 1.356 0.136 2.00e-02 2.50e+03 4.61e+01 ... (remaining 160192 not shown) Histogram of bond angle deviations from ideal: 93.58 - 102.20: 4117 102.20 - 110.82: 78017 110.82 - 119.43: 76359 119.43 - 128.05: 69471 128.05 - 136.67: 6198 Bond angle restraints: 234162 Sorted by residual: angle pdb=" N GLY e1364 " pdb=" CA GLY e1364 " pdb=" C GLY e1364 " ideal model delta sigma weight residual 112.49 126.20 -13.71 1.21e+00 6.83e-01 1.28e+02 angle pdb=" N SER e1460 " pdb=" CA SER e1460 " pdb=" C SER e1460 " ideal model delta sigma weight residual 111.36 123.48 -12.12 1.09e+00 8.42e-01 1.24e+02 angle pdb=" N ASN e1004 " pdb=" CA ASN e1004 " pdb=" C ASN e1004 " ideal model delta sigma weight residual 111.36 123.40 -12.04 1.09e+00 8.42e-01 1.22e+02 angle pdb=" N GLN e 553 " pdb=" CA GLN e 553 " pdb=" C GLN e 553 " ideal model delta sigma weight residual 109.14 93.58 15.56 1.49e+00 4.50e-01 1.09e+02 angle pdb=" N SER e1524 " pdb=" CA SER e1524 " pdb=" C SER e1524 " ideal model delta sigma weight residual 111.14 121.26 -10.12 1.08e+00 8.57e-01 8.78e+01 ... (remaining 234157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 91984 35.99 - 71.98: 8420 71.98 - 107.97: 865 107.97 - 143.96: 20 143.96 - 179.95: 57 Dihedral angle restraints: 101346 sinusoidal: 74528 harmonic: 26818 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 -84.65 -95.35 0 5.00e+00 4.00e-02 3.64e+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 -124.94 -55.06 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA GLY O 20 " pdb=" C GLY O 20 " pdb=" N ILE O 21 " pdb=" CA ILE O 21 " ideal model delta harmonic sigma weight residual -180.00 -132.46 -47.54 0 5.00e+00 4.00e-02 9.04e+01 ... (remaining 101343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 28596 0.149 - 0.297: 581 0.297 - 0.446: 48 0.446 - 0.595: 5 0.595 - 0.743: 1 Chirality restraints: 29231 Sorted by residual: chirality pdb=" CB ILE U 118 " pdb=" CA ILE U 118 " pdb=" CG1 ILE U 118 " pdb=" CG2 ILE U 118 " both_signs ideal model delta sigma weight residual False 2.64 1.90 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA ASN e 79 " pdb=" N ASN e 79 " pdb=" C ASN e 79 " pdb=" CB ASN e 79 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.29e+00 chirality pdb=" CA SER e1460 " pdb=" N SER e1460 " pdb=" C SER e1460 " pdb=" CB SER e1460 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.14e+00 ... (remaining 29228 not shown) Planarity restraints: 16185 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 7.03e+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 " 0.818 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 " 0.319 2.00e-02 2.50e+03 3.20e-01 2.30e+03 pdb=" C2' I x 34 " -0.395 2.00e-02 2.50e+03 pdb=" C3' I x 34 " -0.461 2.00e-02 2.50e+03 pdb=" C4' I x 34 " 0.338 2.00e-02 2.50e+03 pdb=" C5' I x 34 " -0.206 2.00e-02 2.50e+03 pdb=" N9 I x 34 " -0.312 2.00e-02 2.50e+03 pdb=" O2' I x 34 " 0.275 2.00e-02 2.50e+03 pdb=" O3' I x 34 " 0.119 2.00e-02 2.50e+03 pdb=" O4' I x 34 " 0.323 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 90 " 0.040 2.00e-02 2.50e+03 7.95e-02 6.32e+01 pdb=" C ARG H 90 " -0.137 2.00e-02 2.50e+03 pdb=" O ARG H 90 " 0.053 2.00e-02 2.50e+03 pdb=" N ASP H 91 " 0.045 2.00e-02 2.50e+03 ... (remaining 16182 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 6 2.02 - 2.74: 17298 2.74 - 3.46: 195771 3.46 - 4.18: 472069 4.18 - 4.90: 664324 Nonbonded interactions: 1349468 Sorted by model distance: nonbonded pdb=" OG SER e 26 " pdb=" O ASP e 31 " model vdw 1.296 2.440 nonbonded pdb=" O3' A x 76 " pdb=" O UNK 1 58 " model vdw 1.378 3.040 nonbonded pdb=" OP1 U f1258 " pdb=" NH1 ARG 0 46 " model vdw 1.522 2.520 nonbonded pdb=" O3' A y 76 " pdb=" O UNK 1 57 " model vdw 1.901 3.040 nonbonded pdb=" OP2 G f1222 " pdb=" OG1 THR 0 57 " model vdw 1.902 2.440 ... (remaining 1349463 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: 6.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 23.250 Check model and map are aligned: 1.640 Set scattering table: 1.080 Process input model: 616.750 Find NCS groups from input model: 3.380 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 665.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 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 0.208 160197 Z= 0.393 Angle : 0.930 21.577 234162 Z= 0.520 Chirality : 0.055 0.743 29231 Planarity : 0.009 0.559 16185 Dihedral : 21.767 179.953 83992 Min Nonbonded Distance : 1.296 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.70 % Favored : 96.19 % Rotamer: Outliers : 2.04 % Allowed : 2.17 % Favored : 95.79 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.01 % Twisted Proline : 0.61 % 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: -0.44 (0.08), residues: 9091 helix: 0.66 (0.08), residues: 3816 sheet: -0.08 (0.15), residues: 1190 loop : -1.25 (0.09), residues: 4085 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 0.003 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) ************************************************ 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1044 time to evaluate : 8.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 136 ARG cc_start: 0.8548 (ttp-170) cc_final: 0.8070 (ttp80) REVERT: E 148 ASP cc_start: 0.8372 (t70) cc_final: 0.8032 (t70) REVERT: N 93 SER cc_start: 0.8469 (p) cc_final: 0.8159 (p) REVERT: P 27 TYR cc_start: 0.8930 (t80) cc_final: 0.8635 (t80) REVERT: P 61 MET cc_start: 0.8545 (tmm) cc_final: 0.8299 (ttp) REVERT: U 30 GLU cc_start: 0.7164 (tp30) cc_final: 0.6957 (tp30) REVERT: U 34 GLN cc_start: 0.8164 (mt0) cc_final: 0.7860 (mt0) REVERT: V 66 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7142 (mt-10) REVERT: X 5 ILE cc_start: 0.9103 (tp) cc_final: 0.8577 (tp) REVERT: b 102 GLN cc_start: 0.8226 (mp10) cc_final: 0.7855 (mp10) REVERT: c 84 ARG cc_start: 0.8406 (tmm-80) cc_final: 0.8070 (ttp80) REVERT: d 17 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7475 (ttmm) REVERT: n 99 GLU cc_start: 0.8159 (pm20) cc_final: 0.7118 (pm20) REVERT: p 173 MET cc_start: 0.8458 (mmm) cc_final: 0.8094 (mmm) REVERT: p 249 ARG cc_start: 0.8444 (ttp-110) cc_final: 0.8006 (ptp90) REVERT: q 160 ASP cc_start: 0.7712 (m-30) cc_final: 0.7505 (m-30) REVERT: s 48 SER cc_start: 0.9212 (m) cc_final: 0.8758 (p) REVERT: s 55 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8626 (mmm-85) REVERT: s 107 ASP cc_start: 0.8525 (m-30) cc_final: 0.7898 (m-30) REVERT: s 131 MET cc_start: 0.8813 (mmm) cc_final: 0.8450 (mmm) REVERT: e 35 ASP cc_start: 0.9199 (OUTLIER) cc_final: 0.8805 (t0) REVERT: e 251 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.7886 (t0) REVERT: e 284 MET cc_start: 0.9216 (ttp) cc_final: 0.8605 (ptm) REVERT: e 809 MET cc_start: 0.9503 (mtp) cc_final: 0.9239 (mpp) REVERT: e 812 LEU cc_start: 0.9697 (OUTLIER) cc_final: 0.9432 (tp) REVERT: e 857 ASP cc_start: 0.9533 (m-30) cc_final: 0.9117 (t0) REVERT: e 862 PHE cc_start: 0.0918 (OUTLIER) cc_final: -0.1172 (m-80) REVERT: e 1094 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8653 (m-80) REVERT: e 1179 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8682 (mt) REVERT: e 1286 MET cc_start: 0.9118 (ttp) cc_final: 0.8467 (tpp) REVERT: e 1461 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8168 (tpt-90) REVERT: v 26 LEU cc_start: 0.8655 (mt) cc_final: 0.8414 (mt) REVERT: v 112 ASP cc_start: 0.8113 (p0) cc_final: 0.7333 (m-30) REVERT: w 73 ASP cc_start: 0.8642 (m-30) cc_final: 0.7970 (t0) REVERT: 0 38 MET cc_start: 0.9345 (mmm) cc_final: 0.8591 (tmm) REVERT: 0 55 LYS cc_start: 0.8707 (tttt) cc_final: 0.8148 (tppp) REVERT: 0 98 ASN cc_start: 0.8846 (m-40) cc_final: 0.8625 (m110) REVERT: 0 191 TYR cc_start: 0.8886 (t80) cc_final: 0.8683 (t80) outliers start: 151 outliers final: 22 residues processed: 1183 average time/residue: 2.1002 time to fit residues: 3637.6304 Evaluate side-chains 781 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 751 time to evaluate : 8.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain K residue 134 ASP Chi-restraints excluded: chain V residue 98 ARG Chi-restraints excluded: chain s residue 29 ARG Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 35 ASP Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 190 GLU Chi-restraints excluded: chain e residue 251 ASN Chi-restraints excluded: chain e residue 264 VAL Chi-restraints excluded: chain e residue 281 LYS Chi-restraints excluded: chain e residue 342 PHE Chi-restraints excluded: chain e residue 705 ASN Chi-restraints excluded: chain e residue 782 TYR Chi-restraints excluded: chain e residue 812 LEU Chi-restraints excluded: chain e residue 862 PHE Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 974 THR Chi-restraints excluded: chain e residue 1006 LEU Chi-restraints excluded: chain e residue 1047 THR Chi-restraints excluded: chain e residue 1094 TYR Chi-restraints excluded: chain e residue 1179 LEU Chi-restraints excluded: chain e residue 1214 GLU Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1425 THR Chi-restraints excluded: chain e residue 1461 ARG Chi-restraints excluded: chain e residue 1508 CYS Chi-restraints excluded: chain w residue 62 ASN Chi-restraints excluded: chain 0 residue 67 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1261 random chunks: chunk 1064 optimal weight: 5.9990 chunk 955 optimal weight: 5.9990 chunk 530 optimal weight: 10.0000 chunk 326 optimal weight: 8.9990 chunk 644 optimal weight: 10.0000 chunk 510 optimal weight: 8.9990 chunk 988 optimal weight: 20.0000 chunk 382 optimal weight: 10.0000 chunk 600 optimal weight: 10.0000 chunk 735 optimal weight: 10.0000 chunk 1145 optimal weight: 30.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN A B 122 GLN A C 28 ASN C 137 ASN ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 GLN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN G 131 GLN G 149 GLN H 109 GLN K 65 GLN L 26 GLN L 42 GLN S 42 GLN U 76 GLN W 13 ASN W 76 ASN Z 120 GLN b 22 GLN ** k 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 361 HIS m 39 GLN p 77 GLN r 51 HIS r 113 GLN s 101 ASN t 114 GLN t 162 ASN u 62 GLN e 21 ASN ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 174 GLN e 233 ASN e 251 ASN e 389 ASN e 719 ASN e 793 ASN ** e 795 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 805 ASN e 875 ASN ** e 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 995 GLN e1005 ASN ** e1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1138 ASN ** e1144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1190 GLN e1273 HIS e1478 HIS ** e1532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 39 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.160 160197 Z= 0.542 Angle : 0.728 14.599 234162 Z= 0.383 Chirality : 0.046 0.384 29231 Planarity : 0.006 0.107 16185 Dihedral : 22.653 179.967 66638 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.81 % Favored : 96.14 % Rotamer: Outliers : 2.59 % Allowed : 9.93 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.01 % Twisted Proline : 0.31 % 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: -0.04 (0.08), residues: 9091 helix: 0.97 (0.08), residues: 3860 sheet: -0.06 (0.14), residues: 1198 loop : -0.95 (0.09), residues: 4033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP n 9 HIS 0.022 0.002 HIS e1478 PHE 0.044 0.002 PHE 0 66 TYR 0.032 0.002 TYR 0 18 ARG 0.013 0.001 ARG I 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 759 time to evaluate : 8.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.7755 (t0) cc_final: 0.7365 (t0) REVERT: F 110 MET cc_start: 0.9127 (mmm) cc_final: 0.8797 (mmm) REVERT: H 18 ASP cc_start: 0.8147 (t0) cc_final: 0.7885 (OUTLIER) REVERT: H 25 ASN cc_start: 0.8900 (m-40) cc_final: 0.8673 (m-40) REVERT: H 44 GLU cc_start: 0.7943 (pm20) cc_final: 0.7726 (pm20) REVERT: H 49 ASN cc_start: 0.8106 (t0) cc_final: 0.7807 (t0) REVERT: H 52 ASN cc_start: 0.8948 (p0) cc_final: 0.8736 (p0) REVERT: I 74 MET cc_start: 0.8557 (ptp) cc_final: 0.8258 (ptp) REVERT: I 108 GLU cc_start: 0.7968 (pm20) cc_final: 0.7763 (pm20) REVERT: J 1 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8318 (ptt) REVERT: M 106 GLN cc_start: 0.8237 (mp10) cc_final: 0.7819 (mp10) REVERT: P 76 GLU cc_start: 0.8115 (pm20) cc_final: 0.7782 (pm20) REVERT: V 59 ASP cc_start: 0.7656 (m-30) cc_final: 0.7372 (m-30) REVERT: X 5 ILE cc_start: 0.9145 (tp) cc_final: 0.8756 (tp) REVERT: Y 30 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8393 (mtp85) REVERT: d 17 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7715 (ttmm) REVERT: k 318 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8406 (mtpp) REVERT: m 206 GLN cc_start: 0.8277 (tm-30) cc_final: 0.8021 (tm-30) REVERT: n 97 ASN cc_start: 0.7920 (t0) cc_final: 0.7719 (t0) REVERT: p 77 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8421 (pt0) REVERT: p 173 MET cc_start: 0.8664 (mmm) cc_final: 0.8356 (mmm) REVERT: r 102 MET cc_start: 0.8719 (mmp) cc_final: 0.8405 (mmp) REVERT: s 60 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8216 (ptm160) REVERT: s 77 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8254 (tm-30) REVERT: s 167 TYR cc_start: 0.8122 (m-80) cc_final: 0.7595 (m-80) REVERT: e 284 MET cc_start: 0.9382 (ttp) cc_final: 0.8612 (ptm) REVERT: e 857 ASP cc_start: 0.9562 (m-30) cc_final: 0.9158 (OUTLIER) REVERT: e 893 MET cc_start: 0.1509 (pmt) cc_final: 0.0405 (pp-130) REVERT: e 1028 PHE cc_start: 0.8032 (m-80) cc_final: 0.7454 (m-80) REVERT: e 1068 MET cc_start: 0.5387 (ptt) cc_final: 0.4348 (pp-130) REVERT: e 1135 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8743 (ptp) REVERT: e 1461 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.8081 (tmt90) REVERT: v 103 MET cc_start: 0.7271 (tmm) cc_final: 0.7042 (tmm) REVERT: w 73 ASP cc_start: 0.8682 (m-30) cc_final: 0.8158 (t0) REVERT: w 174 MET cc_start: 0.6452 (mpt) cc_final: 0.6200 (mpt) REVERT: 0 22 TYR cc_start: 0.8375 (m-80) cc_final: 0.8011 (m-80) REVERT: 0 43 LYS cc_start: 0.9170 (tmmt) cc_final: 0.8500 (tppp) REVERT: 0 55 LYS cc_start: 0.8661 (tttt) cc_final: 0.8338 (tppp) outliers start: 191 outliers final: 74 residues processed: 877 average time/residue: 2.1015 time to fit residues: 2709.1185 Evaluate side-chains 782 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 703 time to evaluate : 8.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 97 ASP Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Y residue 30 ARG Chi-restraints excluded: chain Z residue 87 SER Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain k residue 140 ASP Chi-restraints excluded: chain k residue 318 LYS Chi-restraints excluded: chain l residue 177 ASP Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain p residue 77 GLN Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 60 ARG Chi-restraints excluded: chain s residue 109 HIS 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 90 VAL Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 190 GLU Chi-restraints excluded: chain e residue 264 VAL Chi-restraints excluded: chain e residue 281 LYS Chi-restraints excluded: chain e residue 342 PHE Chi-restraints excluded: chain e residue 710 LYS Chi-restraints excluded: chain e residue 761 SER Chi-restraints excluded: chain e residue 782 TYR Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 989 GLU Chi-restraints excluded: chain e residue 1006 LEU Chi-restraints excluded: chain e residue 1135 MET Chi-restraints excluded: chain e residue 1282 THR Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1425 THR Chi-restraints excluded: chain e residue 1461 ARG Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 157 ASP Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 197 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1261 random chunks: chunk 636 optimal weight: 7.9990 chunk 355 optimal weight: 7.9990 chunk 953 optimal weight: 10.0000 chunk 779 optimal weight: 1.9990 chunk 315 optimal weight: 0.0070 chunk 1147 optimal weight: 7.9990 chunk 1239 optimal weight: 10.0000 chunk 1021 optimal weight: 9.9990 chunk 1137 optimal weight: 7.9990 chunk 391 optimal weight: 7.9990 chunk 920 optimal weight: 0.9990 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN G 131 GLN G 149 GLN L 26 GLN L 42 GLN Q 87 ASN T 98 GLN ** k 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 38 GLN p 59 GLN p 77 GLN r 113 GLN t 114 GLN t 162 ASN a 141 HIS a 407 GLN ** e1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1138 ASN e1189 ASN e1190 GLN ** e1532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 160197 Z= 0.277 Angle : 0.607 15.733 234162 Z= 0.322 Chirality : 0.038 0.327 29231 Planarity : 0.005 0.114 16185 Dihedral : 22.642 179.773 66600 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 2.25 % Allowed : 11.71 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.01 % Twisted Proline : 0.61 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.09), residues: 9091 helix: 1.22 (0.08), residues: 3860 sheet: 0.05 (0.14), residues: 1187 loop : -0.88 (0.09), residues: 4044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 944 HIS 0.006 0.001 HIS l 311 PHE 0.040 0.002 PHE e1055 TYR 0.025 0.002 TYR e1123 ARG 0.012 0.000 ARG I 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 727 time to evaluate : 8.352 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: C 53 ASP cc_start: 0.7733 (t0) cc_final: 0.7288 (t0) REVERT: C 120 ASN cc_start: 0.8482 (OUTLIER) cc_final: 0.7880 (p0) REVERT: C 128 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7731 (ptm-80) REVERT: F 110 MET cc_start: 0.9138 (mmm) cc_final: 0.8848 (mmm) REVERT: H 25 ASN cc_start: 0.8987 (m-40) cc_final: 0.8509 (m-40) REVERT: H 49 ASN cc_start: 0.8101 (t0) cc_final: 0.7747 (t0) REVERT: M 84 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.7783 (ptp90) REVERT: Q 86 LYS cc_start: 0.8253 (pptt) cc_final: 0.7983 (pptt) REVERT: Q 87 ASN cc_start: 0.8373 (m110) cc_final: 0.7752 (m110) REVERT: V 59 ASP cc_start: 0.7578 (m-30) cc_final: 0.7351 (m-30) REVERT: X 5 ILE cc_start: 0.9063 (tp) cc_final: 0.8797 (tp) REVERT: Y 30 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8397 (mtp85) REVERT: m 206 GLN cc_start: 0.8204 (tm-30) cc_final: 0.7972 (tm-30) REVERT: n 111 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8364 (mt) REVERT: p 173 MET cc_start: 0.8627 (mmm) cc_final: 0.8332 (mmm) REVERT: e 284 MET cc_start: 0.9410 (ttp) cc_final: 0.8675 (ptm) REVERT: e 857 ASP cc_start: 0.9522 (m-30) cc_final: 0.9105 (OUTLIER) REVERT: e 862 PHE cc_start: 0.1151 (OUTLIER) cc_final: 0.0273 (t80) REVERT: e 893 MET cc_start: 0.1622 (pmt) cc_final: 0.0842 (pp-130) REVERT: e 922 ASP cc_start: 0.3249 (OUTLIER) cc_final: 0.2752 (p0) REVERT: e 1068 MET cc_start: 0.5326 (ptt) cc_final: 0.4299 (ptt) REVERT: e 1135 MET cc_start: 0.8977 (mtm) cc_final: 0.8714 (ptp) REVERT: e 1286 MET cc_start: 0.8909 (tpt) cc_final: 0.8334 (tpt) REVERT: e 1289 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9078 (pt) REVERT: e 1461 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8128 (tmt90) REVERT: w 73 ASP cc_start: 0.8631 (m-30) cc_final: 0.8124 (t0) REVERT: w 174 MET cc_start: 0.5923 (mpt) cc_final: 0.5640 (mpt) REVERT: 0 8 LYS cc_start: 0.8525 (mttm) cc_final: 0.8275 (mttm) REVERT: 0 22 TYR cc_start: 0.8372 (m-80) cc_final: 0.8158 (m-80) REVERT: 0 26 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8309 (t80) REVERT: 0 31 ASP cc_start: 0.9338 (t0) cc_final: 0.9097 (t0) REVERT: 0 53 MET cc_start: 0.7507 (mpm) cc_final: 0.7233 (mpm) REVERT: 0 55 LYS cc_start: 0.8504 (tttt) cc_final: 0.8277 (tppp) REVERT: 0 189 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7790 (tp-100) REVERT: 0 191 TYR cc_start: 0.8511 (t80) cc_final: 0.8190 (t80) outliers start: 166 outliers final: 75 residues processed: 828 average time/residue: 2.0435 time to fit residues: 2500.6807 Evaluate side-chains 781 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 697 time to evaluate : 8.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 128 ARG Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 27 LYS Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain Y residue 30 ARG Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 102 ASN Chi-restraints excluded: chain n residue 111 LEU Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 57 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 207 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 28 ASP Chi-restraints excluded: chain s residue 65 ILE Chi-restraints excluded: chain t residue 4 SER Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 124 ILE 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 u residue 15 VAL Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 190 GLU Chi-restraints excluded: chain e residue 281 LYS Chi-restraints excluded: chain e residue 342 PHE Chi-restraints excluded: chain e residue 710 LYS Chi-restraints excluded: chain e residue 782 TYR Chi-restraints excluded: chain e residue 794 THR Chi-restraints excluded: chain e residue 862 PHE Chi-restraints excluded: chain e residue 922 ASP Chi-restraints excluded: chain e residue 924 VAL Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1282 THR Chi-restraints excluded: chain e residue 1289 ILE Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1425 THR Chi-restraints excluded: chain e residue 1461 ARG Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 157 ASP Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 94 THR Chi-restraints excluded: chain 0 residue 197 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1261 random chunks: chunk 1133 optimal weight: 0.7980 chunk 862 optimal weight: 6.9990 chunk 595 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 547 optimal weight: 10.0000 chunk 770 optimal weight: 0.7980 chunk 1151 optimal weight: 30.0000 chunk 1218 optimal weight: 40.0000 chunk 601 optimal weight: 8.9990 chunk 1091 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 overall best weight: 5.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN C 55 GLN E 92 GLN F 138 GLN G 127 GLN G 131 GLN G 149 GLN H 52 ASN L 26 GLN L 42 GLN j 132 ASN ** k 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 225 GLN p 59 GLN ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 114 GLN t 162 ASN a 438 ASN ** e 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 160197 Z= 0.369 Angle : 0.627 18.496 234162 Z= 0.332 Chirality : 0.040 0.308 29231 Planarity : 0.005 0.111 16185 Dihedral : 22.559 179.992 66593 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 2.84 % Allowed : 12.55 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.01 % Twisted Proline : 0.31 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.09), residues: 9091 helix: 1.31 (0.08), residues: 3872 sheet: -0.02 (0.14), residues: 1214 loop : -0.82 (0.09), residues: 4005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP u 85 HIS 0.008 0.001 HIS l 311 PHE 0.043 0.002 PHE e1028 TYR 0.022 0.002 TYR l 194 ARG 0.012 0.001 ARG I 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 714 time to evaluate : 8.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9063 (tt) REVERT: C 53 ASP cc_start: 0.7813 (t0) cc_final: 0.7360 (t0) REVERT: H 25 ASN cc_start: 0.9040 (m-40) cc_final: 0.8266 (m110) REVERT: J 1 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8211 (ptt) REVERT: M 84 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8137 (ptp90) REVERT: M 106 GLN cc_start: 0.8270 (mp10) cc_final: 0.7945 (mp10) REVERT: Q 87 ASN cc_start: 0.8366 (m110) cc_final: 0.7951 (m110) REVERT: V 59 ASP cc_start: 0.7576 (m-30) cc_final: 0.7362 (m-30) REVERT: Y 30 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8375 (mtp85) REVERT: j 73 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: k 318 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8504 (mtpp) REVERT: m 206 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7989 (tm-30) REVERT: p 173 MET cc_start: 0.8681 (mmm) cc_final: 0.8440 (mmm) REVERT: a 612 MET cc_start: 0.6215 (tmm) cc_final: 0.5913 (ppp) REVERT: e 125 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8660 (mp) REVERT: e 284 MET cc_start: 0.9442 (ttp) cc_final: 0.8694 (ptm) REVERT: e 809 MET cc_start: 0.9310 (mpt) cc_final: 0.8921 (mpt) REVERT: e 857 ASP cc_start: 0.9520 (m-30) cc_final: 0.9087 (t0) REVERT: e 879 ILE cc_start: 0.5232 (OUTLIER) cc_final: 0.4665 (tp) REVERT: e 893 MET cc_start: 0.1888 (pmt) cc_final: 0.0934 (pp-130) REVERT: e 922 ASP cc_start: 0.3454 (OUTLIER) cc_final: 0.2879 (p0) REVERT: e 1068 MET cc_start: 0.5243 (ptt) cc_final: 0.4048 (ptt) REVERT: e 1286 MET cc_start: 0.8877 (tpt) cc_final: 0.8401 (tpt) REVERT: e 1289 ILE cc_start: 0.9532 (OUTLIER) cc_final: 0.9139 (pt) REVERT: w 73 ASP cc_start: 0.8597 (m-30) cc_final: 0.8094 (t0) REVERT: w 174 MET cc_start: 0.5873 (mpt) cc_final: 0.5559 (mpt) REVERT: 0 26 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.8438 (t80) REVERT: 0 31 ASP cc_start: 0.9386 (t0) cc_final: 0.9096 (t0) REVERT: 0 43 LYS cc_start: 0.9236 (tmmt) cc_final: 0.8601 (ptpt) REVERT: 0 44 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8637 (pp20) REVERT: 0 64 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8865 (mpp80) REVERT: 0 189 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7849 (tp-100) outliers start: 210 outliers final: 117 residues processed: 847 average time/residue: 2.0479 time to fit residues: 2556.7111 Evaluate side-chains 822 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 693 time to evaluate : 8.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 54 ASP 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 80 LEU Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain T residue 81 CYS Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Y residue 30 ARG Chi-restraints excluded: chain Z residue 87 SER 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 11 LYS Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 140 ASP Chi-restraints excluded: chain k residue 318 LYS Chi-restraints excluded: chain l residue 177 ASP Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain l residue 323 VAL Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 57 THR Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 60 ARG Chi-restraints excluded: chain s residue 65 ILE Chi-restraints excluded: chain s residue 117 ASP 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 124 ILE Chi-restraints excluded: chain t residue 138 VAL 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 u residue 15 VAL Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 248 LYS Chi-restraints excluded: chain e residue 281 LYS Chi-restraints excluded: chain e residue 342 PHE Chi-restraints excluded: chain e residue 710 LYS Chi-restraints excluded: chain e residue 782 TYR Chi-restraints excluded: chain e residue 794 THR Chi-restraints excluded: chain e residue 879 ILE Chi-restraints excluded: chain e residue 922 ASP Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1289 ILE Chi-restraints excluded: chain e residue 1296 GLU Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1425 THR Chi-restraints excluded: chain e residue 1452 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 157 ASP Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 64 ARG Chi-restraints excluded: chain 0 residue 66 PHE Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 197 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1261 random chunks: chunk 1015 optimal weight: 6.9990 chunk 691 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 907 optimal weight: 8.9990 chunk 502 optimal weight: 10.0000 chunk 1040 optimal weight: 4.9990 chunk 842 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 622 optimal weight: 10.0000 chunk 1094 optimal weight: 2.9990 chunk 307 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 G 131 GLN G 149 GLN L 26 GLN L 42 GLN ** k 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 GLN ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 114 GLN t 162 ASN e 79 ASN e 793 ASN e1005 ASN ** e1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 199 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 160197 Z= 0.188 Angle : 0.567 15.081 234162 Z= 0.300 Chirality : 0.036 0.300 29231 Planarity : 0.004 0.111 16185 Dihedral : 22.560 179.679 66586 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 2.55 % Allowed : 13.47 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.01 % Twisted Proline : 0.61 % 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: 0.47 (0.09), residues: 9091 helix: 1.50 (0.08), residues: 3848 sheet: 0.07 (0.15), residues: 1190 loop : -0.74 (0.09), residues: 4053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP a 621 HIS 0.006 0.001 HIS N 40 PHE 0.030 0.001 PHE 0 66 TYR 0.024 0.001 TYR e1156 ARG 0.007 0.000 ARG I 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 741 time to evaluate : 8.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9004 (tt) REVERT: C 53 ASP cc_start: 0.7753 (t0) cc_final: 0.7312 (t0) REVERT: E 34 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7346 (mp-120) REVERT: H 66 VAL cc_start: 0.9349 (OUTLIER) cc_final: 0.9149 (m) REVERT: M 84 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.7796 (ptp90) REVERT: M 106 GLN cc_start: 0.8262 (mp10) cc_final: 0.7990 (mp10) REVERT: Q 86 LYS cc_start: 0.8221 (pptt) cc_final: 0.7996 (pptt) REVERT: Q 87 ASN cc_start: 0.8379 (m110) cc_final: 0.7857 (m110) REVERT: Y 30 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8407 (mtp85) REVERT: k 318 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8499 (mtpp) REVERT: m 206 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7924 (tm-30) REVERT: p 173 MET cc_start: 0.8618 (mmm) cc_final: 0.8327 (mmm) REVERT: s 167 TYR cc_start: 0.7884 (m-80) cc_final: 0.7641 (m-80) REVERT: a 414 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8506 (ttp) REVERT: a 612 MET cc_start: 0.6378 (tmm) cc_final: 0.6122 (ppp) REVERT: e 284 MET cc_start: 0.9455 (ttp) cc_final: 0.8684 (ptm) REVERT: e 809 MET cc_start: 0.9209 (mpt) cc_final: 0.9002 (mpt) REVERT: e 857 ASP cc_start: 0.9550 (m-30) cc_final: 0.9143 (t0) REVERT: e 893 MET cc_start: 0.1970 (OUTLIER) cc_final: 0.1242 (pp-130) REVERT: e 922 ASP cc_start: 0.3144 (OUTLIER) cc_final: 0.2661 (p0) REVERT: e 1028 PHE cc_start: 0.7386 (m-80) cc_final: 0.6807 (m-80) REVERT: e 1068 MET cc_start: 0.5407 (ptt) cc_final: 0.4186 (ptt) REVERT: e 1156 TYR cc_start: 0.9161 (t80) cc_final: 0.8925 (t80) REVERT: e 1286 MET cc_start: 0.8830 (tpt) cc_final: 0.8448 (tpt) REVERT: e 1289 ILE cc_start: 0.9554 (OUTLIER) cc_final: 0.9184 (pp) REVERT: e 1435 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7230 (t0) REVERT: w 73 ASP cc_start: 0.8600 (m-30) cc_final: 0.8085 (t0) REVERT: w 174 MET cc_start: 0.6007 (mpt) cc_final: 0.5753 (mpt) REVERT: 0 8 LYS cc_start: 0.8838 (mttp) cc_final: 0.8497 (mtpm) REVERT: 0 22 TYR cc_start: 0.8401 (m-80) cc_final: 0.8094 (m-80) REVERT: 0 26 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8524 (t80) REVERT: 0 31 ASP cc_start: 0.9308 (t0) cc_final: 0.8827 (m-30) REVERT: 0 43 LYS cc_start: 0.9165 (tmmt) cc_final: 0.8472 (ptpt) REVERT: 0 44 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8685 (pp20) REVERT: 0 55 LYS cc_start: 0.8004 (tppp) cc_final: 0.7618 (tppt) REVERT: 0 64 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8783 (mpp80) REVERT: 0 189 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7796 (tp-100) outliers start: 188 outliers final: 93 residues processed: 857 average time/residue: 2.0749 time to fit residues: 2642.3433 Evaluate side-chains 819 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 713 time to evaluate : 7.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 34 GLN Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 27 LYS Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 68 SER Chi-restraints excluded: chain Y residue 30 ARG Chi-restraints excluded: chain Z residue 126 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 11 LYS Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 140 ASP Chi-restraints excluded: chain k residue 318 LYS Chi-restraints excluded: chain l residue 216 VAL Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 59 GLU Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 181 VAL 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 60 ARG Chi-restraints excluded: chain s residue 117 ASP 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 124 ILE 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 u residue 15 VAL Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 116 MET Chi-restraints excluded: chain e residue 248 LYS Chi-restraints excluded: chain e residue 281 LYS Chi-restraints excluded: chain e residue 342 PHE Chi-restraints excluded: chain e residue 710 LYS Chi-restraints excluded: chain e residue 782 TYR Chi-restraints excluded: chain e residue 794 THR Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 922 ASP Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1282 THR Chi-restraints excluded: chain e residue 1289 ILE Chi-restraints excluded: chain e residue 1296 GLU Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1425 THR Chi-restraints excluded: chain e residue 1435 ASP Chi-restraints excluded: chain e residue 1452 THR Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 157 ASP Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 64 ARG Chi-restraints excluded: chain 0 residue 66 PHE Chi-restraints excluded: chain 0 residue 67 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1261 random chunks: chunk 410 optimal weight: 10.0000 chunk 1097 optimal weight: 40.0000 chunk 240 optimal weight: 8.9990 chunk 715 optimal weight: 9.9990 chunk 300 optimal weight: 5.9990 chunk 1220 optimal weight: 80.0000 chunk 1012 optimal weight: 5.9990 chunk 564 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 403 optimal weight: 10.0000 chunk 640 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 45 ASN E 118 HIS F 138 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN G 131 GLN G 149 GLN L 26 GLN L 42 GLN ** k 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 GLN ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 114 GLN t 162 ASN a 517 ASN ** e 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.124 160197 Z= 0.540 Angle : 0.692 15.037 234162 Z= 0.362 Chirality : 0.045 0.331 29231 Planarity : 0.006 0.111 16185 Dihedral : 22.489 179.310 66586 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.43 % Favored : 95.52 % Rotamer: Outliers : 2.84 % Allowed : 14.29 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.01 % Twisted Proline : 0.31 % Twisted General : 0.09 % 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: 9091 helix: 1.40 (0.08), residues: 3885 sheet: -0.04 (0.15), residues: 1210 loop : -0.77 (0.09), residues: 3996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP a 621 HIS 0.010 0.001 HIS l 311 PHE 0.036 0.002 PHE o 229 TYR 0.026 0.002 TYR D 33 ARG 0.009 0.001 ARG k 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 705 time to evaluate : 8.561 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: B 84 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9108 (tt) REVERT: C 53 ASP cc_start: 0.7851 (t0) cc_final: 0.7441 (t0) REVERT: C 120 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8325 (p0) REVERT: E 140 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7730 (mp0) REVERT: H 24 GLU cc_start: 0.8211 (pp20) cc_final: 0.7964 (pp20) REVERT: H 25 ASN cc_start: 0.9172 (m-40) cc_final: 0.8498 (m-40) REVERT: H 39 ASP cc_start: 0.8362 (p0) cc_final: 0.8138 (p0) REVERT: H 88 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8466 (mp10) REVERT: L 74 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: M 84 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8000 (ptp90) REVERT: M 106 GLN cc_start: 0.8324 (mp10) cc_final: 0.8048 (mp10) REVERT: Q 87 ASN cc_start: 0.8420 (m110) cc_final: 0.8020 (m110) REVERT: Y 30 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8393 (mtp85) REVERT: j 73 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: k 318 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8529 (mtpp) REVERT: k 369 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8276 (mtp85) REVERT: m 206 GLN cc_start: 0.8233 (tm-30) cc_final: 0.8033 (tm-30) REVERT: s 81 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8314 (mm-30) REVERT: s 167 TYR cc_start: 0.8121 (m-80) cc_final: 0.7768 (m-80) REVERT: a 414 MET cc_start: 0.8871 (ttp) cc_final: 0.8667 (ttp) REVERT: e 284 MET cc_start: 0.9461 (ttp) cc_final: 0.8735 (ptm) REVERT: e 893 MET cc_start: 0.2053 (OUTLIER) cc_final: 0.1415 (pp-130) REVERT: e 922 ASP cc_start: 0.3539 (OUTLIER) cc_final: 0.3038 (p0) REVERT: e 1068 MET cc_start: 0.5495 (ptt) cc_final: 0.4169 (ptt) REVERT: e 1156 TYR cc_start: 0.9195 (t80) cc_final: 0.8967 (t80) REVERT: e 1286 MET cc_start: 0.8873 (tpt) cc_final: 0.8525 (tpt) REVERT: e 1289 ILE cc_start: 0.9559 (OUTLIER) cc_final: 0.9192 (pp) REVERT: e 1435 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7292 (t0) REVERT: w 73 ASP cc_start: 0.8580 (m-30) cc_final: 0.8116 (t0) REVERT: w 174 MET cc_start: 0.5995 (mpt) cc_final: 0.5579 (mpt) REVERT: 0 8 LYS cc_start: 0.8828 (mttp) cc_final: 0.8457 (mtpm) REVERT: 0 22 TYR cc_start: 0.8404 (m-80) cc_final: 0.8059 (m-80) REVERT: 0 26 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8523 (t80) REVERT: 0 31 ASP cc_start: 0.9322 (t0) cc_final: 0.8948 (m-30) REVERT: 0 64 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8721 (mpp80) REVERT: 0 88 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.6385 (m-10) outliers start: 210 outliers final: 123 residues processed: 839 average time/residue: 2.0704 time to fit residues: 2567.7642 Evaluate side-chains 830 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 691 time to evaluate : 8.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 88 GLN Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 54 LEU Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 58 GLU Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 81 CYS Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 67 GLN Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Y residue 30 ARG 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 11 LYS Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 140 ASP Chi-restraints excluded: chain k residue 318 LYS Chi-restraints excluded: chain k residue 369 ARG Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 216 VAL Chi-restraints excluded: chain l residue 299 ILE Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 57 THR Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 60 ARG Chi-restraints excluded: chain s residue 65 ILE 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 124 ILE Chi-restraints excluded: chain t residue 138 VAL 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 u residue 15 VAL Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 281 LYS Chi-restraints excluded: chain e residue 342 PHE Chi-restraints excluded: chain e residue 710 LYS Chi-restraints excluded: chain e residue 782 TYR Chi-restraints excluded: chain e residue 794 THR Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 922 ASP Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1003 LEU Chi-restraints excluded: chain e residue 1282 THR Chi-restraints excluded: chain e residue 1289 ILE Chi-restraints excluded: chain e residue 1296 GLU Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1425 THR Chi-restraints excluded: chain e residue 1435 ASP Chi-restraints excluded: chain e residue 1452 THR Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 157 ASP Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 64 ARG Chi-restraints excluded: chain 0 residue 66 PHE Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 88 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1261 random chunks: chunk 1176 optimal weight: 20.0000 chunk 137 optimal weight: 9.9990 chunk 695 optimal weight: 0.9990 chunk 890 optimal weight: 9.9990 chunk 690 optimal weight: 0.7980 chunk 1027 optimal weight: 7.9990 chunk 681 optimal weight: 0.8980 chunk 1215 optimal weight: 6.9990 chunk 760 optimal weight: 0.9980 chunk 740 optimal weight: 5.9990 chunk 561 optimal weight: 20.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN E 92 GLN F 138 GLN G 127 GLN G 131 GLN G 149 GLN H 25 ASN L 26 GLN L 42 GLN N 120 ASN Q 87 ASN ** k 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 97 ASN p 59 GLN ** r 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 114 GLN t 162 ASN e 233 ASN ** e 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 188 ASN ** 0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 160197 Z= 0.188 Angle : 0.581 17.503 234162 Z= 0.306 Chirality : 0.036 0.291 29231 Planarity : 0.004 0.110 16185 Dihedral : 22.545 179.703 66586 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 2.25 % Allowed : 15.21 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.01 % Twisted Proline : 0.31 % 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: 0.53 (0.09), residues: 9091 helix: 1.56 (0.08), residues: 3858 sheet: 0.05 (0.15), residues: 1200 loop : -0.72 (0.09), residues: 4033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 944 HIS 0.005 0.001 HIS N 40 PHE 0.032 0.001 PHE 0 66 TYR 0.018 0.001 TYR e1123 ARG 0.008 0.000 ARG E 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 726 time to evaluate : 8.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9009 (tt) REVERT: C 53 ASP cc_start: 0.7836 (t0) cc_final: 0.7510 (t0) REVERT: E 92 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8527 (tt0) REVERT: H 24 GLU cc_start: 0.8192 (pp20) cc_final: 0.7988 (pp20) REVERT: H 25 ASN cc_start: 0.9074 (m110) cc_final: 0.8464 (m-40) REVERT: L 74 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: M 84 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.7818 (ptp90) REVERT: M 106 GLN cc_start: 0.8255 (mp10) cc_final: 0.8034 (mp10) REVERT: Q 87 ASN cc_start: 0.8511 (m-40) cc_final: 0.8155 (m110) REVERT: Y 30 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8446 (mtp85) REVERT: j 73 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: k 318 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8479 (mtpp) REVERT: k 369 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8274 (mtp85) REVERT: m 206 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7884 (tm-30) REVERT: a 414 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8609 (ttp) REVERT: e 284 MET cc_start: 0.9458 (ttp) cc_final: 0.8712 (ptm) REVERT: e 893 MET cc_start: 0.1836 (OUTLIER) cc_final: 0.1330 (pp-130) REVERT: e 922 ASP cc_start: 0.3132 (OUTLIER) cc_final: 0.2692 (p0) REVERT: e 1028 PHE cc_start: 0.7486 (m-80) cc_final: 0.7003 (m-80) REVERT: e 1068 MET cc_start: 0.5144 (ptt) cc_final: 0.3804 (ptt) REVERT: e 1154 LYS cc_start: 0.9695 (mmtt) cc_final: 0.9456 (tttt) REVERT: e 1286 MET cc_start: 0.8814 (tpt) cc_final: 0.8441 (tpt) REVERT: e 1289 ILE cc_start: 0.9568 (OUTLIER) cc_final: 0.9222 (pp) REVERT: e 1435 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7293 (t0) REVERT: w 73 ASP cc_start: 0.8614 (m-30) cc_final: 0.8129 (t0) REVERT: w 174 MET cc_start: 0.5924 (mpt) cc_final: 0.5531 (mpt) REVERT: 0 8 LYS cc_start: 0.8880 (mttp) cc_final: 0.8511 (mtpm) REVERT: 0 22 TYR cc_start: 0.8346 (m-80) cc_final: 0.8015 (m-80) REVERT: 0 26 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8563 (t80) REVERT: 0 31 ASP cc_start: 0.9317 (t0) cc_final: 0.8964 (m-30) REVERT: 0 43 LYS cc_start: 0.9245 (tmmt) cc_final: 0.8522 (ptpp) REVERT: 0 44 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8575 (pp20) REVERT: 0 64 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8724 (mpp80) REVERT: 0 88 PHE cc_start: 0.6729 (OUTLIER) cc_final: 0.6335 (m-10) outliers start: 166 outliers final: 109 residues processed: 830 average time/residue: 2.1673 time to fit residues: 2658.3130 Evaluate side-chains 830 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 705 time to evaluate : 8.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain T residue 81 CYS Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 67 GLN Chi-restraints excluded: chain Y residue 30 ARG Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain Z residue 126 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 11 LYS Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 140 ASP Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 318 LYS Chi-restraints excluded: chain k residue 369 ARG Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 216 VAL Chi-restraints excluded: chain l residue 299 ILE Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 85 ILE Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 181 VAL 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 60 ARG 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 124 ILE Chi-restraints excluded: chain t residue 138 VAL 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 u residue 15 VAL Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 248 LYS Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 281 LYS Chi-restraints excluded: chain e residue 342 PHE Chi-restraints excluded: chain e residue 782 TYR Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 922 ASP Chi-restraints excluded: chain e residue 924 VAL Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1086 MET Chi-restraints excluded: chain e residue 1282 THR Chi-restraints excluded: chain e residue 1289 ILE Chi-restraints excluded: chain e residue 1296 GLU Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1425 THR Chi-restraints excluded: chain e residue 1435 ASP Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 157 ASP Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 40 GLU Chi-restraints excluded: chain 0 residue 64 ARG Chi-restraints excluded: chain 0 residue 66 PHE Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 88 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1261 random chunks: chunk 751 optimal weight: 2.9990 chunk 485 optimal weight: 10.0000 chunk 725 optimal weight: 4.9990 chunk 366 optimal weight: 10.0000 chunk 238 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 chunk 772 optimal weight: 8.9990 chunk 828 optimal weight: 0.6980 chunk 600 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 955 optimal weight: 30.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 138 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN G 149 GLN L 26 GLN N 120 ASN Q 87 ASN ** X 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 97 ASN ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 114 GLN t 162 ASN ** e1004 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 160197 Z= 0.284 Angle : 0.599 15.510 234162 Z= 0.316 Chirality : 0.038 0.283 29231 Planarity : 0.005 0.110 16185 Dihedral : 22.477 179.877 66586 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.23 % Favored : 95.73 % Rotamer: Outliers : 2.34 % Allowed : 15.68 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.01 % Twisted Proline : 0.31 % 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: 0.54 (0.09), residues: 9091 helix: 1.56 (0.08), residues: 3864 sheet: 0.06 (0.15), residues: 1195 loop : -0.71 (0.09), residues: 4032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP a 658 HIS 0.005 0.001 HIS l 311 PHE 0.034 0.001 PHE 0 66 TYR 0.026 0.001 TYR e1156 ARG 0.017 0.000 ARG e 945 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 710 time to evaluate : 8.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9049 (tt) REVERT: C 53 ASP cc_start: 0.7857 (t0) cc_final: 0.7541 (t0) REVERT: H 25 ASN cc_start: 0.9134 (m110) cc_final: 0.8557 (m-40) REVERT: L 74 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.8272 (m-80) REVERT: M 84 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.7766 (ptp90) REVERT: Q 87 ASN cc_start: 0.8551 (m110) cc_final: 0.8041 (m110) REVERT: Y 30 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8441 (mtp85) REVERT: j 73 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7515 (tm-30) REVERT: k 318 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8497 (mtpp) REVERT: k 369 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8290 (mtp85) REVERT: m 206 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7873 (tm-30) REVERT: s 81 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8125 (mm-30) REVERT: s 167 TYR cc_start: 0.7917 (m-80) cc_final: 0.7607 (m-80) REVERT: a 414 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8579 (ttp) REVERT: e 284 MET cc_start: 0.9464 (ttp) cc_final: 0.8716 (ptm) REVERT: e 893 MET cc_start: 0.1777 (OUTLIER) cc_final: 0.1353 (pp-130) REVERT: e 922 ASP cc_start: 0.3370 (OUTLIER) cc_final: 0.2818 (p0) REVERT: e 1028 PHE cc_start: 0.7458 (m-80) cc_final: 0.7052 (m-80) REVERT: e 1068 MET cc_start: 0.4994 (ptt) cc_final: 0.3682 (ptt) REVERT: e 1156 TYR cc_start: 0.9060 (t80) cc_final: 0.8849 (t80) REVERT: e 1286 MET cc_start: 0.8819 (tpt) cc_final: 0.8448 (tpt) REVERT: e 1289 ILE cc_start: 0.9568 (OUTLIER) cc_final: 0.9225 (pp) REVERT: e 1435 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7279 (t0) REVERT: v 26 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7028 (mt) REVERT: v 93 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7625 (mm) REVERT: w 73 ASP cc_start: 0.8553 (m-30) cc_final: 0.8057 (t0) REVERT: w 174 MET cc_start: 0.5857 (mpt) cc_final: 0.5387 (mpt) REVERT: 0 8 LYS cc_start: 0.8860 (mttp) cc_final: 0.8443 (mtpm) REVERT: 0 26 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8580 (t80) REVERT: 0 31 ASP cc_start: 0.9312 (t0) cc_final: 0.8959 (m-30) REVERT: 0 43 LYS cc_start: 0.9185 (tmmt) cc_final: 0.8425 (ptpp) REVERT: 0 44 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8571 (pp20) REVERT: 0 64 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8728 (mpp80) outliers start: 173 outliers final: 123 residues processed: 824 average time/residue: 2.1155 time to fit residues: 2576.1603 Evaluate side-chains 840 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 701 time to evaluate : 8.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain D residue 22 ASP Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain T residue 81 CYS Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 10 GLN Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 67 GLN Chi-restraints excluded: chain Y residue 30 ARG Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain Z residue 126 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 73 GLU Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 140 ASP Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 318 LYS Chi-restraints excluded: chain k residue 369 ARG Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 216 VAL Chi-restraints excluded: chain l residue 299 ILE Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 53 VAL 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 60 ARG 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 124 ILE Chi-restraints excluded: chain t residue 138 VAL 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 u residue 15 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 248 LYS Chi-restraints excluded: chain e residue 267 LEU Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 281 LYS Chi-restraints excluded: chain e residue 342 PHE Chi-restraints excluded: chain e residue 710 LYS Chi-restraints excluded: chain e residue 782 TYR Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 922 ASP Chi-restraints excluded: chain e residue 924 VAL Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1248 VAL Chi-restraints excluded: chain e residue 1282 THR Chi-restraints excluded: chain e residue 1289 ILE Chi-restraints excluded: chain e residue 1296 GLU Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1425 THR Chi-restraints excluded: chain e residue 1435 ASP Chi-restraints excluded: chain v residue 26 LEU 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 93 LEU Chi-restraints excluded: chain v residue 157 ASP Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 40 GLU Chi-restraints excluded: chain 0 residue 64 ARG Chi-restraints excluded: chain 0 residue 66 PHE Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 193 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1261 random chunks: chunk 1105 optimal weight: 50.0000 chunk 1164 optimal weight: 20.0000 chunk 1062 optimal weight: 7.9990 chunk 1132 optimal weight: 40.0000 chunk 681 optimal weight: 8.9990 chunk 493 optimal weight: 10.0000 chunk 889 optimal weight: 0.9990 chunk 347 optimal weight: 10.0000 chunk 1023 optimal weight: 0.9990 chunk 1071 optimal weight: 30.0000 chunk 1128 optimal weight: 10.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN E 92 GLN F 138 GLN G 127 GLN G 131 GLN G 149 GLN H 25 ASN L 26 GLN L 42 GLN N 120 ASN ** X 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 97 ASN ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 114 GLN t 162 ASN ** e 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 188 ASN ** 0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 160197 Z= 0.394 Angle : 0.644 14.833 234162 Z= 0.339 Chirality : 0.041 0.301 29231 Planarity : 0.005 0.110 16185 Dihedral : 22.474 179.743 66586 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.48 % Favored : 95.49 % Rotamer: Outliers : 2.30 % Allowed : 16.03 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.01 % Twisted Proline : 0.31 % 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: 0.49 (0.09), residues: 9091 helix: 1.53 (0.08), residues: 3854 sheet: 0.02 (0.15), residues: 1214 loop : -0.73 (0.09), residues: 4023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP a 621 HIS 0.008 0.001 HIS l 311 PHE 0.035 0.002 PHE 0 66 TYR 0.033 0.002 TYR e1156 ARG 0.012 0.001 ARG e 945 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 710 time to evaluate : 8.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9065 (tt) REVERT: C 53 ASP cc_start: 0.7871 (t0) cc_final: 0.7562 (t0) REVERT: C 120 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8081 (p0) REVERT: H 24 GLU cc_start: 0.8259 (pp20) cc_final: 0.8049 (pp20) REVERT: H 25 ASN cc_start: 0.9243 (m-40) cc_final: 0.8551 (m-40) REVERT: L 74 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8327 (m-80) REVERT: M 84 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.7987 (ptp90) REVERT: Q 87 ASN cc_start: 0.8399 (m110) cc_final: 0.8015 (m110) REVERT: Y 30 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8394 (mtp85) REVERT: j 73 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7566 (tm-30) REVERT: k 318 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8500 (mtpp) REVERT: k 369 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8266 (mtp85) REVERT: m 206 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7871 (tm-30) REVERT: s 60 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.8017 (mtp-110) REVERT: s 167 TYR cc_start: 0.7974 (m-80) cc_final: 0.7678 (m-80) REVERT: a 414 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8631 (ttp) REVERT: a 589 MET cc_start: 0.8818 (mmp) cc_final: 0.7441 (ppp) REVERT: e 284 MET cc_start: 0.9478 (ttp) cc_final: 0.8739 (ptm) REVERT: e 893 MET cc_start: 0.1748 (OUTLIER) cc_final: 0.1415 (pp-130) REVERT: e 922 ASP cc_start: 0.3441 (OUTLIER) cc_final: 0.2907 (p0) REVERT: e 1060 MET cc_start: 0.7398 (mmt) cc_final: 0.7106 (mpm) REVERT: e 1068 MET cc_start: 0.5129 (ptt) cc_final: 0.3833 (ptt) REVERT: e 1286 MET cc_start: 0.8831 (tpt) cc_final: 0.8464 (tpt) REVERT: e 1289 ILE cc_start: 0.9530 (OUTLIER) cc_final: 0.9171 (pp) REVERT: e 1435 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7271 (t0) REVERT: v 93 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7741 (mm) REVERT: w 73 ASP cc_start: 0.8602 (m-30) cc_final: 0.8089 (t0) REVERT: w 174 MET cc_start: 0.5820 (mpt) cc_final: 0.5355 (mpt) REVERT: 0 8 LYS cc_start: 0.8898 (mttp) cc_final: 0.8550 (mtpm) REVERT: 0 26 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8289 (t80) REVERT: 0 31 ASP cc_start: 0.9278 (t0) cc_final: 0.8910 (m-30) REVERT: 0 38 MET cc_start: 0.9406 (mmm) cc_final: 0.8596 (tmm) REVERT: 0 43 LYS cc_start: 0.9100 (tmmt) cc_final: 0.8254 (ptpt) REVERT: 0 44 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8573 (pp20) REVERT: 0 55 LYS cc_start: 0.8198 (tppt) cc_final: 0.7881 (tppt) REVERT: 0 64 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8713 (mpp80) REVERT: 0 74 GLU cc_start: 0.9361 (pm20) cc_final: 0.9073 (pm20) REVERT: 0 88 PHE cc_start: 0.7668 (m-10) cc_final: 0.7269 (m-10) outliers start: 170 outliers final: 119 residues processed: 818 average time/residue: 2.1252 time to fit residues: 2576.5257 Evaluate side-chains 836 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 700 time to evaluate : 7.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 92 ILE Chi-restraints excluded: chain P residue 98 SER Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain T residue 81 CYS Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 67 GLN Chi-restraints excluded: chain Y residue 30 ARG Chi-restraints excluded: chain Z residue 83 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 73 GLU Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 140 ASP Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 318 LYS Chi-restraints excluded: chain k residue 369 ARG Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 216 VAL Chi-restraints excluded: chain l residue 299 ILE Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 57 THR Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 36 LEU 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 44 THR Chi-restraints excluded: chain s residue 60 ARG Chi-restraints excluded: chain s residue 65 ILE 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 124 ILE Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain a residue 422 LEU Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 267 LEU Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 281 LYS Chi-restraints excluded: chain e residue 342 PHE Chi-restraints excluded: chain e residue 710 LYS Chi-restraints excluded: chain e residue 782 TYR Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 922 ASP Chi-restraints excluded: chain e residue 924 VAL Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1248 VAL Chi-restraints excluded: chain e residue 1282 THR Chi-restraints excluded: chain e residue 1289 ILE Chi-restraints excluded: chain e residue 1296 GLU Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1425 THR Chi-restraints excluded: chain e residue 1435 ASP Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 93 LEU Chi-restraints excluded: chain v residue 157 ASP Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 26 PHE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 64 ARG Chi-restraints excluded: chain 0 residue 66 PHE Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 193 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1261 random chunks: chunk 743 optimal weight: 3.9990 chunk 1197 optimal weight: 8.9990 chunk 730 optimal weight: 8.9990 chunk 568 optimal weight: 8.9990 chunk 832 optimal weight: 5.9990 chunk 1256 optimal weight: 20.0000 chunk 1156 optimal weight: 7.9990 chunk 1000 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 772 optimal weight: 0.9990 chunk 613 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 34 GLN F 138 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN G 149 GLN L 26 GLN L 42 GLN N 120 ASN ** k 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 97 ASN q 125 ASN r 113 GLN ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 114 GLN t 162 ASN ** e 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 160197 Z= 0.308 Angle : 0.621 14.565 234162 Z= 0.327 Chirality : 0.039 0.377 29231 Planarity : 0.005 0.110 16185 Dihedral : 22.493 179.938 66586 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.32 % Favored : 95.67 % Rotamer: Outliers : 2.06 % Allowed : 16.40 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.01 % Twisted Proline : 0.61 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.09), residues: 9091 helix: 1.56 (0.08), residues: 3849 sheet: 0.03 (0.15), residues: 1206 loop : -0.72 (0.09), residues: 4036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP a 621 HIS 0.006 0.001 HIS l 311 PHE 0.049 0.001 PHE e1028 TYR 0.033 0.001 TYR 0 22 ARG 0.012 0.000 ARG e 945 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18182 Ramachandran restraints generated. 9091 Oldfield, 0 Emsley, 9091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 712 time to evaluate : 8.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9056 (tt) REVERT: C 53 ASP cc_start: 0.7879 (t0) cc_final: 0.7566 (t0) REVERT: H 24 GLU cc_start: 0.8261 (pp20) cc_final: 0.8012 (pp20) REVERT: H 25 ASN cc_start: 0.9245 (m-40) cc_final: 0.8483 (m-40) REVERT: H 44 GLU cc_start: 0.8080 (pm20) cc_final: 0.7324 (pm20) REVERT: L 74 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: M 84 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8022 (ptp90) REVERT: Q 80 ASN cc_start: 0.9056 (t0) cc_final: 0.8841 (t0) REVERT: Q 87 ASN cc_start: 0.8327 (m110) cc_final: 0.7956 (m110) REVERT: X 10 GLN cc_start: 0.8642 (pt0) cc_final: 0.8385 (pt0) REVERT: Y 30 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8406 (mtp85) REVERT: j 73 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7524 (tm-30) REVERT: k 318 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8493 (mtpp) REVERT: k 369 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8259 (mtp85) REVERT: m 206 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7854 (tm-30) REVERT: s 60 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7872 (mtp-110) REVERT: a 414 MET cc_start: 0.8932 (OUTLIER) cc_final: 0.8651 (ttp) REVERT: a 589 MET cc_start: 0.8878 (mmp) cc_final: 0.7367 (ppp) REVERT: e 284 MET cc_start: 0.9482 (ttp) cc_final: 0.8735 (ptm) REVERT: e 893 MET cc_start: 0.1780 (OUTLIER) cc_final: 0.1496 (pp-130) REVERT: e 922 ASP cc_start: 0.3460 (OUTLIER) cc_final: 0.2948 (p0) REVERT: e 1028 PHE cc_start: 0.7565 (m-80) cc_final: 0.7050 (m-80) REVERT: e 1068 MET cc_start: 0.5120 (ptt) cc_final: 0.3850 (ptt) REVERT: e 1156 TYR cc_start: 0.9023 (t80) cc_final: 0.8655 (t80) REVERT: e 1286 MET cc_start: 0.8821 (tpt) cc_final: 0.8458 (tpt) REVERT: e 1289 ILE cc_start: 0.9546 (OUTLIER) cc_final: 0.9139 (pp) REVERT: e 1435 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7440 (t0) REVERT: v 93 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7806 (mm) REVERT: w 73 ASP cc_start: 0.8602 (m-30) cc_final: 0.8087 (t0) REVERT: w 174 MET cc_start: 0.5816 (mpt) cc_final: 0.5361 (mpt) REVERT: 0 8 LYS cc_start: 0.8889 (mttp) cc_final: 0.8436 (mtpm) REVERT: 0 22 TYR cc_start: 0.8024 (m-80) cc_final: 0.7357 (t80) REVERT: 0 31 ASP cc_start: 0.9272 (t0) cc_final: 0.8876 (m-30) REVERT: 0 43 LYS cc_start: 0.9154 (tmmt) cc_final: 0.8347 (ptpp) REVERT: 0 44 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8571 (pp20) REVERT: 0 64 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8710 (mpp80) REVERT: 0 74 GLU cc_start: 0.9337 (pm20) cc_final: 0.9033 (pm20) REVERT: 0 88 PHE cc_start: 0.7459 (m-10) cc_final: 0.6826 (m-10) REVERT: 0 97 LYS cc_start: 0.8806 (tmmt) cc_final: 0.8404 (pttp) outliers start: 152 outliers final: 119 residues processed: 814 average time/residue: 2.1354 time to fit residues: 2581.3376 Evaluate side-chains 833 residues out of total 7922 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 699 time to evaluate : 8.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 157 GLN Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 27 LYS Chi-restraints excluded: chain J residue 47 ARG Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 54 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain T residue 81 CYS Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 16 ARG Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 50 SER Chi-restraints excluded: chain X residue 67 GLN Chi-restraints excluded: chain Y residue 30 ARG Chi-restraints excluded: chain Z residue 83 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 73 GLU Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 93 VAL Chi-restraints excluded: chain k residue 137 TYR Chi-restraints excluded: chain k residue 140 ASP Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 318 LYS Chi-restraints excluded: chain k residue 369 ARG Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 216 VAL Chi-restraints excluded: chain l residue 299 ILE Chi-restraints excluded: chain m residue 153 THR Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 15 VAL Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 57 THR Chi-restraints excluded: chain o residue 115 THR Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 126 SER Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 57 VAL Chi-restraints excluded: chain q residue 181 VAL Chi-restraints excluded: chain r residue 36 LEU 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 44 THR Chi-restraints excluded: chain s residue 60 ARG Chi-restraints excluded: chain s residue 65 ILE 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 124 ILE Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 90 VAL Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain e residue 114 THR Chi-restraints excluded: chain e residue 267 LEU Chi-restraints excluded: chain e residue 277 MET Chi-restraints excluded: chain e residue 281 LYS Chi-restraints excluded: chain e residue 342 PHE Chi-restraints excluded: chain e residue 710 LYS Chi-restraints excluded: chain e residue 782 TYR Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 922 ASP Chi-restraints excluded: chain e residue 924 VAL Chi-restraints excluded: chain e residue 971 ASP Chi-restraints excluded: chain e residue 1248 VAL Chi-restraints excluded: chain e residue 1282 THR Chi-restraints excluded: chain e residue 1289 ILE Chi-restraints excluded: chain e residue 1296 GLU Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1425 THR Chi-restraints excluded: chain e residue 1435 ASP 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 93 LEU Chi-restraints excluded: chain v residue 157 ASP Chi-restraints excluded: chain w residue 34 LEU Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 30 VAL Chi-restraints excluded: chain 0 residue 64 ARG Chi-restraints excluded: chain 0 residue 66 PHE Chi-restraints excluded: chain 0 residue 67 LEU Chi-restraints excluded: chain 0 residue 193 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1261 random chunks: chunk 794 optimal weight: 3.9990 chunk 1065 optimal weight: 8.9990 chunk 306 optimal weight: 8.9990 chunk 922 optimal weight: 9.9990 chunk 147 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 1001 optimal weight: 0.9980 chunk 419 optimal weight: 10.0000 chunk 1028 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 G 131 GLN G 149 GLN H 49 ASN L 26 GLN L 42 GLN j 97 ASN ** k 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 296 GLN ** s 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 114 GLN t 162 ASN a 599 GLN ** e1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 22 GLN ** 0 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.072703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.041497 restraints weight = 467619.471| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 2.09 r_work: 0.2527 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2441 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2434 r_free = 0.2434 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2436 r_free = 0.2436 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9214 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 160197 Z= 0.255 Angle : 0.610 14.533 234162 Z= 0.322 Chirality : 0.038 0.428 29231 Planarity : 0.005 0.110 16185 Dihedral : 22.502 179.549 66586 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.40 % Favored : 95.59 % Rotamer: Outliers : 2.00 % Allowed : 16.44 % Favored : 81.56 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.14 % Cis-general : 0.01 % Twisted Proline : 0.61 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.09), residues: 9091 helix: 1.55 (0.08), residues: 3848 sheet: 0.03 (0.15), residues: 1204 loop : -0.72 (0.09), residues: 4039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP a 944 HIS 0.005 0.001 HIS l 311 PHE 0.047 0.001 PHE e1028 TYR 0.032 0.001 TYR e1156 ARG 0.010 0.000 ARG e 945 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 50622.76 seconds wall clock time: 878 minutes 58.47 seconds (52738.47 seconds total)