Starting phenix.real_space_refine on Sat Mar 16 13:43:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8j_0369/03_2024/6n8j_0369_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8j_0369/03_2024/6n8j_0369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8j_0369/03_2024/6n8j_0369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8j_0369/03_2024/6n8j_0369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8j_0369/03_2024/6n8j_0369_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n8j_0369/03_2024/6n8j_0369_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians P 3332 5.49 5 Mg 2 5.21 5 S 140 5.16 5 C 70559 2.51 5 N 24382 2.21 5 O 34139 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 22": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D ARG 140": "NH1" <-> "NH2" Residue "D ARG 158": "NH1" <-> "NH2" Residue "J ARG 29": "NH1" <-> "NH2" Residue "J ARG 51": "NH1" <-> "NH2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J ARG 61": "NH1" <-> "NH2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 200": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "a ARG 117": "NH1" <-> "NH2" Residue "a ARG 139": "NH1" <-> "NH2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 300": "NH1" <-> "NH2" Residue "B TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "b ARG 24": "NH1" <-> "NH2" Residue "b ARG 27": "NH1" <-> "NH2" Residue "b ARG 34": "NH1" <-> "NH2" Residue "b ARG 43": "NH1" <-> "NH2" Residue "b ARG 79": "NH1" <-> "NH2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b ARG 135": "NH1" <-> "NH2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 154": "NH1" <-> "NH2" Residue "b PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 332": "NH1" <-> "NH2" Residue "b TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 510": "NH1" <-> "NH2" Residue "b TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 613": "NH1" <-> "NH2" Residue "b ARG 615": "NH1" <-> "NH2" Residue "b ARG 624": "NH1" <-> "NH2" Residue "b PHE 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 647": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "f PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "g ARG 60": "NH1" <-> "NH2" Residue "I ARG 3": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 75": "NH1" <-> "NH2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "H ARG 166": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H ARG 173": "NH1" <-> "NH2" Residue "h TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "k ARG 3": "NH1" <-> "NH2" Residue "k ARG 39": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 49": "NH1" <-> "NH2" Residue "m ARG 82": "NH1" <-> "NH2" Residue "m ARG 147": "NH1" <-> "NH2" Residue "m ARG 149": "NH1" <-> "NH2" Residue "m ARG 238": "NH1" <-> "NH2" Residue "m ARG 389": "NH1" <-> "NH2" Residue "m ARG 437": "NH1" <-> "NH2" Residue "m ARG 459": "NH1" <-> "NH2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "L ARG 171": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 77": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "p ARG 36": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "u TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 23": "NH1" <-> "NH2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u ARG 43": "NH1" <-> "NH2" Residue "u ARG 44": "NH1" <-> "NH2" Residue "u ARG 56": "NH1" <-> "NH2" Residue "u ARG 75": "NH1" <-> "NH2" Residue "u ARG 80": "NH1" <-> "NH2" Residue "u ARG 83": "NH1" <-> "NH2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "u ARG 111": "NH1" <-> "NH2" Residue "u ARG 113": "NH1" <-> "NH2" Residue "u ARG 122": "NH1" <-> "NH2" Residue "u ARG 135": "NH1" <-> "NH2" Residue "O PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "P ARG 126": "NH1" <-> "NH2" Residue "P ARG 181": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "R ARG 62": "NH1" <-> "NH2" Residue "R ARG 104": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "r TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 9": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "r ARG 126": "NH1" <-> "NH2" Residue "r ARG 149": "NH1" <-> "NH2" Residue "r ARG 251": "NH1" <-> "NH2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 108": "NH1" <-> "NH2" Residue "T ARG 139": "NH1" <-> "NH2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "W ARG 31": "NH1" <-> "NH2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W ARG 126": "NH1" <-> "NH2" Residue "W ARG 166": "NH1" <-> "NH2" Residue "W ARG 198": "NH1" <-> "NH2" Residue "X ARG 33": "NH1" <-> "NH2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 125": "NH1" <-> "NH2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "y ARG 85": "NH1" <-> "NH2" Residue "y ARG 100": "NH1" <-> "NH2" Residue "y TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 84": "NH1" <-> "NH2" Residue "Z ARG 135": "NH1" <-> "NH2" Residue "z ARG 6": "NH1" <-> "NH2" Residue "z ARG 19": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "K ARG 67": "NH1" <-> "NH2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "q ARG 18": "NH1" <-> "NH2" Residue "q ARG 71": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 132554 Number of models: 1 Model: "" Number of chains: 51 Chain: "D" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2047 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 245} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1283 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1863 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 233} Chain: "a" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 742 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "B" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3081 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Chain: "b" Number of atoms: 5215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5215 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 622} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2749 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain: "c" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 743 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "d" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 873 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1274 Classifications: {'peptide': 160} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 151} Chain breaks: 1 Chain: "e" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1020 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "F" 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: "f" 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: "G" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1798 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 12, 'TRANS': 217} Chain: "g" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 881 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "I" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1056 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1493 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain: "h" 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: "i" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "j" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "k" 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: "m" Number of atoms: 3006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3006 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 19, 'TRANS': 358} Chain breaks: 6 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 29 Chain: "L" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1491 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 178} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "l" 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: "M" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1059 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "p" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "N" 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: "u" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1256 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1438 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1191 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "R" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1241 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain: "r" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1647 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain breaks: 1 Chain: "S" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1425 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "T" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 476 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 5, 'TRANS': 55} Chain: "U" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 826 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain: "V" 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: "W" Number of atoms: 1814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1814 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "X" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "Y" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 993 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "y" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1826 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 233} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 444 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "K" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 821 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain breaks: 1 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'UNK:plan-1': 92, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 113 Chain: "q" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 783 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "o" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "1" Number of atoms: 65181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3047, 65181 Classifications: {'RNA': 3047} Modifications used: {'rna2p_pur': 320, 'rna2p_pyr': 226, 'rna3p_pur': 1372, 'rna3p_pyr': 1129} Link IDs: {'rna2p': 546, 'rna3p': 2500} Chain breaks: 6 Chain: "2" 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: "3" 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: "b" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N VAL O 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 13 " occ=0.50 residue: pdb=" N HIS O 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2 HIS O 14 " occ=0.50 ... (remaining 185 not shown) Time building chain proxies: 49.80, per 1000 atoms: 0.38 Number of scatterers: 132554 At special positions: 0 Unit cell: (236.5, 221.1, 254.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 140 16.00 P 3332 15.00 Mg 2 11.99 O 34139 8.00 N 24382 7.00 C 70559 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 47 " distance=2.02 Simple disulfide: pdb=" SG CYS g 44 " - pdb=" SG CYS g 81 " distance=2.03 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 81 " distance=2.01 Simple disulfide: pdb=" SG CYS g 47 " - pdb=" SG CYS g 84 " distance=2.04 Simple disulfide: pdb=" SG CYS j 22 " - pdb=" SG CYS j 37 " distance=2.03 Simple disulfide: pdb=" SG CYS p 39 " - pdb=" SG CYS p 57 " distance=2.04 Simple disulfide: pdb=" SG CYS p 42 " - pdb=" SG CYS p 59 " distance=2.03 Simple disulfide: pdb=" SG CYS u 6 " - pdb=" SG CYS u 9 " distance=2.02 Simple disulfide: pdb=" SG CYS u 6 " - pdb=" SG CYS u 32 " distance=2.05 Simple disulfide: pdb=" SG CYS u 9 " - pdb=" SG CYS u 32 " distance=2.02 Simple disulfide: pdb=" SG CYS u 9 " - pdb=" SG CYS u 36 " distance=2.01 Simple disulfide: pdb=" SG CYS u 32 " - pdb=" SG CYS u 36 " distance=2.62 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: 45.34 Conformation dependent library (CDL) restraints added in 9.1 seconds 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14554 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: 273 helices and 62 sheets defined 44.2% alpha, 12.1% beta 768 base pairs and 1737 stacking pairs defined. Time for finding SS restraints: 66.96 Creating SS restraints... Processing helix chain 'D' and resid 9 through 16 removed outlier: 3.573A pdb=" N ARG D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE D 16 " --> pdb=" O TYR D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 26 removed outlier: 3.584A pdb=" N GLU D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 4.441A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR D 38 " --> pdb=" O LYS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 4.187A pdb=" N LEU D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 114 removed outlier: 3.507A pdb=" N ALA D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 removed outlier: 5.218A pdb=" N TYR D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LYS D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 115 through 120' Processing helix chain 'D' and resid 157 through 170 removed outlier: 4.057A pdb=" N GLY D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP D 168 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.580A pdb=" N SER D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE D 200 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY D 201 " --> pdb=" O SER D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 209 removed outlier: 3.943A pdb=" N TYR D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 224 removed outlier: 4.912A pdb=" N PHE D 223 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 219 through 224' Processing helix chain 'D' and resid 225 through 230 removed outlier: 3.634A pdb=" N ASP D 230 " --> pdb=" O TYR D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 250 removed outlier: 4.440A pdb=" N GLU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR D 241 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG D 248 " --> pdb=" O HIS D 244 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 273 removed outlier: 3.716A pdb=" N TYR D 265 " --> pdb=" O THR D 261 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU D 268 " --> pdb=" O GLN D 264 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D 269 " --> pdb=" O TYR D 265 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR D 272 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG D 273 " --> pdb=" O SER D 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 42 removed outlier: 3.977A pdb=" N VAL J 36 " --> pdb=" O ARG J 32 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 88 removed outlier: 3.741A pdb=" N GLU J 77 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU J 78 " --> pdb=" O PRO J 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE J 79 " --> pdb=" O LYS J 75 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU J 81 " --> pdb=" O GLU J 77 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL J 86 " --> pdb=" O ARG J 82 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS J 87 " --> pdb=" O GLY J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 113 removed outlier: 4.729A pdb=" N LEU J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLY J 113 " --> pdb=" O HIS J 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 108 through 113' Processing helix chain 'J' and resid 136 through 141 removed outlier: 3.518A pdb=" N ARG J 140 " --> pdb=" O ALA J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 167 removed outlier: 3.702A pdb=" N THR J 159 " --> pdb=" O THR J 155 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN J 165 " --> pdb=" O SER J 161 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR J 167 " --> pdb=" O PHE J 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.502A pdb=" N ARG A 9 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLY A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.696A pdb=" N VAL A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.577A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG A 193 " --> pdb=" O TYR A 189 " (cutoff:3.500A) Processing helix chain 'a' and resid 64 through 69 removed outlier: 4.564A pdb=" N PHE a 68 " --> pdb=" O GLN a 64 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TRP a 69 " --> pdb=" O GLN a 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 64 through 69' Processing helix chain 'a' and resid 74 through 83 removed outlier: 4.029A pdb=" N LEU a 78 " --> pdb=" O ASN a 74 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) Proline residue: a 83 - end of helix No H-bonds generated for 'chain 'a' and resid 74 through 83' Processing helix chain 'a' and resid 84 through 94 removed outlier: 3.773A pdb=" N ASP a 88 " --> pdb=" O GLU a 84 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLN a 89 " --> pdb=" O ASP a 85 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR a 90 " --> pdb=" O LYS a 86 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU a 91 " --> pdb=" O ARG a 87 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER a 93 " --> pdb=" O GLN a 89 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA a 94 " --> pdb=" O TYR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 108 removed outlier: 3.531A pdb=" N ALA a 107 " --> pdb=" O ASP a 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 131 through 142 removed outlier: 3.507A pdb=" N ILE a 138 " --> pdb=" O ALA a 134 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA a 141 " --> pdb=" O LYS a 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 removed outlier: 4.594A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.661A pdb=" N SER B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ALA B 138 " --> pdb=" O SER B 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 130 through 138' Processing helix chain 'B' and resid 141 through 154 removed outlier: 5.965A pdb=" N GLU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 removed outlier: 4.203A pdb=" N THR B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix No H-bonds generated for 'chain 'B' and resid 165 through 170' Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.789A pdb=" N LYS B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 4.808A pdb=" N VAL B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 347 through 352 removed outlier: 4.397A pdb=" N LEU B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 347 through 352' Processing helix chain 'B' and resid 372 through 381 removed outlier: 3.564A pdb=" N LYS B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 381 " --> pdb=" O HIS B 377 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 29 removed outlier: 3.586A pdb=" N ASP b 19 " --> pdb=" O ASN b 15 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL b 21 " --> pdb=" O LEU b 17 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU b 22 " --> pdb=" O LEU b 18 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN b 23 " --> pdb=" O ASP b 19 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN b 26 " --> pdb=" O LEU b 22 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR b 29 " --> pdb=" O THR b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 66 removed outlier: 3.522A pdb=" N TYR b 46 " --> pdb=" O ILE b 42 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG b 48 " --> pdb=" O ALA b 44 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS b 49 " --> pdb=" O PHE b 45 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS b 51 " --> pdb=" O MET b 47 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL b 58 " --> pdb=" O GLY b 54 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS b 60 " --> pdb=" O GLY b 56 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP b 63 " --> pdb=" O GLU b 59 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS b 66 " --> pdb=" O GLU b 62 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 86 removed outlier: 3.984A pdb=" N ASP b 80 " --> pdb=" O PRO b 76 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET b 82 " --> pdb=" O HIS b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 119 removed outlier: 3.520A pdb=" N LEU b 95 " --> pdb=" O TYR b 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER b 103 " --> pdb=" O SER b 99 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL b 105 " --> pdb=" O ALA b 101 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG b 114 " --> pdb=" O ARG b 110 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU b 116 " --> pdb=" O TYR b 112 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS b 117 " --> pdb=" O VAL b 113 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N PHE b 118 " --> pdb=" O ARG b 114 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLY b 119 " --> pdb=" O LEU b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 145 removed outlier: 4.563A pdb=" N GLN b 127 " --> pdb=" O PHE b 123 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET b 136 " --> pdb=" O ALA b 132 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE b 139 " --> pdb=" O ARG b 135 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG b 144 " --> pdb=" O VAL b 140 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASP b 145 " --> pdb=" O LYS b 141 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 160 removed outlier: 3.638A pdb=" N GLN b 152 " --> pdb=" O ALA b 148 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS b 156 " --> pdb=" O GLN b 152 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARG b 159 " --> pdb=" O GLN b 155 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU b 160 " --> pdb=" O HIS b 156 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 Processing helix chain 'b' and resid 233 through 246 removed outlier: 3.596A pdb=" N GLN b 238 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE b 240 " --> pdb=" O GLU b 236 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR b 241 " --> pdb=" O MET b 237 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA b 242 " --> pdb=" O GLN b 238 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU b 246 " --> pdb=" O ALA b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 279 removed outlier: 3.702A pdb=" N GLN b 267 " --> pdb=" O THR b 263 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL b 268 " --> pdb=" O ILE b 264 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS b 269 " --> pdb=" O GLU b 265 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU b 270 " --> pdb=" O ALA b 266 " (cutoff:3.500A) Proline residue: b 276 - end of helix removed outlier: 4.272A pdb=" N ALA b 279 " --> pdb=" O LYS b 275 " (cutoff:3.500A) Processing helix chain 'b' and resid 289 through 294 removed outlier: 3.871A pdb=" N ILE b 293 " --> pdb=" O LYS b 289 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 312 removed outlier: 3.889A pdb=" N LEU b 306 " --> pdb=" O ARG b 302 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS b 310 " --> pdb=" O LEU b 306 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N VAL b 312 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 351 removed outlier: 4.291A pdb=" N VAL b 328 " --> pdb=" O LEU b 324 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET b 329 " --> pdb=" O GLU b 325 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG b 332 " --> pdb=" O VAL b 328 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS b 334 " --> pdb=" O GLU b 330 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU b 339 " --> pdb=" O ALA b 335 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER b 342 " --> pdb=" O LYS b 338 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU b 345 " --> pdb=" O ALA b 341 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS b 349 " --> pdb=" O GLU b 345 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N SER b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLN b 351 " --> pdb=" O LYS b 347 " (cutoff:3.500A) Processing helix chain 'b' and resid 352 through 362 removed outlier: 5.199A pdb=" N ASN b 356 " --> pdb=" O SER b 352 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN b 359 " --> pdb=" O ASN b 355 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS b 360 " --> pdb=" O ASN b 356 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 removed outlier: 3.586A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 407 removed outlier: 3.962A pdb=" N ILE b 402 " --> pdb=" O LEU b 398 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU b 405 " --> pdb=" O ASP b 401 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN b 406 " --> pdb=" O ILE b 402 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY b 407 " --> pdb=" O GLU b 403 " (cutoff:3.500A) Processing helix chain 'b' and resid 424 through 429 removed outlier: 4.495A pdb=" N LYS b 428 " --> pdb=" O ASP b 424 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASN b 429 " --> pdb=" O ASP b 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 424 through 429' Processing helix chain 'b' and resid 440 through 445 removed outlier: 4.308A pdb=" N PHE b 444 " --> pdb=" O ASN b 440 " (cutoff:3.500A) Processing helix chain 'b' and resid 448 through 467 removed outlier: 4.011A pdb=" N ALA b 455 " --> pdb=" O ALA b 451 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU b 456 " --> pdb=" O LYS b 452 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU b 459 " --> pdb=" O ALA b 455 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU b 461 " --> pdb=" O GLU b 457 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN b 465 " --> pdb=" O GLU b 461 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU b 466 " --> pdb=" O LYS b 462 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY b 467 " --> pdb=" O LEU b 463 " (cutoff:3.500A) Processing helix chain 'b' and resid 482 through 511 removed outlier: 3.753A pdb=" N ALA b 494 " --> pdb=" O LYS b 490 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN b 498 " --> pdb=" O ALA b 494 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE b 504 " --> pdb=" O GLN b 500 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASN b 509 " --> pdb=" O ALA b 505 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG b 510 " --> pdb=" O GLU b 506 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS b 511 " --> pdb=" O ALA b 507 " (cutoff:3.500A) Processing helix chain 'b' and resid 520 through 525 removed outlier: 5.203A pdb=" N THR b 525 " --> pdb=" O ARG b 521 " (cutoff:3.500A) Processing helix chain 'b' and resid 527 through 539 removed outlier: 3.677A pdb=" N MET b 531 " --> pdb=" O SER b 527 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU b 533 " --> pdb=" O GLY b 529 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS b 534 " --> pdb=" O LYS b 530 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET b 535 " --> pdb=" O MET b 531 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER b 536 " --> pdb=" O GLU b 532 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR b 537 " --> pdb=" O GLU b 533 " (cutoff:3.500A) Processing helix chain 'b' and resid 543 through 557 removed outlier: 4.043A pdb=" N ASP b 547 " --> pdb=" O SER b 543 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS b 548 " --> pdb=" O ALA b 544 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN b 549 " --> pdb=" O LEU b 545 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG b 554 " --> pdb=" O ASN b 550 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG b 557 " --> pdb=" O ALA b 553 " (cutoff:3.500A) Processing helix chain 'b' and resid 561 through 568 removed outlier: 3.648A pdb=" N VAL b 565 " --> pdb=" O ARG b 561 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL b 566 " --> pdb=" O GLY b 562 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE b 567 " --> pdb=" O SER b 563 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY b 568 " --> pdb=" O ASP b 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 561 through 568' Processing helix chain 'b' and resid 587 through 592 removed outlier: 5.436A pdb=" N GLY b 592 " --> pdb=" O ARG b 588 " (cutoff:3.500A) Processing helix chain 'b' and resid 595 through 617 removed outlier: 3.769A pdb=" N ARG b 604 " --> pdb=" O SER b 600 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET b 605 " --> pdb=" O LYS b 601 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA b 606 " --> pdb=" O ALA b 602 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS b 607 " --> pdb=" O ASP b 603 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG b 610 " --> pdb=" O ALA b 606 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG b 611 " --> pdb=" O LYS b 607 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU b 612 " --> pdb=" O MET b 608 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG b 613 " --> pdb=" O GLU b 609 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS b 616 " --> pdb=" O GLU b 612 " (cutoff:3.500A) Processing helix chain 'b' and resid 631 through 636 removed outlier: 4.109A pdb=" N PHE b 635 " --> pdb=" O SER b 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 46 removed outlier: 3.566A pdb=" N HIS C 36 " --> pdb=" O PRO C 32 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS C 44 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASN C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS C 46 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 132 removed outlier: 3.543A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 removed outlier: 3.558A pdb=" N GLY C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 removed outlier: 4.366A pdb=" N SER C 158 " --> pdb=" O THR C 154 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 154 through 159' Processing helix chain 'C' and resid 161 through 173 removed outlier: 3.905A pdb=" N ALA C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL C 172 " --> pdb=" O ALA C 168 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.902A pdb=" N VAL C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C 184 " --> pdb=" O LYS C 180 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 removed outlier: 4.310A pdb=" N ARG C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 196' Processing helix chain 'C' and resid 214 through 221 removed outlier: 3.946A pdb=" N ARG C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 240 Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 251 through 261 removed outlier: 3.560A pdb=" N LYS C 257 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.988A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 300 removed outlier: 4.759A pdb=" N ALA C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 299 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ARG C 300 " --> pdb=" O GLN C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 328 removed outlier: 3.644A pdb=" N LEU C 324 " --> pdb=" O ASN C 320 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 327 " --> pdb=" O VAL C 323 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN C 328 " --> pdb=" O LEU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.696A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA C 336 " --> pdb=" O LYS C 332 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 338 " --> pdb=" O PHE C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 361 removed outlier: 3.543A pdb=" N THR C 356 " --> pdb=" O ALA C 352 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 21 removed outlier: 3.703A pdb=" N LYS c 13 " --> pdb=" O SER c 9 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU c 16 " --> pdb=" O GLN c 12 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS c 19 " --> pdb=" O ALA c 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 37 removed outlier: 3.675A pdb=" N THR c 30 " --> pdb=" O GLY c 26 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER c 33 " --> pdb=" O SER c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 64 removed outlier: 3.536A pdb=" N LEU c 56 " --> pdb=" O ARG c 52 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET c 61 " --> pdb=" O GLU c 57 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU c 62 " --> pdb=" O TYR c 58 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 82 removed outlier: 3.533A pdb=" N LEU c 77 " --> pdb=" O GLY c 73 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY c 78 " --> pdb=" O ASN c 74 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR c 79 " --> pdb=" O ASN c 75 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 21 removed outlier: 3.972A pdb=" N ARG d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N HIS d 21 " --> pdb=" O HIS d 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 44 removed outlier: 5.308A pdb=" N ALA d 29 " --> pdb=" O PHE d 25 " (cutoff:3.500A) Proline residue: d 30 - end of helix removed outlier: 3.740A pdb=" N VAL d 33 " --> pdb=" O ALA d 29 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N HIS d 43 " --> pdb=" O PHE d 39 " (cutoff:3.500A) Processing helix chain 'd' and resid 52 through 61 removed outlier: 3.638A pdb=" N ALA d 58 " --> pdb=" O GLU d 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 removed outlier: 4.405A pdb=" N PHE E 106 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA E 107 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LYS E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 108' Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.526A pdb=" N GLN E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E 141 " --> pdb=" O ASP E 137 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.698A pdb=" N SER E 160 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA E 161 " --> pdb=" O GLN E 157 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N SER E 162 " --> pdb=" O TYR E 158 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 26 removed outlier: 3.699A pdb=" N TYR e 25 " --> pdb=" O HIS e 21 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N HIS e 26 " --> pdb=" O SER e 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 21 through 26' Processing helix chain 'e' and resid 40 through 45 removed outlier: 3.790A pdb=" N ARG e 44 " --> pdb=" O SER e 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 78 through 87 removed outlier: 3.680A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU e 85 " --> pdb=" O ASP e 81 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR e 86 " --> pdb=" O LEU e 82 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N MET e 87 " --> pdb=" O GLU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.581A pdb=" N ARG e 105 " --> pdb=" O SER e 101 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS e 113 " --> pdb=" O LEU e 109 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 73 removed outlier: 5.257A pdb=" N ARG F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE F 44 " --> pdb=" O LYS F 40 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA F 50 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.691A pdb=" N VAL F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 131 removed outlier: 3.663A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 150 Processing helix chain 'F' and resid 165 through 173 removed outlier: 3.966A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 191 removed outlier: 3.692A pdb=" N LEU F 184 " --> pdb=" O SER F 180 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE F 188 " --> pdb=" O LEU F 184 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL F 191 " --> pdb=" O GLU F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 203 removed outlier: 3.548A pdb=" N ALA F 198 " --> pdb=" O HIS F 194 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU F 202 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP F 203 " --> pdb=" O ASN F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 244 removed outlier: 4.502A pdb=" N LYS F 238 " --> pdb=" O GLU F 234 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 45 removed outlier: 4.451A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N TYR f 44 " --> pdb=" O ASP f 40 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU f 45 " --> pdb=" O ALA f 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 69 removed outlier: 3.746A pdb=" N GLN G 61 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE G 64 " --> pdb=" O ARG G 60 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 78 removed outlier: 4.313A pdb=" N ALA G 76 " --> pdb=" O PRO G 72 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN G 77 " --> pdb=" O PRO G 73 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N PHE G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 72 through 78' Processing helix chain 'G' and resid 83 through 98 removed outlier: 3.620A pdb=" N ALA G 88 " --> pdb=" O ARG G 84 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU G 89 " --> pdb=" O ASN G 85 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG G 98 " --> pdb=" O PHE G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 119 removed outlier: 3.816A pdb=" N THR G 110 " --> pdb=" O LYS G 106 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA G 114 " --> pdb=" O THR G 110 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA G 117 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 146 removed outlier: 3.733A pdb=" N ALA G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU G 144 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS G 146 " --> pdb=" O LEU G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 174 removed outlier: 4.710A pdb=" N VAL G 163 " --> pdb=" O PRO G 159 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL G 164 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU G 166 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Proline residue: G 167 - end of helix Processing helix chain 'G' and resid 182 through 191 removed outlier: 3.885A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY G 187 " --> pdb=" O LYS G 183 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 222 removed outlier: 5.208A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU G 211 " --> pdb=" O ASP G 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR G 217 " --> pdb=" O LYS G 213 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA G 220 " --> pdb=" O SER G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 232 removed outlier: 5.438A pdb=" N ASP G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N GLU G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS G 230 " --> pdb=" O TYR G 226 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HIS G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 253 removed outlier: 3.660A pdb=" N ARG G 249 " --> pdb=" O LYS G 245 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 66 removed outlier: 3.741A pdb=" N TYR g 62 " --> pdb=" O ARG g 58 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ALA g 63 " --> pdb=" O PRO g 59 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL g 65 " --> pdb=" O GLN g 61 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N SER g 66 " --> pdb=" O TYR g 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 58 through 66' Processing helix chain 'g' and resid 81 through 113 removed outlier: 6.099A pdb=" N VAL g 85 " --> pdb=" O CYS g 81 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS g 86 " --> pdb=" O ALA g 82 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU g 87 " --> pdb=" O ASN g 83 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE g 90 " --> pdb=" O LYS g 86 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA g 92 " --> pdb=" O ARG g 88 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU g 96 " --> pdb=" O ALA g 92 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE g 100 " --> pdb=" O GLU g 96 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL g 101 " --> pdb=" O GLU g 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 9 removed outlier: 4.619A pdb=" N VAL I 6 " --> pdb=" O GLY I 2 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG I 8 " --> pdb=" O TYR I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 27 removed outlier: 3.752A pdb=" N ILE I 21 " --> pdb=" O ASP I 17 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR I 27 " --> pdb=" O ASN I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 37 removed outlier: 3.751A pdb=" N GLN I 32 " --> pdb=" O LYS I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 removed outlier: 3.523A pdb=" N LEU I 64 " --> pdb=" O THR I 60 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS I 65 " --> pdb=" O ALA I 61 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS I 67 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY I 70 " --> pdb=" O THR I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 81 removed outlier: 3.915A pdb=" N ARG I 76 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS I 78 " --> pdb=" O LYS I 74 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 95 removed outlier: 4.303A pdb=" N SER I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA I 94 " --> pdb=" O SER I 90 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY I 95 " --> pdb=" O ASP I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 131 removed outlier: 3.618A pdb=" N ARG I 104 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLY I 113 " --> pdb=" O THR I 109 " (cutoff:3.500A) Proline residue: I 114 - end of helix removed outlier: 4.117A pdb=" N LEU I 122 " --> pdb=" O SER I 118 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS I 124 " --> pdb=" O GLU I 120 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP I 128 " --> pdb=" O LYS I 124 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER I 129 " --> pdb=" O GLU I 125 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU I 131 " --> pdb=" O LEU I 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 84 removed outlier: 4.134A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS H 72 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN H 77 " --> pdb=" O SER H 73 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL H 82 " --> pdb=" O MET H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 166 removed outlier: 3.874A pdb=" N GLN H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU H 161 " --> pdb=" O ASN H 157 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN H 162 " --> pdb=" O ALA H 158 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 5.411A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 13 removed outlier: 3.853A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG h 10 " --> pdb=" O ALA h 6 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS h 12 " --> pdb=" O GLU h 8 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N SER h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 5 through 13' Processing helix chain 'h' and resid 14 through 38 removed outlier: 3.616A pdb=" N ASP h 23 " --> pdb=" O SER h 19 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU h 27 " --> pdb=" O ASP h 23 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL h 33 " --> pdb=" O ALA h 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS h 35 " --> pdb=" O LEU h 31 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LEU h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER h 37 " --> pdb=" O VAL h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 71 removed outlier: 4.458A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE h 51 " --> pdb=" O VAL h 47 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA h 52 " --> pdb=" O ARG h 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG h 63 " --> pdb=" O ASN h 59 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN h 68 " --> pdb=" O GLU h 64 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 82 removed outlier: 5.644A pdb=" N ALA h 82 " --> pdb=" O LYS h 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 92 removed outlier: 4.338A pdb=" N ALA h 91 " --> pdb=" O ALA h 87 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU h 92 " --> pdb=" O LEU h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 25 through 30 removed outlier: 4.691A pdb=" N LYS i 29 " --> pdb=" O LYS i 25 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS i 30 " --> pdb=" O ILE i 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 25 through 30' Processing helix chain 'i' and resid 34 through 49 removed outlier: 4.067A pdb=" N LYS i 38 " --> pdb=" O SER i 34 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE i 39 " --> pdb=" O ASN i 35 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU i 46 " --> pdb=" O SER i 42 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE i 47 " --> pdb=" O LEU i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 64 removed outlier: 3.727A pdb=" N ARG i 56 " --> pdb=" O PRO i 52 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE i 58 " --> pdb=" O GLU i 54 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG i 62 " --> pdb=" O ILE i 58 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN i 63 " --> pdb=" O ASP i 59 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 77 removed outlier: 4.189A pdb=" N ALA i 69 " --> pdb=" O GLY i 65 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS i 71 " --> pdb=" O LYS i 67 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS i 75 " --> pdb=" O LYS i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 98 removed outlier: 3.856A pdb=" N ALA i 83 " --> pdb=" O SER i 79 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA i 85 " --> pdb=" O THR i 81 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG i 98 " --> pdb=" O ILE i 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 11 removed outlier: 4.305A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS j 10 " --> pdb=" O PRO j 6 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.733A pdb=" N LYS j 54 " --> pdb=" O GLY j 50 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG j 55 " --> pdb=" O ALA j 51 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N HIS j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 77 removed outlier: 3.625A pdb=" N LYS j 68 " --> pdb=" O MET j 64 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N HIS j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL j 70 " --> pdb=" O TYR j 66 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER j 71 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS j 75 " --> pdb=" O SER j 71 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 18 removed outlier: 3.948A pdb=" N PHE k 11 " --> pdb=" O ASP k 7 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU k 13 " --> pdb=" O LYS k 9 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU k 14 " --> pdb=" O GLN k 10 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR k 15 " --> pdb=" O PHE k 11 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG k 16 " --> pdb=" O LEU k 12 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG k 17 " --> pdb=" O GLU k 13 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ALA k 18 " --> pdb=" O LEU k 14 " (cutoff:3.500A) Processing helix chain 'k' and resid 58 through 69 removed outlier: 3.903A pdb=" N ALA k 62 " --> pdb=" O ASP k 58 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE k 66 " --> pdb=" O ALA k 62 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN k 67 " --> pdb=" O LYS k 63 " (cutoff:3.500A) Processing helix chain 'm' and resid 6 through 15 removed outlier: 4.031A pdb=" N ILE m 12 " --> pdb=" O LYS m 8 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG m 13 " --> pdb=" O SER m 9 " (cutoff:3.500A) Processing helix chain 'm' and resid 32 through 45 removed outlier: 4.888A pdb=" N VAL m 36 " --> pdb=" O ASP m 32 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS m 37 " --> pdb=" O SER m 33 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET m 41 " --> pdb=" O LYS m 37 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR m 42 " --> pdb=" O PHE m 38 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THR m 43 " --> pdb=" O LEU m 39 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER m 44 " --> pdb=" O ASN m 40 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLY m 45 " --> pdb=" O MET m 41 " (cutoff:3.500A) Processing helix chain 'm' and resid 130 through 135 removed outlier: 4.146A pdb=" N THR m 134 " --> pdb=" O ARG m 130 " (cutoff:3.500A) Processing helix chain 'm' and resid 136 through 141 removed outlier: 5.679A pdb=" N ALA m 140 " --> pdb=" O SER m 136 " (cutoff:3.500A) Processing helix chain 'm' and resid 157 through 176 removed outlier: 4.315A pdb=" N LYS m 162 " --> pdb=" O GLU m 158 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA m 163 " --> pdb=" O ASP m 159 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR m 169 " --> pdb=" O ASN m 165 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR m 171 " --> pdb=" O ASP m 167 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU m 173 " --> pdb=" O THR m 169 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN m 175 " --> pdb=" O TYR m 171 " (cutoff:3.500A) Processing helix chain 'm' and resid 208 through 222 removed outlier: 3.824A pdb=" N TRP m 212 " --> pdb=" O SER m 208 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU m 215 " --> pdb=" O ILE m 211 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS m 217 " --> pdb=" O ASN m 213 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP m 220 " --> pdb=" O TYR m 216 " (cutoff:3.500A) Processing helix chain 'm' and resid 233 through 238 Processing helix chain 'm' and resid 239 through 249 removed outlier: 5.943A pdb=" N GLU m 243 " --> pdb=" O CYS m 239 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU m 244 " --> pdb=" O LYS m 240 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS m 247 " --> pdb=" O GLU m 243 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS m 248 " --> pdb=" O GLU m 244 " (cutoff:3.500A) Processing helix chain 'm' and resid 261 through 266 removed outlier: 4.360A pdb=" N VAL m 265 " --> pdb=" O LYS m 261 " (cutoff:3.500A) Proline residue: m 266 - end of helix No H-bonds generated for 'chain 'm' and resid 261 through 266' Processing helix chain 'm' and resid 267 through 279 removed outlier: 3.561A pdb=" N VAL m 274 " --> pdb=" O ALA m 270 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS m 275 " --> pdb=" O ALA m 271 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS m 279 " --> pdb=" O LYS m 275 " (cutoff:3.500A) Processing helix chain 'm' and resid 295 through 311 removed outlier: 3.582A pdb=" N ILE m 300 " --> pdb=" O LYS m 296 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN m 305 " --> pdb=" O GLN m 301 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE m 306 " --> pdb=" O LEU m 302 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER m 307 " --> pdb=" O LEU m 303 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN m 308 " --> pdb=" O ARG m 304 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU m 309 " --> pdb=" O GLN m 305 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR m 311 " --> pdb=" O SER m 307 " (cutoff:3.500A) Processing helix chain 'm' and resid 327 through 337 removed outlier: 3.624A pdb=" N ILE m 331 " --> pdb=" O GLY m 327 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE m 332 " --> pdb=" O LYS m 328 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN m 333 " --> pdb=" O SER m 329 " (cutoff:3.500A) Processing helix chain 'm' and resid 380 through 386 removed outlier: 3.662A pdb=" N PHE m 384 " --> pdb=" O GLU m 380 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLY m 386 " --> pdb=" O ILE m 382 " (cutoff:3.500A) Processing helix chain 'm' and resid 396 through 407 removed outlier: 4.042A pdb=" N ILE m 400 " --> pdb=" O PRO m 396 " (cutoff:3.500A) Proline residue: m 401 - end of helix removed outlier: 3.768A pdb=" N LYS m 405 " --> pdb=" O PRO m 401 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG m 406 " --> pdb=" O GLY m 402 " (cutoff:3.500A) Processing helix chain 'm' and resid 408 through 417 removed outlier: 3.769A pdb=" N THR m 415 " --> pdb=" O HIS m 411 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR m 416 " --> pdb=" O LEU m 412 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU m 417 " --> pdb=" O GLU m 413 " (cutoff:3.500A) Processing helix chain 'm' and resid 423 through 436 removed outlier: 3.863A pdb=" N PHE m 427 " --> pdb=" O ASP m 423 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU m 429 " --> pdb=" O THR m 425 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS m 434 " --> pdb=" O ILE m 430 " (cutoff:3.500A) Processing helix chain 'm' and resid 445 through 460 removed outlier: 3.518A pdb=" N SER m 450 " --> pdb=" O GLU m 446 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN m 452 " --> pdb=" O GLY m 448 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN m 458 " --> pdb=" O LEU m 454 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY m 460 " --> pdb=" O ASP m 456 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 22 removed outlier: 4.484A pdb=" N ARG L 21 " --> pdb=" O HIS L 17 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL L 22 " --> pdb=" O TRP L 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 17 through 22' Processing helix chain 'L' and resid 27 through 47 removed outlier: 3.674A pdb=" N LYS L 32 " --> pdb=" O GLN L 28 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL L 33 " --> pdb=" O ALA L 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN L 37 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA L 38 " --> pdb=" O SER L 34 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA L 47 " --> pdb=" O ALA L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 removed outlier: 3.858A pdb=" N VAL L 80 " --> pdb=" O THR L 76 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS L 81 " --> pdb=" O LEU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 94 removed outlier: 4.129A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 124 removed outlier: 3.777A pdb=" N SER L 121 " --> pdb=" O LYS L 117 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE L 124 " --> pdb=" O GLN L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 146 removed outlier: 4.123A pdb=" N THR L 144 " --> pdb=" O SER L 140 " (cutoff:3.500A) Proline residue: L 146 - end of helix Processing helix chain 'L' and resid 165 through 180 removed outlier: 5.673A pdb=" N THR L 169 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU L 170 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 193 removed outlier: 4.048A pdb=" N ALA L 193 " --> pdb=" O GLU L 189 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 21 removed outlier: 3.936A pdb=" N LYS l 12 " --> pdb=" O ARG l 8 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS l 15 " --> pdb=" O GLN l 11 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN l 20 " --> pdb=" O ALA l 16 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ARG l 21 " --> pdb=" O LYS l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.033A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ARG l 30 " --> pdb=" O TRP l 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 24 through 30' Processing helix chain 'M' and resid 59 through 64 removed outlier: 3.871A pdb=" N VAL M 63 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL M 64 " --> pdb=" O LEU M 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 59 through 64' Processing helix chain 'M' and resid 77 through 89 removed outlier: 3.586A pdb=" N ALA M 86 " --> pdb=" O SER M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 98 removed outlier: 4.062A pdb=" N ALA M 95 " --> pdb=" O CYS M 91 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA M 96 " --> pdb=" O GLU M 92 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N SER M 98 " --> pdb=" O TRP M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 112 removed outlier: 3.525A pdb=" N ALA M 104 " --> pdb=" O ALA M 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA M 111 " --> pdb=" O GLU M 107 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU M 112 " --> pdb=" O ARG M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 136 removed outlier: 3.599A pdb=" N ARG M 128 " --> pdb=" O ARG M 124 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR M 129 " --> pdb=" O LYS M 125 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR M 130 " --> pdb=" O GLN M 126 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS M 133 " --> pdb=" O TYR M 129 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ALA M 136 " --> pdb=" O LYS M 132 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.565A pdb=" N GLN p 25 " --> pdb=" O SER p 21 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS p 27 " --> pdb=" O ARG p 23 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN p 32 " --> pdb=" O LYS p 28 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS p 34 " --> pdb=" O GLU p 30 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA p 35 " --> pdb=" O ILE p 31 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 removed outlier: 3.962A pdb=" N THR p 78 " --> pdb=" O ALA p 74 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG p 80 " --> pdb=" O ALA p 76 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER p 81 " --> pdb=" O ALA p 77 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU p 88 " --> pdb=" O ARG p 84 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET p 89 " --> pdb=" O ARG p 85 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL p 90 " --> pdb=" O LEU p 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 14 removed outlier: 3.673A pdb=" N LEU N 10 " --> pdb=" O TYR N 6 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG N 12 " --> pdb=" O GLU N 8 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 3.885A pdb=" N PHE N 21 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG N 24 " --> pdb=" O ARG N 20 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG N 31 " --> pdb=" O VAL N 27 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASN N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 removed outlier: 3.694A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY N 52 " --> pdb=" O ALA N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 88 removed outlier: 4.365A pdb=" N GLN N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLY N 88 " --> pdb=" O PRO N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 83 through 88' Processing helix chain 'N' and resid 97 through 111 removed outlier: 3.715A pdb=" N VAL N 106 " --> pdb=" O ALA N 102 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA N 111 " --> pdb=" O GLY N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 145 removed outlier: 3.573A pdb=" N ARG N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 163 removed outlier: 3.743A pdb=" N ARG N 162 " --> pdb=" O HIS N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 173 removed outlier: 3.763A pdb=" N LYS N 170 " --> pdb=" O ALA N 166 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY N 173 " --> pdb=" O LYS N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 196 removed outlier: 3.932A pdb=" N GLN N 194 " --> pdb=" O THR N 190 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR N 196 " --> pdb=" O LYS N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 153 removed outlier: 4.795A pdb=" N TRP N 150 " --> pdb=" O ARG N 147 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE N 151 " --> pdb=" O TYR N 148 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS N 152 " --> pdb=" O ASN N 149 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP N 153 " --> pdb=" O TRP N 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 147 through 153' Processing helix chain 'u' and resid 33 through 43 removed outlier: 3.724A pdb=" N GLN u 42 " --> pdb=" O LYS u 38 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG u 43 " --> pdb=" O ALA u 39 " (cutoff:3.500A) Processing helix chain 'u' and resid 45 through 50 removed outlier: 6.064A pdb=" N LYS u 50 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 60 removed outlier: 3.648A pdb=" N ARG u 56 " --> pdb=" O THR u 52 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY u 60 " --> pdb=" O ARG u 56 " (cutoff:3.500A) Processing helix chain 'u' and resid 66 through 71 removed outlier: 3.914A pdb=" N THR u 70 " --> pdb=" O ASP u 66 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N PHE u 71 " --> pdb=" O SER u 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 66 through 71' Processing helix chain 'u' and resid 82 through 131 removed outlier: 3.564A pdb=" N VAL u 86 " --> pdb=" O ASN u 82 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR u 88 " --> pdb=" O GLU u 84 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU u 97 " --> pdb=" O MET u 93 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU u 98 " --> pdb=" O ALA u 94 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA u 106 " --> pdb=" O LYS u 102 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN u 110 " --> pdb=" O ALA u 106 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG u 111 " --> pdb=" O PHE u 107 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY u 114 " --> pdb=" O ASN u 110 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN u 115 " --> pdb=" O ARG u 111 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYS u 116 " --> pdb=" O MET u 112 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLU u 117 " --> pdb=" O ARG u 113 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS u 118 " --> pdb=" O GLY u 114 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS u 125 " --> pdb=" O LEU u 121 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN u 130 " --> pdb=" O LEU u 126 " (cutoff:3.500A) Proline residue: u 131 - end of helix Processing helix chain 'u' and resid 132 through 149 removed outlier: 3.686A pdb=" N ILE u 136 " --> pdb=" O GLU u 132 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU u 138 " --> pdb=" O LEU u 134 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL u 139 " --> pdb=" O ARG u 135 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU u 148 " --> pdb=" O LYS u 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 removed outlier: 3.558A pdb=" N VAL O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN O 26 " --> pdb=" O VAL O 22 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.595A pdb=" N LEU O 52 " --> pdb=" O PHE O 48 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP O 56 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE O 57 " --> pdb=" O LYS O 53 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS O 60 " --> pdb=" O ASP O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 4.102A pdb=" N GLY O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Proline residue: O 70 - end of helix No H-bonds generated for 'chain 'O' and resid 65 through 70' Processing helix chain 'O' and resid 75 through 89 removed outlier: 3.501A pdb=" N PHE O 80 " --> pdb=" O PRO O 76 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER O 89 " --> pdb=" O ARG O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 103 removed outlier: 3.803A pdb=" N LYS O 96 " --> pdb=" O THR O 92 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG O 101 " --> pdb=" O ALA O 97 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 116 removed outlier: 8.305A pdb=" N LYS O 114 " --> pdb=" O PRO O 110 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS O 116 " --> pdb=" O TYR O 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 110 through 116' Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 137 through 146 removed outlier: 3.535A pdb=" N SER O 144 " --> pdb=" O LYS O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 184 removed outlier: 3.747A pdb=" N LYS O 155 " --> pdb=" O ASP O 151 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA O 158 " --> pdb=" O ALA O 154 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL O 162 " --> pdb=" O ALA O 158 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR O 167 " --> pdb=" O SER O 163 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS O 170 " --> pdb=" O GLU O 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 198 removed outlier: 3.567A pdb=" N GLN O 193 " --> pdb=" O ASP O 189 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU O 194 " --> pdb=" O VAL O 190 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA O 195 " --> pdb=" O ALA O 191 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA O 196 " --> pdb=" O LYS O 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 15 removed outlier: 4.009A pdb=" N SER P 14 " --> pdb=" O ASN P 10 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA P 15 " --> pdb=" O PRO P 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 10 through 15' Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.704A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE P 36 " --> pdb=" O THR P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 54 removed outlier: 3.777A pdb=" N LYS P 46 " --> pdb=" O THR P 42 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU P 49 " --> pdb=" O GLN P 45 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN P 50 " --> pdb=" O LYS P 46 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP P 53 " --> pdb=" O GLU P 49 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS P 54 " --> pdb=" O GLN P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.659A pdb=" N VAL P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA P 104 " --> pdb=" O ALA P 100 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS P 105 " --> pdb=" O ASN P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 169 through 184 removed outlier: 3.753A pdb=" N ARG P 175 " --> pdb=" O ARG P 171 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE P 176 " --> pdb=" O GLN P 172 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ALA P 184 " --> pdb=" O LYS P 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 76 removed outlier: 3.979A pdb=" N GLY P 73 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 40 removed outlier: 3.501A pdb=" N LEU Q 28 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 54 removed outlier: 4.515A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL Q 47 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 60 Proline residue: Q 60 - end of helix Processing helix chain 'Q' and resid 63 through 73 removed outlier: 3.626A pdb=" N ILE Q 67 " --> pdb=" O SER Q 63 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLN Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 118 removed outlier: 3.608A pdb=" N LYS Q 113 " --> pdb=" O GLY Q 109 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL Q 115 " --> pdb=" O ARG Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 131 removed outlier: 3.762A pdb=" N LEU Q 127 " --> pdb=" O THR Q 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 36 removed outlier: 4.002A pdb=" N ALA R 33 " --> pdb=" O THR R 29 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN R 34 " --> pdb=" O SER R 30 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ASN R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 removed outlier: 3.632A pdb=" N LYS R 43 " --> pdb=" O ASN R 39 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS R 46 " --> pdb=" O ARG R 42 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY R 48 " --> pdb=" O LEU R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 73 removed outlier: 3.825A pdb=" N GLU R 72 " --> pdb=" O GLN R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 82 removed outlier: 3.703A pdb=" N ARG R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LYS R 82 " --> pdb=" O TYR R 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 77 through 82' Processing helix chain 'R' and resid 84 through 113 Proline residue: R 90 - end of helix removed outlier: 6.477A pdb=" N VAL R 93 " --> pdb=" O LEU R 89 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP R 95 " --> pdb=" O SER R 91 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG R 104 " --> pdb=" O ARG R 100 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU R 106 " --> pdb=" O LEU R 102 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS R 108 " --> pdb=" O ARG R 104 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA R 112 " --> pdb=" O LYS R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 removed outlier: 3.536A pdb=" N HIS R 121 " --> pdb=" O LYS R 117 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL R 122 " --> pdb=" O HIS R 118 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS R 125 " --> pdb=" O HIS R 121 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN R 130 " --> pdb=" O GLU R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 155 removed outlier: 3.605A pdb=" N GLU R 140 " --> pdb=" O ARG R 136 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS R 141 " --> pdb=" O ALA R 137 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 14 removed outlier: 4.238A pdb=" N ARG r 9 " --> pdb=" O ASP r 5 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 35 removed outlier: 3.644A pdb=" N ARG r 25 " --> pdb=" O GLU r 21 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU r 28 " --> pdb=" O LYS r 24 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA r 29 " --> pdb=" O ARG r 25 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG r 30 " --> pdb=" O LYS r 26 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 68 removed outlier: 6.051A pdb=" N LYS r 48 " --> pdb=" O GLY r 44 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE r 50 " --> pdb=" O LYS r 46 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA r 51 " --> pdb=" O GLY r 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS r 58 " --> pdb=" O ARG r 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL r 59 " --> pdb=" O TYR r 55 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS r 64 " --> pdb=" O SER r 60 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS r 68 " --> pdb=" O LYS r 64 " (cutoff:3.500A) Processing helix chain 'r' and resid 129 through 135 removed outlier: 4.887A pdb=" N MET r 133 " --> pdb=" O SER r 129 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE r 134 " --> pdb=" O GLU r 130 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS r 135 " --> pdb=" O GLU r 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 129 through 135' Processing helix chain 'r' and resid 206 through 213 removed outlier: 4.792A pdb=" N THR r 210 " --> pdb=" O SER r 206 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN r 211 " --> pdb=" O PRO r 207 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU r 212 " --> pdb=" O MET r 208 " (cutoff:3.500A) Processing helix chain 'r' and resid 248 through 253 removed outlier: 4.086A pdb=" N ASP r 252 " --> pdb=" O GLU r 248 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLY r 253 " --> pdb=" O PRO r 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 248 through 253' Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.653A pdb=" N ALA S 37 " --> pdb=" O ASN S 33 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR S 43 " --> pdb=" O SER S 39 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU S 48 " --> pdb=" O PHE S 44 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS S 49 " --> pdb=" O LEU S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 114 removed outlier: 3.593A pdb=" N VAL S 103 " --> pdb=" O ARG S 99 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR S 105 " --> pdb=" O ALA S 101 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN S 108 " --> pdb=" O GLU S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 137 through 145 removed outlier: 3.935A pdb=" N LYS S 141 " --> pdb=" O ARG S 137 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N PHE S 143 " --> pdb=" O TYR S 139 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU S 144 " --> pdb=" O VAL S 140 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR S 145 " --> pdb=" O LYS S 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 123 removed outlier: 5.030A pdb=" N GLN T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG T 108 " --> pdb=" O GLU T 104 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS T 110 " --> pdb=" O LEU T 106 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY T 123 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 19 through 26 removed outlier: 3.706A pdb=" N ASN U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 41 removed outlier: 4.077A pdb=" N TYR U 33 " --> pdb=" O ASP U 29 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS U 35 " --> pdb=" O ALA U 31 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE U 38 " --> pdb=" O ALA U 34 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP U 39 " --> pdb=" O LYS U 35 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N HIS U 40 " --> pdb=" O TYR U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 88 removed outlier: 3.628A pdb=" N THR U 80 " --> pdb=" O LEU U 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS U 82 " --> pdb=" O TYR U 78 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN U 87 " --> pdb=" O TYR U 83 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN U 88 " --> pdb=" O LEU U 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 71 removed outlier: 6.262A pdb=" N LYS V 71 " --> pdb=" O PRO V 67 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 127 Proline residue: V 127 - end of helix Processing helix chain 'V' and resid 128 through 133 removed outlier: 3.768A pdb=" N ASN V 132 " --> pdb=" O ARG V 128 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 37 removed outlier: 4.291A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG W 25 " --> pdb=" O GLU W 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE W 26 " --> pdb=" O ASN W 22 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG W 31 " --> pdb=" O PHE W 27 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU W 34 " --> pdb=" O VAL W 30 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR W 36 " --> pdb=" O GLU W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 61 removed outlier: 3.681A pdb=" N THR W 58 " --> pdb=" O GLN W 54 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP W 60 " --> pdb=" O ILE W 56 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ALA W 61 " --> pdb=" O ARG W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 89 through 96 removed outlier: 3.512A pdb=" N SER W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS W 94 " --> pdb=" O TYR W 90 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS W 96 " --> pdb=" O LEU W 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 89 through 96' Processing helix chain 'W' and resid 108 through 119 removed outlier: 4.087A pdb=" N VAL W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS W 113 " --> pdb=" O VAL W 109 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE W 116 " --> pdb=" O VAL W 112 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS W 117 " --> pdb=" O LYS W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 168 removed outlier: 3.959A pdb=" N GLU W 162 " --> pdb=" O ILE W 158 " (cutoff:3.500A) Proline residue: W 163 - end of helix Processing helix chain 'W' and resid 196 through 207 Processing helix chain 'X' and resid 58 through 64 removed outlier: 3.681A pdb=" N ILE X 63 " --> pdb=" O SER X 59 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU X 64 " --> pdb=" O TYR X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 69 through 79 removed outlier: 3.659A pdb=" N LYS X 74 " --> pdb=" O GLU X 70 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS X 75 " --> pdb=" O THR X 71 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU X 77 " --> pdb=" O MET X 73 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP X 78 " --> pdb=" O LYS X 74 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY X 79 " --> pdb=" O LYS X 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 103 removed outlier: 3.965A pdb=" N LYS X 100 " --> pdb=" O LYS X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 140 removed outlier: 3.640A pdb=" N ILE X 135 " --> pdb=" O ASP X 131 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA X 136 " --> pdb=" O ALA X 132 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN X 137 " --> pdb=" O LEU X 133 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE X 139 " --> pdb=" O ILE X 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 22 removed outlier: 3.656A pdb=" N LYS Y 17 " --> pdb=" O ARG Y 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR Y 21 " --> pdb=" O LYS Y 17 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA Y 22 " --> pdb=" O ALA Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 32 removed outlier: 3.707A pdb=" N ARG Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER Y 32 " --> pdb=" O ARG Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 removed outlier: 3.627A pdb=" N ALA Y 41 " --> pdb=" O LYS Y 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 105 removed outlier: 4.221A pdb=" N LEU Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 123 removed outlier: 3.569A pdb=" N GLY Y 123 " --> pdb=" O ILE Y 119 " (cutoff:3.500A) Processing helix chain 'y' and resid 12 through 17 removed outlier: 4.462A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 42 removed outlier: 3.815A pdb=" N SER y 36 " --> pdb=" O GLU y 32 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU y 39 " --> pdb=" O TYR y 35 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 removed outlier: 3.691A pdb=" N MET y 62 " --> pdb=" O ILE y 58 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR y 63 " --> pdb=" O ILE y 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 58 through 63' Processing helix chain 'y' and resid 77 through 89 removed outlier: 3.589A pdb=" N LEU y 84 " --> pdb=" O GLU y 80 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG y 85 " --> pdb=" O LEU y 81 " (cutoff:3.500A) Proline residue: y 89 - end of helix Processing helix chain 'y' and resid 103 through 108 removed outlier: 3.725A pdb=" N VAL y 107 " --> pdb=" O ALA y 103 " (cutoff:3.500A) Processing helix chain 'y' and resid 122 through 133 removed outlier: 3.559A pdb=" N GLU y 127 " --> pdb=" O ARG y 123 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER y 130 " --> pdb=" O GLU y 126 " (cutoff:3.500A) Processing helix chain 'y' and resid 147 through 152 removed outlier: 3.710A pdb=" N TYR y 151 " --> pdb=" O LEU y 147 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS y 152 " --> pdb=" O VAL y 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 147 through 152' Processing helix chain 'y' and resid 166 through 178 removed outlier: 3.600A pdb=" N GLU y 171 " --> pdb=" O VAL y 167 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU y 176 " --> pdb=" O GLU y 172 " (cutoff:3.500A) Processing helix chain 'y' and resid 192 through 197 removed outlier: 3.815A pdb=" N MET y 197 " --> pdb=" O VAL y 193 " (cutoff:3.500A) Processing helix chain 'y' and resid 211 through 223 removed outlier: 3.533A pdb=" N SER y 216 " --> pdb=" O ALA y 212 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL y 217 " --> pdb=" O PRO y 213 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE y 218 " --> pdb=" O GLU y 214 " (cutoff:3.500A) Processing helix chain 'y' and resid 230 through 238 removed outlier: 4.834A pdb=" N GLY y 234 " --> pdb=" O GLU y 230 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN y 235 " --> pdb=" O SER y 231 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG y 237 " --> pdb=" O SER y 233 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASP y 238 " --> pdb=" O GLY y 234 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 67 removed outlier: 4.408A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 3.770A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU Z 81 " --> pdb=" O TYR Z 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 76 through 81' Processing helix chain 'Z' and resid 92 through 97 removed outlier: 3.865A pdb=" N VAL Z 96 " --> pdb=" O PHE Z 92 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 92 through 97' Processing helix chain 'Z' and resid 98 through 103 removed outlier: 4.847A pdb=" N GLU Z 102 " --> pdb=" O THR Z 98 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLN Z 103 " --> pdb=" O GLU Z 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 98 through 103' Processing helix chain 'Z' and resid 104 through 125 removed outlier: 4.265A pdb=" N GLU Z 108 " --> pdb=" O PRO Z 104 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL Z 113 " --> pdb=" O GLU Z 109 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL Z 114 " --> pdb=" O ALA Z 110 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG Z 121 " --> pdb=" O ALA Z 117 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA Z 124 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY Z 125 " --> pdb=" O ARG Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 133 removed outlier: 3.905A pdb=" N PHE Z 131 " --> pdb=" O ASN Z 127 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LYS Z 133 " --> pdb=" O TRP Z 129 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 56 removed outlier: 3.585A pdb=" N LYS z 17 " --> pdb=" O ALA z 13 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG z 19 " --> pdb=" O SER z 15 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL z 21 " --> pdb=" O LYS z 17 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N PHE z 22 " --> pdb=" O ARG z 18 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN z 23 " --> pdb=" O ARG z 19 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS z 24 " --> pdb=" O GLY z 20 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL z 26 " --> pdb=" O PHE z 22 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN z 31 " --> pdb=" O ASP z 27 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER z 34 " --> pdb=" O GLU z 30 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS z 36 " --> pdb=" O ARG z 32 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU z 41 " --> pdb=" O LEU z 37 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU z 42 " --> pdb=" O LYS z 38 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU z 46 " --> pdb=" O LEU z 42 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP z 48 " --> pdb=" O GLN z 44 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS z 51 " --> pdb=" O GLU z 47 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 86 removed outlier: 3.767A pdb=" N LEU K 85 " --> pdb=" O VAL K 81 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 37 through 49 removed outlier: 3.571A pdb=" N ARG q 41 " --> pdb=" O ALA q 37 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLY q 49 " --> pdb=" O ARG q 45 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 20 removed outlier: 4.596A pdb=" N LYS o 15 " --> pdb=" O ASN o 11 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS o 17 " --> pdb=" O THR o 13 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG o 18 " --> pdb=" O ARG o 14 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASN o 19 " --> pdb=" O LYS o 15 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY o 20 " --> pdb=" O ALA o 16 " (cutoff:3.500A) Processing helix chain 'o' and resid 36 through 57 removed outlier: 3.591A pdb=" N ASN o 42 " --> pdb=" O LYS o 38 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N HIS o 45 " --> pdb=" O ARG o 41 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS o 48 " --> pdb=" O LYS o 44 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR o 50 " --> pdb=" O ALA o 46 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA o 51 " --> pdb=" O LEU o 47 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU o 54 " --> pdb=" O THR o 50 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA o 56 " --> pdb=" O LYS o 52 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'D' and resid 72 through 75 removed outlier: 3.631A pdb=" N VAL D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE D 64 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 145 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 53 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'J' and resid 11 through 14 removed outlier: 3.768A pdb=" N VAL J 130 " --> pdb=" O LYS J 16 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS J 16 " --> pdb=" O VAL J 130 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL J 23 " --> pdb=" O ILE J 65 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE J 65 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA J 66 " --> pdb=" O SER J 48 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'J' and resid 101 through 107 Processing sheet with id= 4, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.881A pdb=" N GLN A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 146 through 150 removed outlier: 4.337A pdb=" N ALA A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 58 through 64 Processing sheet with id= 7, first strand: chain 'B' and resid 45 through 51 removed outlier: 3.954A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 53 through 59 removed outlier: 5.124A pdb=" N ASN B 319 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 288 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE B 321 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 286 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 98 through 101 removed outlier: 3.760A pdb=" N GLY B 98 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL B 87 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 107 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 178 through 182 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'B' and resid 84 through 91 removed outlier: 6.281A pdb=" N LEU B 161 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 89 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG B 159 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY B 91 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL B 157 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'b' and resid 204 through 210 removed outlier: 3.738A pdb=" N TYR b 205 " --> pdb=" O ASP b 220 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR b 221 " --> pdb=" O ILE b 172 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY b 174 " --> pdb=" O THR b 221 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N CYS b 249 " --> pdb=" O THR b 169 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER b 282 " --> pdb=" O SER b 248 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL b 250 " --> pdb=" O SER b 282 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU b 316 " --> pdb=" O VAL b 283 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 224 through 229 removed outlier: 3.518A pdb=" N GLU C 226 " --> pdb=" O PRO C 205 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE C 247 " --> pdb=" O GLY C 204 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'c' and resid 22 through 25 removed outlier: 6.675A pdb=" N LYS c 22 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU c 41 " --> pdb=" O ILE c 92 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS c 66 " --> pdb=" O LYS c 40 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE c 42 " --> pdb=" O LYS c 66 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'd' and resid 48 through 51 removed outlier: 5.958A pdb=" N ASP d 48 " --> pdb=" O LEU d 89 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER d 91 " --> pdb=" O ASP d 48 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL d 8 " --> pdb=" O ARG d 77 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR d 9 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL d 107 " --> pdb=" O GLU d 11 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 49 through 54 removed outlier: 4.415A pdb=" N LYS E 50 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 42 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 62 through 66 Processing sheet with id= 18, first strand: chain 'e' and resid 71 through 76 Processing sheet with id= 19, first strand: chain 'F' and resid 133 through 138 removed outlier: 7.940A pdb=" N TYR F 133 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL F 87 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY F 137 " --> pdb=" O PHE F 85 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS F 82 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL F 119 " --> pdb=" O LYS F 82 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASN F 112 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'f' and resid 11 through 14 removed outlier: 6.797A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ARG f 82 " --> pdb=" O THR f 72 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR f 72 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LYS f 63 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS f 47 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'f' and resid 8 through 14 removed outlier: 4.028A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 176 through 181 removed outlier: 3.782A pdb=" N VAL G 151 " --> pdb=" O PRO G 176 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN G 155 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU G 150 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'g' and resid 19 through 24 removed outlier: 4.415A pdb=" N LYS g 19 " --> pdb=" O VAL g 35 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL g 35 " --> pdb=" O LYS g 19 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 5 through 12 removed outlier: 3.511A pdb=" N VAL H 57 " --> pdb=" O THR H 6 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN H 8 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN H 51 " --> pdb=" O VAL H 12 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'H' and resid 17 through 20 Processing sheet with id= 26, first strand: chain 'H' and resid 100 through 105 Processing sheet with id= 27, first strand: chain 'H' and resid 143 through 149 removed outlier: 7.890A pdb=" N GLY H 85 " --> pdb=" O ILE H 187 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'k' and resid 2 through 5 removed outlier: 4.615A pdb=" N VAL k 55 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N SER k 50 " --> pdb=" O GLY k 47 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THR k 22 " --> pdb=" O ARG k 46 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE k 27 " --> pdb=" O LEU k 78 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'm' and resid 283 through 286 removed outlier: 3.690A pdb=" N HIS m 254 " --> pdb=" O ASP m 223 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL m 225 " --> pdb=" O HIS m 254 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL m 224 " --> pdb=" O SER m 317 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY m 319 " --> pdb=" O VAL m 224 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS m 367 " --> pdb=" O PHE m 320 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY m 322 " --> pdb=" O CYS m 367 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASP m 366 " --> pdb=" O GLN m 354 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLN m 354 " --> pdb=" O ASP m 366 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'L' and resid 56 through 59 removed outlier: 3.575A pdb=" N GLY L 72 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'M' and resid 19 through 24 removed outlier: 4.466A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS M 31 " --> pdb=" O ILE M 23 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'M' and resid 36 through 39 removed outlier: 6.674A pdb=" N LYS M 43 " --> pdb=" O ILE M 39 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'p' and resid 46 through 49 removed outlier: 8.385A pdb=" N THR p 46 " --> pdb=" O SER p 58 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'N' and resid 35 through 39 removed outlier: 6.500A pdb=" N VAL N 35 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY N 58 " --> pdb=" O ASP N 136 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'N' and resid 117 through 121 removed outlier: 7.130A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'u' and resid 3 through 6 removed outlier: 4.095A pdb=" N TYR u 4 " --> pdb=" O CYS u 13 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SER u 11 " --> pdb=" O CYS u 6 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'u' and resid 18 through 22 removed outlier: 3.806A pdb=" N ILE u 19 " --> pdb=" O PHE u 31 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 39, first strand: chain 'P' and resid 16 through 20 Processing sheet with id= 40, first strand: chain 'P' and resid 124 through 132 removed outlier: 5.507A pdb=" N LYS P 124 " --> pdb=" O SER P 141 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER P 141 " --> pdb=" O LYS P 124 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG P 126 " --> pdb=" O TYR P 139 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR P 139 " --> pdb=" O ARG P 126 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ARG P 128 " --> pdb=" O ASN P 137 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ASN P 137 " --> pdb=" O ARG P 128 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TYR P 130 " --> pdb=" O ARG P 135 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ARG P 135 " --> pdb=" O TYR P 130 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA P 132 " --> pdb=" O HIS P 133 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'Q' and resid 79 through 83 Processing sheet with id= 42, first strand: chain 'R' and resid 21 through 24 removed outlier: 6.071A pdb=" N LYS R 21 " --> pdb=" O LYS R 53 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS R 53 " --> pdb=" O LYS R 21 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL R 51 " --> pdb=" O TRP R 23 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'r' and resid 148 through 151 Processing sheet with id= 44, first strand: chain 'r' and resid 190 through 195 removed outlier: 3.695A pdb=" N VAL r 191 " --> pdb=" O HIS r 186 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASN r 256 " --> pdb=" O THR r 246 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N THR r 219 " --> pdb=" O VAL r 245 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'S' and resid 24 through 31 removed outlier: 6.764A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU S 57 " --> pdb=" O ARG S 12 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'S' and resid 87 through 96 removed outlier: 3.570A pdb=" N TYR S 81 " --> pdb=" O HIS S 88 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER S 120 " --> pdb=" O ASP S 82 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'S' and resid 6 through 10 removed outlier: 4.691A pdb=" N GLU S 6 " --> pdb=" O ILE S 64 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE S 10 " --> pdb=" O SER S 60 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER S 60 " --> pdb=" O ILE S 10 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'S' and resid 74 through 78 removed outlier: 4.733A pdb=" N ASN S 74 " --> pdb=" O ILE S 129 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS S 125 " --> pdb=" O TRP S 78 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'U' and resid 53 through 58 removed outlier: 7.877A pdb=" N ALA U 53 " --> pdb=" O THR U 68 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASN U 101 " --> pdb=" O THR U 14 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR U 16 " --> pdb=" O ASN U 101 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLU U 102 " --> pdb=" O THR U 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG U 94 " --> pdb=" O ALA U 106 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'V' and resid 21 through 24 removed outlier: 4.576A pdb=" N ALA V 21 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE V 36 " --> pdb=" O ALA V 21 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'V' and resid 56 through 60 removed outlier: 4.415A pdb=" N ASP V 56 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASP V 97 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA V 82 " --> pdb=" O ASP V 97 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'W' and resid 63 through 67 removed outlier: 5.068A pdb=" N VAL W 99 " --> pdb=" O LEU W 45 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU W 43 " --> pdb=" O GLY W 101 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR W 105 " --> pdb=" O TYR W 39 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ARG W 38 " --> pdb=" O ASP W 222 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP W 222 " --> pdb=" O ARG W 38 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL W 40 " --> pdb=" O TYR W 220 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR W 220 " --> pdb=" O VAL W 40 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL W 42 " --> pdb=" O SER W 218 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'X' and resid 81 through 86 removed outlier: 3.796A pdb=" N LYS X 120 " --> pdb=" O VAL X 86 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS X 109 " --> pdb=" O ARG X 125 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'Y' and resid 72 through 75 removed outlier: 3.767A pdb=" N SER Y 72 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'Y' and resid 86 through 89 removed outlier: 4.663A pdb=" N ALA Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'y' and resid 2 through 5 Processing sheet with id= 57, first strand: chain 'y' and resid 23 through 27 Processing sheet with id= 58, first strand: chain 'y' and resid 69 through 73 Processing sheet with id= 59, first strand: chain 'y' and resid 114 through 117 Processing sheet with id= 60, first strand: chain 'Z' and resid 9 through 13 removed outlier: 4.903A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL Z 13 " --> pdb=" O LYS Z 21 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Z' and resid 42 through 45 Processing sheet with id= 62, first strand: chain 'q' and resid 23 through 28 removed outlier: 4.804A pdb=" N VAL q 68 " --> pdb=" O LEU q 85 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS q 74 " --> pdb=" O THR q 79 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N THR q 79 " --> pdb=" O CYS q 74 " (cutoff:3.500A) 1858 hydrogen bonds defined for protein. 5526 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1823 hydrogen bonds 3022 hydrogen bond angles 0 basepair planarities 768 basepair parallelities 1737 stacking parallelities Total time for adding SS restraints: 154.52 Time building geometry restraints manager: 49.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 25077 1.33 - 1.46: 57089 1.46 - 1.59: 54498 1.59 - 1.72: 5199 1.72 - 1.85: 222 Bond restraints: 142085 Sorted by residual: bond pdb=" CA ARG O 68 " pdb=" C ARG O 68 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.41e-02 5.03e+03 1.85e+01 bond pdb=" CA PHE B 130 " pdb=" C PHE B 130 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.40e-02 5.10e+03 1.41e+01 bond pdb=" N ALA W 177 " pdb=" CA ALA W 177 " ideal model delta sigma weight residual 1.457 1.502 -0.044 1.29e-02 6.01e+03 1.17e+01 bond pdb=" C ASP b 437 " pdb=" N GLY b 438 " ideal model delta sigma weight residual 1.333 1.303 0.031 9.60e-03 1.09e+04 1.03e+01 bond pdb=" N LEU Y 126 " pdb=" CA LEU Y 126 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.17e-02 7.31e+03 8.04e+00 ... (remaining 142080 not shown) Histogram of bond angle deviations from ideal: 97.27 - 105.13: 16013 105.13 - 113.00: 84125 113.00 - 120.87: 67627 120.87 - 128.74: 36840 128.74 - 136.60: 3469 Bond angle restraints: 208074 Sorted by residual: angle pdb=" N ASP m 377 " pdb=" CA ASP m 377 " pdb=" C ASP m 377 " ideal model delta sigma weight residual 110.80 131.21 -20.41 2.13e+00 2.20e-01 9.18e+01 angle pdb=" C ASN b 515 " pdb=" N LYS b 516 " pdb=" CA LYS b 516 " ideal model delta sigma weight residual 121.90 112.30 9.60 1.26e+00 6.30e-01 5.80e+01 angle pdb=" N ALA a 66 " pdb=" CA ALA a 66 " pdb=" C ALA a 66 " ideal model delta sigma weight residual 114.56 105.71 8.85 1.27e+00 6.20e-01 4.85e+01 angle pdb=" O3' U 1 979 " pdb=" C3' U 1 979 " pdb=" C2' U 1 979 " ideal model delta sigma weight residual 109.50 119.40 -9.90 1.50e+00 4.44e-01 4.35e+01 angle pdb=" N TYR i 28 " pdb=" CA TYR i 28 " pdb=" C TYR i 28 " ideal model delta sigma weight residual 114.31 105.84 8.47 1.29e+00 6.01e-01 4.31e+01 ... (remaining 208069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 81830 35.88 - 71.76: 7262 71.76 - 107.65: 847 107.65 - 143.53: 28 143.53 - 179.41: 62 Dihedral angle restraints: 90029 sinusoidal: 67518 harmonic: 22511 Sorted by residual: dihedral pdb=" CA LYS m 376 " pdb=" C LYS m 376 " pdb=" N ASP m 377 " pdb=" CA ASP m 377 " ideal model delta harmonic sigma weight residual -180.00 -58.19 -121.81 0 5.00e+00 4.00e-02 5.93e+02 dihedral pdb=" CA THR G 30 " pdb=" C THR G 30 " pdb=" N PRO G 31 " pdb=" CA PRO G 31 " ideal model delta harmonic sigma weight residual -180.00 -121.48 -58.52 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CA VAL T 154 " pdb=" C VAL T 154 " pdb=" N PRO T 155 " pdb=" CA PRO T 155 " ideal model delta harmonic sigma weight residual -180.00 -124.17 -55.83 0 5.00e+00 4.00e-02 1.25e+02 ... (remaining 90026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 24647 0.096 - 0.193: 1220 0.193 - 0.289: 82 0.289 - 0.385: 22 0.385 - 0.481: 5 Chirality restraints: 25976 Sorted by residual: chirality pdb=" C3' C 13350 " pdb=" C4' C 13350 " pdb=" O3' C 13350 " pdb=" C2' C 13350 " both_signs ideal model delta sigma weight residual False -2.74 -2.26 -0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" C3' A 1 715 " pdb=" C4' A 1 715 " pdb=" O3' A 1 715 " pdb=" C2' A 1 715 " both_signs ideal model delta sigma weight residual False -2.74 -2.31 -0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" CB THR L 76 " pdb=" CA THR L 76 " pdb=" OG1 THR L 76 " pdb=" CG2 THR L 76 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 25973 not shown) Planarity restraints: 14023 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA W 177 " 0.028 2.00e-02 2.50e+03 5.35e-02 2.87e+01 pdb=" C ALA W 177 " -0.093 2.00e-02 2.50e+03 pdb=" O ALA W 177 " 0.034 2.00e-02 2.50e+03 pdb=" N GLY W 178 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS W 176 " 0.022 2.00e-02 2.50e+03 4.35e-02 1.90e+01 pdb=" C LYS W 176 " -0.075 2.00e-02 2.50e+03 pdb=" O LYS W 176 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA W 177 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG b 369 " -0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C ARG b 369 " 0.074 2.00e-02 2.50e+03 pdb=" O ARG b 369 " -0.028 2.00e-02 2.50e+03 pdb=" N ASP b 370 " -0.025 2.00e-02 2.50e+03 ... (remaining 14020 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 12 2.02 - 2.74: 18208 2.74 - 3.46: 164974 3.46 - 4.18: 382332 4.18 - 4.90: 562735 Nonbonded interactions: 1128261 Sorted by model distance: nonbonded pdb=" O UNK K 120 " pdb=" N UNK K 122 " model vdw 1.297 2.520 nonbonded pdb=" O GLY K 102 " pdb=" N UNK K 141 " model vdw 1.299 2.520 nonbonded pdb=" CB UNK K 135 " pdb=" O2 C 11254 " model vdw 1.375 3.440 nonbonded pdb=" O ILE K 104 " pdb=" C UNK K 142 " model vdw 1.382 3.270 nonbonded pdb=" CB UNK K 17 " pdb=" NE2 GLN K 61 " model vdw 1.429 3.520 ... (remaining 1128256 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.21 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 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: 0.110 Extract box with map and model: 16.500 Check model and map are aligned: 1.470 Set scattering table: 0.880 Process input model: 408.270 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.310 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: 0.010 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 434.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 142085 Z= 0.450 Angle : 0.945 20.411 208074 Z= 0.513 Chirality : 0.048 0.481 25976 Planarity : 0.006 0.097 14023 Dihedral : 21.495 179.412 75439 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.32 % Favored : 92.35 % Rotamer: Outliers : 0.51 % Allowed : 4.95 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 1.04 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.07), residues: 7557 helix: -4.49 (0.04), residues: 2534 sheet: -1.47 (0.16), residues: 955 loop : -2.53 (0.08), residues: 4068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP M 99 HIS 0.023 0.002 HIS r 154 PHE 0.044 0.003 PHE N 180 TYR 0.044 0.003 TYR P 21 ARG 0.020 0.001 ARG b 639 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2057 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 2024 time to evaluate : 7.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 15 ARG cc_start: 0.8060 (ptp-110) cc_final: 0.7723 (mtt180) REVERT: D 63 GLN cc_start: 0.8842 (mt0) cc_final: 0.8418 (pm20) REVERT: D 79 TYR cc_start: 0.8633 (m-80) cc_final: 0.8409 (m-10) REVERT: D 126 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7692 (tm-30) REVERT: D 143 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8413 (ttmt) REVERT: D 148 ILE cc_start: 0.8642 (tt) cc_final: 0.8349 (tp) REVERT: D 151 GLN cc_start: 0.8447 (tp-100) cc_final: 0.7918 (mp10) REVERT: D 177 GLU cc_start: 0.8680 (pm20) cc_final: 0.8319 (pm20) REVERT: J 9 MET cc_start: 0.8047 (ttt) cc_final: 0.7431 (ttm) REVERT: J 17 LEU cc_start: 0.8531 (tp) cc_final: 0.8326 (mt) REVERT: J 41 SER cc_start: 0.6164 (p) cc_final: 0.5749 (p) REVERT: J 48 SER cc_start: 0.7578 (m) cc_final: 0.7294 (p) REVERT: J 68 HIS cc_start: 0.7926 (p-80) cc_final: 0.7520 (p90) REVERT: J 89 TYR cc_start: 0.7826 (m-80) cc_final: 0.7432 (m-10) REVERT: J 132 ASN cc_start: 0.8183 (p0) cc_final: 0.7234 (m110) REVERT: A 33 ASP cc_start: 0.8590 (p0) cc_final: 0.8176 (p0) REVERT: A 221 LYS cc_start: 0.7573 (mmpt) cc_final: 0.7158 (mttt) REVERT: a 70 LYS cc_start: 0.9334 (ttmt) cc_final: 0.9100 (ttmm) REVERT: B 7 GLU cc_start: 0.6793 (mp0) cc_final: 0.6364 (mp0) REVERT: B 319 ASN cc_start: 0.8765 (m-40) cc_final: 0.8495 (m-40) REVERT: b 16 ASP cc_start: 0.8072 (m-30) cc_final: 0.7843 (m-30) REVERT: b 55 GLU cc_start: 0.8598 (tp30) cc_final: 0.8078 (tp30) REVERT: b 136 MET cc_start: 0.8769 (mtt) cc_final: 0.8531 (mtp) REVERT: b 152 GLN cc_start: 0.8642 (mt0) cc_final: 0.8142 (tp40) REVERT: b 189 LYS cc_start: 0.7390 (ttmp) cc_final: 0.6943 (tttm) REVERT: b 265 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8148 (tm-30) REVERT: b 307 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7974 (tp30) REVERT: b 403 GLU cc_start: 0.8464 (tt0) cc_final: 0.8088 (tt0) REVERT: b 547 ASP cc_start: 0.6944 (m-30) cc_final: 0.6576 (p0) REVERT: b 632 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7903 (tptm) REVERT: C 159 ILE cc_start: 0.9356 (mt) cc_final: 0.8919 (mt) REVERT: C 221 ASN cc_start: 0.8526 (t160) cc_final: 0.8320 (t0) REVERT: c 27 TYR cc_start: 0.8693 (t80) cc_final: 0.8431 (t80) REVERT: c 40 LYS cc_start: 0.9064 (mptm) cc_final: 0.8822 (mmpt) REVERT: c 97 ASP cc_start: 0.7431 (t70) cc_final: 0.7140 (t0) REVERT: d 27 LYS cc_start: 0.9026 (mttt) cc_final: 0.8761 (mttp) REVERT: d 34 LYS cc_start: 0.8791 (mttm) cc_final: 0.8576 (mttp) REVERT: d 94 GLU cc_start: 0.8372 (pt0) cc_final: 0.8136 (pt0) REVERT: E 169 ASP cc_start: 0.8362 (m-30) cc_final: 0.8118 (m-30) REVERT: e 109 LEU cc_start: 0.9031 (mt) cc_final: 0.8810 (mp) REVERT: F 140 SER cc_start: 0.9268 (p) cc_final: 0.8909 (p) REVERT: F 243 MET cc_start: 0.9302 (mtp) cc_final: 0.9075 (mtm) REVERT: f 15 SER cc_start: 0.9386 (t) cc_final: 0.9018 (m) REVERT: f 65 ARG cc_start: 0.8502 (mtt180) cc_final: 0.8283 (mtt180) REVERT: f 70 LYS cc_start: 0.8884 (pttt) cc_final: 0.8645 (pttt) REVERT: G 83 ASP cc_start: 0.8398 (p0) cc_final: 0.7603 (p0) REVERT: G 124 ASP cc_start: 0.7180 (m-30) cc_final: 0.6039 (p0) REVERT: G 232 HIS cc_start: 0.7018 (p90) cc_final: 0.6748 (p-80) REVERT: g 97 GLU cc_start: 0.8635 (tp30) cc_final: 0.8169 (tp30) REVERT: g 108 GLN cc_start: 0.8717 (mt0) cc_final: 0.8306 (mm-40) REVERT: I 39 LEU cc_start: 0.8093 (pp) cc_final: 0.7676 (mp) REVERT: I 78 LYS cc_start: 0.8373 (mttt) cc_final: 0.8170 (mtpt) REVERT: I 106 GLN cc_start: 0.8651 (tp-100) cc_final: 0.7820 (tp40) REVERT: H 8 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8823 (mm110) REVERT: H 9 GLN cc_start: 0.8663 (mt0) cc_final: 0.8440 (mt0) REVERT: H 19 SER cc_start: 0.8923 (m) cc_final: 0.8628 (p) REVERT: H 52 LEU cc_start: 0.8831 (tt) cc_final: 0.8597 (tt) REVERT: H 86 TYR cc_start: 0.8845 (m-80) cc_final: 0.8629 (m-80) REVERT: H 171 ASP cc_start: 0.7711 (t70) cc_final: 0.7446 (t0) REVERT: h 32 LYS cc_start: 0.9242 (mtmt) cc_final: 0.8937 (mttm) REVERT: h 79 ASP cc_start: 0.8316 (p0) cc_final: 0.8103 (p0) REVERT: h 93 THR cc_start: 0.9288 (p) cc_final: 0.9085 (p) REVERT: i 42 SER cc_start: 0.9390 (t) cc_final: 0.9171 (p) REVERT: i 62 ARG cc_start: 0.8657 (mtt180) cc_final: 0.8340 (mtt-85) REVERT: i 88 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8594 (tm-30) REVERT: j 46 SER cc_start: 0.9282 (p) cc_final: 0.8924 (p) REVERT: j 54 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8580 (mttp) REVERT: j 76 ASN cc_start: 0.8847 (m-40) cc_final: 0.8629 (m-40) REVERT: m 8 LYS cc_start: 0.6579 (mmtt) cc_final: 0.6365 (mmmt) REVERT: m 263 ASP cc_start: 0.6960 (m-30) cc_final: 0.6231 (t0) REVERT: m 351 LYS cc_start: 0.5008 (tmmt) cc_final: 0.4543 (mmtt) REVERT: m 359 MET cc_start: 0.5863 (mmm) cc_final: 0.4888 (mmm) REVERT: m 360 LYS cc_start: 0.8488 (ttmp) cc_final: 0.8159 (pttm) REVERT: m 433 ARG cc_start: 0.7790 (mmt90) cc_final: 0.7575 (mmt90) REVERT: m 435 GLN cc_start: 0.6893 (mm-40) cc_final: 0.5717 (mm-40) REVERT: m 452 GLN cc_start: 0.7669 (tp40) cc_final: 0.7156 (tp40) REVERT: L 162 ASN cc_start: 0.7473 (p0) cc_final: 0.7227 (m-40) REVERT: M 6 ILE cc_start: 0.9286 (mm) cc_final: 0.9062 (mt) REVERT: p 7 LYS cc_start: 0.8893 (ptpt) cc_final: 0.8656 (ptpp) REVERT: p 37 TYR cc_start: 0.8567 (m-80) cc_final: 0.8200 (m-80) REVERT: N 46 ASP cc_start: 0.8415 (p0) cc_final: 0.8195 (p0) REVERT: u 140 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7702 (tm-30) REVERT: O 48 PHE cc_start: 0.7722 (t80) cc_final: 0.7373 (t80) REVERT: O 62 THR cc_start: 0.9218 (m) cc_final: 0.8987 (t) REVERT: R 76 SER cc_start: 0.9328 (m) cc_final: 0.8996 (p) REVERT: R 148 ASP cc_start: 0.8123 (m-30) cc_final: 0.6314 (m-30) REVERT: R 150 GLN cc_start: 0.8432 (tp-100) cc_final: 0.8045 (tm-30) REVERT: r 23 ARG cc_start: 0.8190 (mmt180) cc_final: 0.7933 (mtp-110) REVERT: r 41 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7271 (mmtt) REVERT: r 64 LYS cc_start: 0.8438 (mttm) cc_final: 0.8147 (pttt) REVERT: r 153 LYS cc_start: 0.7102 (mtmp) cc_final: 0.6870 (mmtt) REVERT: T 102 ARG cc_start: 0.8937 (tpt-90) cc_final: 0.6775 (ptt180) REVERT: T 122 GLN cc_start: 0.7067 (tm-30) cc_final: 0.6698 (tm-30) REVERT: U 88 GLN cc_start: 0.8621 (mp10) cc_final: 0.8409 (mt0) REVERT: V 33 ASN cc_start: 0.9166 (p0) cc_final: 0.8903 (p0) REVERT: V 71 LYS cc_start: 0.9101 (mtpm) cc_final: 0.8631 (mmmt) REVERT: W 5 LYS cc_start: 0.8943 (ptpp) cc_final: 0.8294 (tptt) REVERT: W 27 PHE cc_start: 0.7769 (t80) cc_final: 0.7321 (t80) REVERT: W 28 ASP cc_start: 0.8335 (m-30) cc_final: 0.7837 (t0) REVERT: W 124 TYR cc_start: 0.7325 (m-80) cc_final: 0.6778 (m-10) REVERT: W 148 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8184 (mm-40) REVERT: X 67 ILE cc_start: 0.9407 (mt) cc_final: 0.9144 (mt) REVERT: X 68 THR cc_start: 0.8689 (p) cc_final: 0.8409 (t) REVERT: X 71 THR cc_start: 0.9491 (t) cc_final: 0.9199 (p) REVERT: Y 86 THR cc_start: 0.9062 (p) cc_final: 0.8680 (t) REVERT: Y 95 VAL cc_start: 0.9350 (t) cc_final: 0.9038 (m) REVERT: y 122 ASP cc_start: 0.7924 (p0) cc_final: 0.7641 (p0) REVERT: y 131 ASP cc_start: 0.8737 (t0) cc_final: 0.8402 (t0) REVERT: y 209 ASP cc_start: 0.8590 (t0) cc_final: 0.8209 (t70) REVERT: Z 99 GLU cc_start: 0.8156 (pp20) cc_final: 0.7612 (tm-30) REVERT: q 53 GLN cc_start: 0.8486 (tp40) cc_final: 0.8129 (tp40) REVERT: q 69 VAL cc_start: 0.8845 (t) cc_final: 0.8437 (t) outliers start: 33 outliers final: 6 residues processed: 2045 average time/residue: 1.3649 time to fit residues: 4709.7727 Evaluate side-chains 1274 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1268 time to evaluate : 6.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 318 VAL Chi-restraints excluded: chain P residue 119 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 906 optimal weight: 10.0000 chunk 813 optimal weight: 10.0000 chunk 451 optimal weight: 7.9990 chunk 277 optimal weight: 9.9990 chunk 548 optimal weight: 0.7980 chunk 434 optimal weight: 7.9990 chunk 841 optimal weight: 20.0000 chunk 325 optimal weight: 4.9990 chunk 511 optimal weight: 0.9980 chunk 625 optimal weight: 4.9990 chunk 974 optimal weight: 30.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 GLN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 GLN J 68 HIS A 97 ASN ** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 217 GLN a 67 HIS a 74 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS B 279 ASN b 70 ASN b 177 ASN b 217 GLN b 272 HIS b 346 ASN ** b 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 415 ASN b 454 GLN b 470 ASN b 509 ASN b 549 GLN b 550 ASN b 579 ASN b 614 ASN C 48 GLN C 58 HIS ** C 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN C 196 ASN C 221 ASN d 17 HIS E 4 GLN E 28 GLN E 127 ASN E 167 ASN e 52 GLN F 61 ASN F 172 ASN F 244 ASN f 77 ASN ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN g 14 ASN I 36 ASN H 163 GLN h 59 ASN j 20 ASN k 57 ASN m 86 GLN m 146 GLN m 175 GLN m 227 HIS m 392 HIS ** m 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 411 HIS m 452 GLN L 114 GLN l 4 GLN l 20 ASN l 43 ASN l 50 ASN N 37 HIS ** u 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 45 ASN u 149 GLN P 97 ASN Q 10 HIS Q 15 HIS Q 45 ASN R 130 ASN r 3 GLN ** r 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 20 HIS r 68 HIS r 203 ASN r 244 GLN S 122 HIS ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 ASN U 87 ASN V 47 ASN V 81 GLN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 GLN W 232 ASN Y 110 HIS y 82 GLN y 162 HIS ** y 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 12 GLN o 43 HIS Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 142085 Z= 0.274 Angle : 0.669 14.327 208074 Z= 0.345 Chirality : 0.040 0.300 25976 Planarity : 0.005 0.089 14023 Dihedral : 22.929 179.856 60058 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.99 % Favored : 92.83 % Rotamer: Outliers : 3.28 % Allowed : 11.64 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.08), residues: 7557 helix: -2.51 (0.08), residues: 2669 sheet: -1.06 (0.16), residues: 956 loop : -2.17 (0.09), residues: 3932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 99 HIS 0.008 0.001 HIS y 118 PHE 0.023 0.002 PHE b 77 TYR 0.027 0.002 TYR P 139 ARG 0.014 0.001 ARG F 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1618 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1406 time to evaluate : 7.071 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: D 15 ARG cc_start: 0.8068 (ptp-110) cc_final: 0.7813 (mtt180) REVERT: D 79 TYR cc_start: 0.8603 (m-80) cc_final: 0.8355 (m-10) REVERT: D 126 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7600 (tm-30) REVERT: D 151 GLN cc_start: 0.8342 (tp-100) cc_final: 0.7844 (mp10) REVERT: D 177 GLU cc_start: 0.8510 (pm20) cc_final: 0.8184 (pm20) REVERT: J 9 MET cc_start: 0.7988 (ttt) cc_final: 0.7671 (ttm) REVERT: J 89 TYR cc_start: 0.7944 (m-80) cc_final: 0.7308 (m-10) REVERT: A 36 GLU cc_start: 0.8603 (tt0) cc_final: 0.8219 (tt0) REVERT: A 221 LYS cc_start: 0.7346 (mmpt) cc_final: 0.7030 (mttt) REVERT: a 70 LYS cc_start: 0.9324 (ttmt) cc_final: 0.9066 (ttmm) REVERT: B 7 GLU cc_start: 0.6550 (mp0) cc_final: 0.6020 (mp0) REVERT: B 25 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8566 (mt) REVERT: B 72 VAL cc_start: 0.9053 (t) cc_final: 0.8822 (m) REVERT: B 214 MET cc_start: 0.7933 (mmm) cc_final: 0.7728 (mtp) REVERT: B 345 ASN cc_start: 0.9043 (t0) cc_final: 0.8665 (t0) REVERT: b 52 TYR cc_start: 0.8921 (t80) cc_final: 0.8660 (t80) REVERT: b 136 MET cc_start: 0.8812 (mtt) cc_final: 0.8559 (mtp) REVERT: b 152 GLN cc_start: 0.8545 (mt0) cc_final: 0.8329 (tp40) REVERT: b 189 LYS cc_start: 0.7579 (ttmp) cc_final: 0.7250 (ttpt) REVERT: b 281 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6732 (mppt) REVERT: b 290 THR cc_start: 0.7952 (p) cc_final: 0.7638 (p) REVERT: b 445 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8481 (pt) REVERT: b 547 ASP cc_start: 0.7069 (m-30) cc_final: 0.6647 (p0) REVERT: b 632 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7799 (tptm) REVERT: C 221 ASN cc_start: 0.8815 (t0) cc_final: 0.7985 (t0) REVERT: c 69 TYR cc_start: 0.8449 (m-80) cc_final: 0.7857 (m-80) REVERT: c 97 ASP cc_start: 0.7550 (t70) cc_final: 0.7138 (t0) REVERT: c 100 ILE cc_start: 0.8776 (mp) cc_final: 0.8560 (mp) REVERT: E 169 ASP cc_start: 0.8330 (m-30) cc_final: 0.8087 (m-30) REVERT: e 109 LEU cc_start: 0.9081 (mt) cc_final: 0.8833 (mp) REVERT: F 140 SER cc_start: 0.8902 (p) cc_final: 0.8509 (p) REVERT: f 14 LEU cc_start: 0.9552 (mt) cc_final: 0.9317 (mt) REVERT: f 15 SER cc_start: 0.9366 (t) cc_final: 0.8966 (m) REVERT: f 70 LYS cc_start: 0.8804 (pttt) cc_final: 0.8560 (pttt) REVERT: f 92 LYS cc_start: 0.9129 (pttt) cc_final: 0.8860 (pttm) REVERT: G 116 VAL cc_start: 0.8613 (t) cc_final: 0.8402 (p) REVERT: G 123 GLN cc_start: 0.8535 (mt0) cc_final: 0.8328 (mt0) REVERT: G 124 ASP cc_start: 0.7044 (m-30) cc_final: 0.6442 (p0) REVERT: G 173 MET cc_start: 0.8709 (mmt) cc_final: 0.8229 (mmt) REVERT: g 29 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8817 (pt) REVERT: I 30 SER cc_start: 0.7643 (p) cc_final: 0.7432 (p) REVERT: H 19 SER cc_start: 0.8838 (m) cc_final: 0.8561 (t) REVERT: H 42 ASP cc_start: 0.8214 (t0) cc_final: 0.7994 (t0) REVERT: H 52 LEU cc_start: 0.8921 (tt) cc_final: 0.8644 (tp) REVERT: H 137 SER cc_start: 0.8506 (t) cc_final: 0.8254 (p) REVERT: H 171 ASP cc_start: 0.7753 (t70) cc_final: 0.7240 (t0) REVERT: h 32 LYS cc_start: 0.9289 (mtmt) cc_final: 0.9048 (mttm) REVERT: h 96 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7782 (mt-10) REVERT: h 102 GLU cc_start: 0.7418 (tp30) cc_final: 0.7187 (tp30) REVERT: i 42 SER cc_start: 0.9462 (t) cc_final: 0.9181 (p) REVERT: i 62 ARG cc_start: 0.8723 (mtt180) cc_final: 0.8295 (mtt180) REVERT: i 70 ARG cc_start: 0.7942 (mtt-85) cc_final: 0.7730 (mtm-85) REVERT: i 92 ASN cc_start: 0.8395 (m-40) cc_final: 0.8176 (t0) REVERT: j 46 SER cc_start: 0.9217 (p) cc_final: 0.8941 (p) REVERT: j 54 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8458 (mttp) REVERT: m 8 LYS cc_start: 0.6627 (mmtt) cc_final: 0.6335 (mmmt) REVERT: m 166 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7750 (tp30) REVERT: m 263 ASP cc_start: 0.7202 (m-30) cc_final: 0.6319 (t0) REVERT: m 359 MET cc_start: 0.6240 (mmm) cc_final: 0.5172 (mmm) REVERT: m 360 LYS cc_start: 0.8624 (ttmp) cc_final: 0.8294 (pttm) REVERT: m 423 ASP cc_start: 0.6787 (t0) cc_final: 0.6579 (t0) REVERT: L 161 ASP cc_start: 0.8285 (t0) cc_final: 0.8020 (t0) REVERT: L 162 ASN cc_start: 0.7642 (p0) cc_final: 0.7118 (m-40) REVERT: N 46 ASP cc_start: 0.8605 (p0) cc_final: 0.8325 (p0) REVERT: u 104 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7729 (tp30) REVERT: u 132 GLU cc_start: 0.8467 (mp0) cc_final: 0.8146 (mp0) REVERT: O 48 PHE cc_start: 0.7651 (t80) cc_final: 0.7117 (t80) REVERT: P 131 ARG cc_start: 0.8599 (mtt-85) cc_final: 0.7622 (mmp-170) REVERT: P 139 TYR cc_start: 0.9182 (t80) cc_final: 0.8882 (t80) REVERT: R 76 SER cc_start: 0.9385 (m) cc_final: 0.9066 (p) REVERT: R 144 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7511 (tm-30) REVERT: R 148 ASP cc_start: 0.7587 (m-30) cc_final: 0.6424 (m-30) REVERT: R 150 GLN cc_start: 0.8378 (tp-100) cc_final: 0.7988 (tm-30) REVERT: r 7 ILE cc_start: 0.7331 (tt) cc_final: 0.7004 (tp) REVERT: r 24 LYS cc_start: 0.8529 (ttmt) cc_final: 0.7989 (tppt) REVERT: r 41 LYS cc_start: 0.7851 (ttmt) cc_final: 0.7325 (mmtt) REVERT: r 64 LYS cc_start: 0.8591 (mttm) cc_final: 0.8295 (pttt) REVERT: r 153 LYS cc_start: 0.7111 (mtmp) cc_final: 0.6839 (mmtt) REVERT: r 168 MET cc_start: 0.8248 (mmp) cc_final: 0.8042 (mmm) REVERT: S 87 THR cc_start: 0.8616 (t) cc_final: 0.8289 (t) REVERT: T 102 ARG cc_start: 0.8738 (tpt-90) cc_final: 0.7011 (mtm180) REVERT: T 122 GLN cc_start: 0.6994 (tm-30) cc_final: 0.6564 (tm-30) REVERT: T 156 TYR cc_start: 0.5690 (t80) cc_final: 0.5398 (t80) REVERT: U 88 GLN cc_start: 0.8527 (mp10) cc_final: 0.8286 (mt0) REVERT: W 5 LYS cc_start: 0.8967 (ptpp) cc_final: 0.8409 (tptt) REVERT: W 149 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7687 (tp) REVERT: W 165 MET cc_start: 0.7127 (mtt) cc_final: 0.6879 (mtm) REVERT: X 67 ILE cc_start: 0.9427 (mt) cc_final: 0.9134 (mt) REVERT: X 71 THR cc_start: 0.9403 (t) cc_final: 0.9111 (p) REVERT: Y 76 LEU cc_start: 0.9641 (OUTLIER) cc_final: 0.9201 (tp) REVERT: Y 86 THR cc_start: 0.8992 (p) cc_final: 0.8721 (t) REVERT: y 131 ASP cc_start: 0.8698 (t0) cc_final: 0.8454 (t0) REVERT: y 145 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8511 (t0) REVERT: y 209 ASP cc_start: 0.8604 (t0) cc_final: 0.8120 (t70) REVERT: Z 106 GLN cc_start: 0.8290 (tm-30) cc_final: 0.8079 (tm-30) REVERT: Z 109 GLU cc_start: 0.8649 (mp0) cc_final: 0.8226 (mp0) REVERT: q 27 GLN cc_start: 0.7669 (tp40) cc_final: 0.7401 (tp40) REVERT: q 38 GLN cc_start: 0.9185 (tp40) cc_final: 0.8965 (tp40) REVERT: q 53 GLN cc_start: 0.8263 (tp40) cc_final: 0.8004 (tp40) REVERT: q 97 LYS cc_start: 0.7072 (tppp) cc_final: 0.5808 (pttp) REVERT: o 52 LYS cc_start: 0.9179 (tptt) cc_final: 0.8920 (tptp) outliers start: 212 outliers final: 134 residues processed: 1522 average time/residue: 1.1542 time to fit residues: 3065.0816 Evaluate side-chains 1352 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1211 time to evaluate : 6.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 224 ILE Chi-restraints excluded: chain b residue 281 LYS Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 371 ASP Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 445 LEU Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain c residue 14 LEU Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain d residue 24 SER Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain e residue 3 SER Chi-restraints excluded: chain e residue 9 ILE Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 22 VAL Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 41 MET Chi-restraints excluded: chain m residue 221 SER Chi-restraints excluded: chain m residue 224 VAL Chi-restraints excluded: chain m residue 226 ILE Chi-restraints excluded: chain m residue 235 LEU Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 318 VAL Chi-restraints excluded: chain m residue 350 THR Chi-restraints excluded: chain m residue 453 ILE Chi-restraints excluded: chain m residue 462 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 91 CYS Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain u residue 4 TYR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 11 SER Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain T residue 109 VAL Chi-restraints excluded: chain T residue 110 LYS Chi-restraints excluded: chain T residue 139 ARG Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain W residue 17 LYS Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 174 LYS Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 145 ASN Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 102 GLU Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain q residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 541 optimal weight: 7.9990 chunk 302 optimal weight: 0.8980 chunk 810 optimal weight: 10.0000 chunk 663 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 976 optimal weight: 20.0000 chunk 1054 optimal weight: 10.0000 chunk 869 optimal weight: 10.0000 chunk 968 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 783 optimal weight: 10.0000 overall best weight: 5.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 GLN ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN ** b 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 515 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN c 12 GLN E 28 GLN f 106 ASN G 138 HIS k 76 ASN ** m 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 50 ASN ** u 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 137 ASN ** r 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN V 47 ASN V 81 GLN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 83 HIS y 162 HIS y 178 GLN Z 36 HIS ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 142085 Z= 0.339 Angle : 0.660 13.748 208074 Z= 0.339 Chirality : 0.040 0.289 25976 Planarity : 0.005 0.090 14023 Dihedral : 22.787 179.884 60058 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.77 % Favored : 92.10 % Rotamer: Outliers : 4.54 % Allowed : 13.58 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.11 % 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: -2.44 (0.09), residues: 7557 helix: -1.35 (0.09), residues: 2645 sheet: -0.98 (0.16), residues: 990 loop : -1.96 (0.09), residues: 3922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP F 203 HIS 0.009 0.001 HIS y 118 PHE 0.024 0.002 PHE g 7 TYR 0.032 0.002 TYR G 134 ARG 0.011 0.001 ARG u 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1535 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1242 time to evaluate : 8.478 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: D 15 ARG cc_start: 0.8121 (ptp-110) cc_final: 0.7860 (mtt180) REVERT: D 79 TYR cc_start: 0.8658 (m-80) cc_final: 0.8369 (m-10) REVERT: D 151 GLN cc_start: 0.8351 (tp-100) cc_final: 0.7751 (mp10) REVERT: D 177 GLU cc_start: 0.8533 (pm20) cc_final: 0.8261 (pm20) REVERT: J 89 TYR cc_start: 0.7915 (m-80) cc_final: 0.7273 (m-10) REVERT: J 128 TYR cc_start: 0.6261 (OUTLIER) cc_final: 0.3355 (m-80) REVERT: J 157 GLU cc_start: 0.6871 (pp20) cc_final: 0.6241 (pm20) REVERT: a 70 LYS cc_start: 0.9326 (ttmt) cc_final: 0.9088 (ttmm) REVERT: B 7 GLU cc_start: 0.6734 (mp0) cc_final: 0.6189 (mp0) REVERT: B 53 MET cc_start: 0.9299 (OUTLIER) cc_final: 0.8967 (mtm) REVERT: B 173 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: B 345 ASN cc_start: 0.9027 (t0) cc_final: 0.8676 (t0) REVERT: B 380 MET cc_start: 0.8770 (mmm) cc_final: 0.8345 (mtt) REVERT: b 136 MET cc_start: 0.8850 (mtt) cc_final: 0.8592 (mtp) REVERT: b 152 GLN cc_start: 0.8579 (mt0) cc_final: 0.8333 (tp40) REVERT: b 175 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.7523 (m-10) REVERT: b 189 LYS cc_start: 0.7759 (ttmp) cc_final: 0.7242 (ttpt) REVERT: b 254 MET cc_start: 0.8029 (tmm) cc_final: 0.7766 (tmm) REVERT: b 330 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8484 (mt-10) REVERT: b 403 GLU cc_start: 0.8613 (tt0) cc_final: 0.8005 (tm-30) REVERT: b 547 ASP cc_start: 0.7285 (m-30) cc_final: 0.6783 (p0) REVERT: b 608 MET cc_start: 0.6735 (mmm) cc_final: 0.6311 (mmt) REVERT: C 54 GLU cc_start: 0.7871 (pt0) cc_final: 0.7663 (pt0) REVERT: C 141 ARG cc_start: 0.8605 (mmt90) cc_final: 0.8393 (mpt-90) REVERT: c 47 ASN cc_start: 0.8880 (p0) cc_final: 0.8635 (p0) REVERT: c 69 TYR cc_start: 0.8567 (m-80) cc_final: 0.7937 (m-80) REVERT: c 97 ASP cc_start: 0.7600 (t70) cc_final: 0.7117 (t0) REVERT: E 169 ASP cc_start: 0.8404 (m-30) cc_final: 0.8093 (m-30) REVERT: e 8 LYS cc_start: 0.8477 (tppt) cc_final: 0.8266 (tppp) REVERT: e 100 ILE cc_start: 0.9333 (mm) cc_final: 0.9133 (mm) REVERT: F 140 SER cc_start: 0.9066 (p) cc_final: 0.8708 (p) REVERT: f 15 SER cc_start: 0.9374 (t) cc_final: 0.8985 (m) REVERT: f 16 TYR cc_start: 0.8972 (m-10) cc_final: 0.8743 (m-80) REVERT: f 70 LYS cc_start: 0.8743 (pttt) cc_final: 0.8518 (pttt) REVERT: g 29 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8801 (pt) REVERT: H 1 MET cc_start: 0.8656 (ptm) cc_final: 0.8326 (ptt) REVERT: H 19 SER cc_start: 0.8867 (m) cc_final: 0.8473 (t) REVERT: H 171 ASP cc_start: 0.7707 (t70) cc_final: 0.7151 (t0) REVERT: h 32 LYS cc_start: 0.9327 (mtmt) cc_final: 0.9047 (mttm) REVERT: i 42 SER cc_start: 0.9540 (t) cc_final: 0.9209 (p) REVERT: i 62 ARG cc_start: 0.8750 (mtt180) cc_final: 0.8333 (mtt180) REVERT: j 46 SER cc_start: 0.9167 (p) cc_final: 0.8879 (p) REVERT: j 54 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8562 (mttp) REVERT: m 8 LYS cc_start: 0.6474 (mmtt) cc_final: 0.6190 (mmmt) REVERT: m 166 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7668 (tp30) REVERT: m 263 ASP cc_start: 0.7132 (m-30) cc_final: 0.6317 (t0) REVERT: m 280 GLU cc_start: 0.5541 (pt0) cc_final: 0.5318 (tp30) REVERT: m 325 ASN cc_start: 0.6559 (t0) cc_final: 0.6170 (m-40) REVERT: m 359 MET cc_start: 0.5838 (mmm) cc_final: 0.4839 (mmm) REVERT: m 360 LYS cc_start: 0.8642 (ttmp) cc_final: 0.8300 (pttm) REVERT: m 452 GLN cc_start: 0.7481 (tp-100) cc_final: 0.7104 (tp40) REVERT: L 34 SER cc_start: 0.9384 (p) cc_final: 0.9064 (t) REVERT: L 161 ASP cc_start: 0.8254 (t0) cc_final: 0.7897 (t0) REVERT: L 162 ASN cc_start: 0.7927 (p0) cc_final: 0.7445 (m-40) REVERT: p 25 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7569 (mm110) REVERT: N 46 ASP cc_start: 0.8641 (p0) cc_final: 0.8358 (p0) REVERT: u 104 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7966 (tm-30) REVERT: u 132 GLU cc_start: 0.8564 (mp0) cc_final: 0.8208 (mp0) REVERT: O 48 PHE cc_start: 0.7643 (t80) cc_final: 0.7116 (t80) REVERT: O 62 THR cc_start: 0.9204 (m) cc_final: 0.8981 (p) REVERT: P 131 ARG cc_start: 0.8579 (mtt-85) cc_final: 0.7591 (mmp-170) REVERT: P 139 TYR cc_start: 0.9243 (t80) cc_final: 0.8988 (t80) REVERT: R 36 ASN cc_start: 0.8904 (p0) cc_final: 0.8651 (p0) REVERT: R 68 GLN cc_start: 0.8686 (tp40) cc_final: 0.8205 (tp40) REVERT: R 76 SER cc_start: 0.9359 (m) cc_final: 0.9085 (p) REVERT: R 150 GLN cc_start: 0.8367 (tp-100) cc_final: 0.7994 (tm-30) REVERT: r 7 ILE cc_start: 0.7624 (tt) cc_final: 0.7348 (tp) REVERT: r 24 LYS cc_start: 0.8547 (ttmt) cc_final: 0.8001 (tppt) REVERT: r 31 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7385 (mm-30) REVERT: r 41 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7343 (mmtt) REVERT: r 64 LYS cc_start: 0.8584 (mttm) cc_final: 0.8298 (pttt) REVERT: r 131 GLU cc_start: 0.4896 (pt0) cc_final: 0.4428 (pt0) REVERT: S 17 GLU cc_start: 0.8252 (tp30) cc_final: 0.8000 (tp30) REVERT: S 82 ASP cc_start: 0.8355 (m-30) cc_final: 0.8109 (m-30) REVERT: S 87 THR cc_start: 0.8625 (t) cc_final: 0.8249 (t) REVERT: S 124 LEU cc_start: 0.9127 (mp) cc_final: 0.8925 (mp) REVERT: T 102 ARG cc_start: 0.8708 (tpt-90) cc_final: 0.7023 (mtm180) REVERT: T 139 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8422 (ptt90) REVERT: T 156 TYR cc_start: 0.5906 (t80) cc_final: 0.5449 (t80) REVERT: U 75 TYR cc_start: 0.8885 (t80) cc_final: 0.8663 (t80) REVERT: U 88 GLN cc_start: 0.8650 (mp10) cc_final: 0.8410 (mt0) REVERT: V 40 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8462 (mtpp) REVERT: W 5 LYS cc_start: 0.8925 (ptpp) cc_final: 0.8441 (tptt) REVERT: W 199 GLN cc_start: 0.8143 (mt0) cc_final: 0.7943 (pt0) REVERT: X 67 ILE cc_start: 0.9333 (mt) cc_final: 0.9055 (mt) REVERT: X 71 THR cc_start: 0.9461 (t) cc_final: 0.9205 (m) REVERT: Y 76 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9203 (tp) REVERT: y 232 ILE cc_start: 0.5826 (OUTLIER) cc_final: 0.5622 (pt) REVERT: Z 49 TYR cc_start: 0.9006 (m-80) cc_final: 0.8797 (m-80) REVERT: Z 99 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7785 (tm-30) REVERT: Z 106 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7545 (tm-30) REVERT: Z 109 GLU cc_start: 0.8658 (mp0) cc_final: 0.8139 (mp0) REVERT: q 97 LYS cc_start: 0.7175 (tppp) cc_final: 0.5876 (pttp) REVERT: o 52 LYS cc_start: 0.9254 (tptt) cc_final: 0.8990 (tptp) outliers start: 293 outliers final: 207 residues processed: 1421 average time/residue: 1.1956 time to fit residues: 2970.1784 Evaluate side-chains 1369 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1153 time to evaluate : 7.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 102 ILE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 175 TYR Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 224 ILE Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 342 SER Chi-restraints excluded: chain b residue 371 ASP Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 531 MET Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain c residue 14 LEU Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 38 ILE Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 67 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain f residue 19 SER Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 105 SER Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 20 ILE Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 46 ASP Chi-restraints excluded: chain g residue 55 SER Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 22 VAL Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 139 ASP Chi-restraints excluded: chain m residue 221 SER Chi-restraints excluded: chain m residue 224 VAL Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 318 VAL Chi-restraints excluded: chain m residue 350 THR Chi-restraints excluded: chain m residue 418 ILE Chi-restraints excluded: chain m residue 453 ILE Chi-restraints excluded: chain m residue 462 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 21 SER Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain u residue 4 TYR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 11 SER Chi-restraints excluded: chain u residue 27 LYS Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain R residue 30 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 136 VAL Chi-restraints excluded: chain r residue 237 VAL Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain T residue 139 ARG Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain W residue 17 LYS Chi-restraints excluded: chain W residue 160 SER Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 202 ILE Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 59 VAL Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 190 SER Chi-restraints excluded: chain y residue 232 ILE Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 89 VAL Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain q residue 6 LYS Chi-restraints excluded: chain q residue 54 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 964 optimal weight: 10.0000 chunk 733 optimal weight: 10.0000 chunk 506 optimal weight: 10.0000 chunk 108 optimal weight: 0.0670 chunk 465 optimal weight: 6.9990 chunk 655 optimal weight: 5.9990 chunk 979 optimal weight: 10.0000 chunk 1037 optimal weight: 10.0000 chunk 511 optimal weight: 1.9990 chunk 928 optimal weight: 10.0000 chunk 279 optimal weight: 7.9990 overall best weight: 4.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 109 HIS ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN c 12 GLN ** d 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN F 80 GLN f 106 ASN L 28 GLN l 50 ASN M 11 ASN N 138 GLN u 5 GLN u 37 HIS P 137 ASN r 3 GLN ** r 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN V 24 ASN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 42 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 142085 Z= 0.293 Angle : 0.621 13.624 208074 Z= 0.320 Chirality : 0.038 0.277 25976 Planarity : 0.005 0.091 14023 Dihedral : 22.711 179.290 60058 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.69 % Favored : 92.19 % Rotamer: Outliers : 4.46 % Allowed : 15.48 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -2.01 (0.09), residues: 7557 helix: -0.77 (0.10), residues: 2645 sheet: -0.90 (0.16), residues: 987 loop : -1.85 (0.09), residues: 3925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP F 203 HIS 0.009 0.001 HIS A 19 PHE 0.020 0.002 PHE F 229 TYR 0.031 0.002 TYR G 134 ARG 0.007 0.001 ARG Z 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1492 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1204 time to evaluate : 6.967 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: D 15 ARG cc_start: 0.8117 (ptp-110) cc_final: 0.7853 (mtt180) REVERT: D 79 TYR cc_start: 0.8600 (m-80) cc_final: 0.8332 (m-10) REVERT: D 151 GLN cc_start: 0.8364 (tp-100) cc_final: 0.7718 (mp10) REVERT: D 177 GLU cc_start: 0.8560 (pm20) cc_final: 0.8279 (pm20) REVERT: J 89 TYR cc_start: 0.7896 (m-80) cc_final: 0.7196 (m-10) REVERT: J 109 HIS cc_start: 0.7266 (p90) cc_final: 0.6988 (p-80) REVERT: J 128 TYR cc_start: 0.6619 (OUTLIER) cc_final: 0.3471 (m-80) REVERT: a 70 LYS cc_start: 0.9331 (ttmt) cc_final: 0.9090 (ttmm) REVERT: B 7 GLU cc_start: 0.6466 (mp0) cc_final: 0.5870 (mp0) REVERT: B 173 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: B 214 MET cc_start: 0.7854 (mtp) cc_final: 0.7649 (mtp) REVERT: B 345 ASN cc_start: 0.9030 (t0) cc_final: 0.8651 (t0) REVERT: B 380 MET cc_start: 0.8697 (mmm) cc_final: 0.8338 (mtt) REVERT: b 62 GLU cc_start: 0.8608 (tp30) cc_final: 0.8170 (tp30) REVERT: b 136 MET cc_start: 0.8921 (mtt) cc_final: 0.8719 (mtp) REVERT: b 175 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7636 (m-10) REVERT: b 254 MET cc_start: 0.7983 (tmm) cc_final: 0.7682 (tmm) REVERT: b 330 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8464 (mt-10) REVERT: b 403 GLU cc_start: 0.8616 (tt0) cc_final: 0.8073 (tm-30) REVERT: b 521 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.7971 (mtm-85) REVERT: b 547 ASP cc_start: 0.7346 (m-30) cc_final: 0.6836 (p0) REVERT: C 194 TYR cc_start: 0.9362 (OUTLIER) cc_final: 0.8535 (p90) REVERT: E 169 ASP cc_start: 0.8334 (m-30) cc_final: 0.8003 (m-30) REVERT: e 8 LYS cc_start: 0.8531 (tppt) cc_final: 0.8296 (tppp) REVERT: e 91 THR cc_start: 0.9658 (OUTLIER) cc_final: 0.9401 (p) REVERT: F 140 SER cc_start: 0.9019 (p) cc_final: 0.8680 (p) REVERT: f 15 SER cc_start: 0.9373 (t) cc_final: 0.8992 (m) REVERT: f 16 TYR cc_start: 0.8984 (m-10) cc_final: 0.8765 (m-80) REVERT: f 70 LYS cc_start: 0.8805 (pttt) cc_final: 0.8603 (pttt) REVERT: G 124 ASP cc_start: 0.7273 (m-30) cc_final: 0.6693 (p0) REVERT: G 173 MET cc_start: 0.8818 (mmt) cc_final: 0.8164 (mmt) REVERT: g 29 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8818 (pt) REVERT: H 1 MET cc_start: 0.8663 (ptm) cc_final: 0.8305 (ptt) REVERT: H 9 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8380 (mm-40) REVERT: H 19 SER cc_start: 0.8858 (m) cc_final: 0.8474 (t) REVERT: H 171 ASP cc_start: 0.7710 (t70) cc_final: 0.7152 (t0) REVERT: h 32 LYS cc_start: 0.9356 (mtmt) cc_final: 0.9062 (mttm) REVERT: h 64 GLU cc_start: 0.8835 (tp30) cc_final: 0.8335 (mm-30) REVERT: i 42 SER cc_start: 0.9542 (t) cc_final: 0.9168 (p) REVERT: j 46 SER cc_start: 0.9162 (p) cc_final: 0.8903 (p) REVERT: j 54 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8541 (mttp) REVERT: k 12 LEU cc_start: 0.8936 (mm) cc_final: 0.8628 (mm) REVERT: m 13 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7581 (ttt180) REVERT: m 166 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7465 (tp30) REVERT: m 263 ASP cc_start: 0.7077 (m-30) cc_final: 0.6230 (t0) REVERT: m 325 ASN cc_start: 0.6646 (t0) cc_final: 0.6141 (m-40) REVERT: m 359 MET cc_start: 0.5813 (mmm) cc_final: 0.4731 (mmm) REVERT: m 360 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8337 (pttm) REVERT: m 452 GLN cc_start: 0.7568 (tp-100) cc_final: 0.7236 (tp40) REVERT: L 10 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8445 (pp) REVERT: L 161 ASP cc_start: 0.8234 (t0) cc_final: 0.7899 (t0) REVERT: L 162 ASN cc_start: 0.7980 (OUTLIER) cc_final: 0.7500 (m-40) REVERT: N 46 ASP cc_start: 0.8591 (p0) cc_final: 0.8333 (p0) REVERT: u 28 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: u 104 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7967 (tm-30) REVERT: u 132 GLU cc_start: 0.8653 (mp0) cc_final: 0.8277 (mp0) REVERT: O 62 THR cc_start: 0.9197 (m) cc_final: 0.8917 (p) REVERT: O 84 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8744 (tt) REVERT: R 36 ASN cc_start: 0.8924 (p0) cc_final: 0.8647 (p0) REVERT: R 68 GLN cc_start: 0.8631 (tp40) cc_final: 0.8119 (tp40) REVERT: R 76 SER cc_start: 0.9356 (m) cc_final: 0.9080 (p) REVERT: R 150 GLN cc_start: 0.8411 (tp-100) cc_final: 0.8003 (tm-30) REVERT: r 16 LYS cc_start: 0.7827 (mmtt) cc_final: 0.7553 (mmtt) REVERT: r 24 LYS cc_start: 0.8532 (ttmt) cc_final: 0.7993 (tppt) REVERT: r 41 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7340 (mmtt) REVERT: r 64 LYS cc_start: 0.8557 (mttm) cc_final: 0.8274 (pttt) REVERT: r 175 SER cc_start: 0.7369 (t) cc_final: 0.7055 (p) REVERT: S 14 LEU cc_start: 0.8044 (mt) cc_final: 0.7828 (mt) REVERT: S 82 ASP cc_start: 0.8372 (m-30) cc_final: 0.8100 (m-30) REVERT: S 87 THR cc_start: 0.8590 (t) cc_final: 0.8238 (t) REVERT: T 102 ARG cc_start: 0.8772 (tpt-90) cc_final: 0.6894 (mtm180) REVERT: T 108 ARG cc_start: 0.8710 (ttp80) cc_final: 0.8382 (ttt-90) REVERT: T 139 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8392 (ptt90) REVERT: U 75 TYR cc_start: 0.8844 (t80) cc_final: 0.8565 (t80) REVERT: V 40 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8462 (mtpp) REVERT: W 5 LYS cc_start: 0.8967 (ptpp) cc_final: 0.8477 (tptt) REVERT: W 148 GLN cc_start: 0.8301 (mm-40) cc_final: 0.8060 (mp10) REVERT: W 149 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7865 (tp) REVERT: W 165 MET cc_start: 0.6684 (ttt) cc_final: 0.6267 (tpp) REVERT: X 67 ILE cc_start: 0.9340 (mt) cc_final: 0.9039 (mt) REVERT: X 71 THR cc_start: 0.9455 (t) cc_final: 0.9194 (m) REVERT: Y 76 LEU cc_start: 0.9617 (OUTLIER) cc_final: 0.9178 (tp) REVERT: Z 49 TYR cc_start: 0.9001 (m-80) cc_final: 0.8798 (m-80) REVERT: Z 106 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8136 (tm-30) REVERT: Z 109 GLU cc_start: 0.8642 (mp0) cc_final: 0.8121 (mp0) REVERT: q 71 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6963 (ptm160) REVERT: q 97 LYS cc_start: 0.7091 (tppp) cc_final: 0.5851 (pttp) REVERT: o 52 LYS cc_start: 0.9238 (tptt) cc_final: 0.8991 (tptp) outliers start: 288 outliers final: 193 residues processed: 1380 average time/residue: 1.1441 time to fit residues: 2757.1079 Evaluate side-chains 1346 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1136 time to evaluate : 6.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 102 ILE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 175 TYR Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 371 ASP Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 436 LEU Chi-restraints excluded: chain b residue 531 MET Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain c residue 14 LEU Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain d residue 24 SER Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain e residue 3 SER Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain e residue 38 ILE Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 67 SER Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 113 LYS Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 77 GLN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 13 ARG Chi-restraints excluded: chain m residue 139 ASP Chi-restraints excluded: chain m residue 221 SER Chi-restraints excluded: chain m residue 224 VAL Chi-restraints excluded: chain m residue 235 LEU Chi-restraints excluded: chain m residue 242 VAL Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 318 VAL Chi-restraints excluded: chain m residue 360 LYS Chi-restraints excluded: chain m residue 462 ILE Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain M residue 116 GLU Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain u residue 4 TYR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 11 SER Chi-restraints excluded: chain u residue 28 GLU Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 136 VAL Chi-restraints excluded: chain r residue 237 VAL Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain T residue 139 ARG Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 185 THR Chi-restraints excluded: chain y residue 190 SER Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 89 VAL Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain q residue 71 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 863 optimal weight: 10.0000 chunk 588 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 772 optimal weight: 10.0000 chunk 427 optimal weight: 0.3980 chunk 885 optimal weight: 8.9990 chunk 716 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 529 optimal weight: 2.9990 chunk 930 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 GLN ** b 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN c 12 GLN F 61 ASN f 106 ASN H 157 ASN H 169 ASN ** j 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 50 ASN N 138 GLN ** r 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 33 HIS T 146 ASN V 24 ASN V 81 GLN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 11 ASN ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 31 GLN ** z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 142085 Z= 0.342 Angle : 0.646 13.287 208074 Z= 0.331 Chirality : 0.039 0.271 25976 Planarity : 0.005 0.092 14023 Dihedral : 22.682 179.664 60058 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.26 % Favored : 91.62 % Rotamer: Outliers : 5.29 % Allowed : 15.91 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -1.82 (0.09), residues: 7557 helix: -0.49 (0.10), residues: 2646 sheet: -0.91 (0.16), residues: 974 loop : -1.81 (0.09), residues: 3937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 203 HIS 0.010 0.001 HIS A 19 PHE 0.025 0.002 PHE Z 136 TYR 0.035 0.002 TYR P 139 ARG 0.009 0.001 ARG A 149 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1512 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 1170 time to evaluate : 7.070 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: D 15 ARG cc_start: 0.8083 (ptp-110) cc_final: 0.7840 (mtt180) REVERT: D 79 TYR cc_start: 0.8596 (m-80) cc_final: 0.8300 (m-10) REVERT: D 151 GLN cc_start: 0.8424 (tp-100) cc_final: 0.7766 (mp10) REVERT: D 177 GLU cc_start: 0.8617 (pm20) cc_final: 0.8290 (pm20) REVERT: D 264 GLN cc_start: 0.5282 (OUTLIER) cc_final: 0.4575 (pt0) REVERT: J 89 TYR cc_start: 0.7949 (m-80) cc_final: 0.7242 (m-10) REVERT: J 109 HIS cc_start: 0.7245 (p90) cc_final: 0.6959 (p-80) REVERT: J 128 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.3211 (m-80) REVERT: J 131 MET cc_start: 0.7848 (mmm) cc_final: 0.7411 (mmm) REVERT: J 132 ASN cc_start: 0.7483 (p0) cc_final: 0.7033 (m110) REVERT: a 70 LYS cc_start: 0.9356 (ttmt) cc_final: 0.9099 (ttmm) REVERT: B 7 GLU cc_start: 0.6558 (mp0) cc_final: 0.5926 (mp0) REVERT: B 67 PHE cc_start: 0.8590 (m-10) cc_final: 0.8319 (m-10) REVERT: B 173 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: B 345 ASN cc_start: 0.9044 (t0) cc_final: 0.8675 (t0) REVERT: B 380 MET cc_start: 0.8769 (mmm) cc_final: 0.8456 (mtt) REVERT: b 62 GLU cc_start: 0.8832 (tp30) cc_final: 0.8622 (tp30) REVERT: b 66 LYS cc_start: 0.8339 (mptt) cc_final: 0.8136 (mptt) REVERT: b 136 MET cc_start: 0.8914 (mtt) cc_final: 0.8709 (mtp) REVERT: b 175 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7782 (m-10) REVERT: b 189 LYS cc_start: 0.7834 (ttmp) cc_final: 0.7222 (tttm) REVERT: b 232 MET cc_start: 0.4742 (tpp) cc_final: 0.4416 (mmp) REVERT: b 254 MET cc_start: 0.8113 (tmm) cc_final: 0.7815 (tmm) REVERT: b 330 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8512 (mt-10) REVERT: b 403 GLU cc_start: 0.8602 (tt0) cc_final: 0.8123 (tm-30) REVERT: b 521 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.8001 (mtm-85) REVERT: b 547 ASP cc_start: 0.7394 (m-30) cc_final: 0.6894 (p0) REVERT: b 598 MET cc_start: 0.6120 (mmp) cc_final: 0.5844 (mtm) REVERT: C 179 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9118 (tp) REVERT: C 194 TYR cc_start: 0.9405 (OUTLIER) cc_final: 0.8660 (p90) REVERT: c 58 TYR cc_start: 0.8433 (t80) cc_final: 0.7902 (t80) REVERT: c 69 TYR cc_start: 0.8549 (m-80) cc_final: 0.8250 (m-80) REVERT: E 169 ASP cc_start: 0.8375 (m-30) cc_final: 0.8037 (m-30) REVERT: F 203 TRP cc_start: 0.8820 (t-100) cc_final: 0.8534 (t60) REVERT: f 15 SER cc_start: 0.9383 (t) cc_final: 0.9006 (m) REVERT: f 70 LYS cc_start: 0.8739 (pttt) cc_final: 0.8522 (pttt) REVERT: f 92 LYS cc_start: 0.9076 (pttm) cc_final: 0.8765 (tttt) REVERT: G 124 ASP cc_start: 0.7349 (m-30) cc_final: 0.6675 (p0) REVERT: G 173 MET cc_start: 0.8836 (mmt) cc_final: 0.8130 (mmt) REVERT: g 29 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8820 (pt) REVERT: H 1 MET cc_start: 0.8728 (ptm) cc_final: 0.8440 (ptt) REVERT: H 19 SER cc_start: 0.8906 (m) cc_final: 0.8457 (t) REVERT: H 171 ASP cc_start: 0.7704 (t70) cc_final: 0.7139 (t0) REVERT: h 32 LYS cc_start: 0.9398 (mtmt) cc_final: 0.9077 (mttm) REVERT: h 64 GLU cc_start: 0.8900 (tp30) cc_final: 0.8425 (mm-30) REVERT: i 42 SER cc_start: 0.9567 (t) cc_final: 0.9194 (p) REVERT: j 46 SER cc_start: 0.9191 (p) cc_final: 0.8917 (p) REVERT: j 54 LYS cc_start: 0.8845 (mtmt) cc_final: 0.8573 (mttp) REVERT: k 12 LEU cc_start: 0.9025 (mm) cc_final: 0.8652 (mm) REVERT: m 166 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7476 (tp30) REVERT: m 263 ASP cc_start: 0.7071 (m-30) cc_final: 0.6228 (t0) REVERT: m 325 ASN cc_start: 0.6687 (t0) cc_final: 0.6185 (m-40) REVERT: m 359 MET cc_start: 0.5729 (mmm) cc_final: 0.4758 (mmm) REVERT: m 360 LYS cc_start: 0.8676 (ttmp) cc_final: 0.8318 (pttm) REVERT: m 452 GLN cc_start: 0.7508 (tp-100) cc_final: 0.7192 (tp40) REVERT: L 34 SER cc_start: 0.9415 (p) cc_final: 0.9097 (t) REVERT: L 120 GLN cc_start: 0.9016 (mt0) cc_final: 0.8795 (mt0) REVERT: L 128 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.6179 (mtt90) REVERT: L 161 ASP cc_start: 0.8180 (t0) cc_final: 0.7857 (t0) REVERT: L 162 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7604 (m-40) REVERT: N 46 ASP cc_start: 0.8608 (p0) cc_final: 0.8361 (p0) REVERT: N 108 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8383 (ttp80) REVERT: u 28 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: u 104 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7921 (tm-30) REVERT: u 132 GLU cc_start: 0.8667 (mp0) cc_final: 0.8310 (mp0) REVERT: O 62 THR cc_start: 0.9183 (m) cc_final: 0.8915 (p) REVERT: O 84 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8743 (tt) REVERT: R 36 ASN cc_start: 0.8949 (p0) cc_final: 0.8659 (p0) REVERT: R 68 GLN cc_start: 0.8604 (tp40) cc_final: 0.8116 (tp40) REVERT: R 76 SER cc_start: 0.9388 (m) cc_final: 0.9101 (p) REVERT: R 86 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: R 99 LEU cc_start: 0.9523 (OUTLIER) cc_final: 0.9237 (tm) REVERT: R 150 GLN cc_start: 0.8429 (tp-100) cc_final: 0.8005 (tm-30) REVERT: r 16 LYS cc_start: 0.7822 (mmtt) cc_final: 0.7486 (mmtt) REVERT: r 24 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8028 (tppt) REVERT: r 31 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7266 (mm-30) REVERT: r 41 LYS cc_start: 0.7942 (ttmt) cc_final: 0.7351 (mmtt) REVERT: r 64 LYS cc_start: 0.8530 (mttm) cc_final: 0.8265 (pttt) REVERT: r 175 SER cc_start: 0.7353 (t) cc_final: 0.7047 (p) REVERT: S 14 LEU cc_start: 0.8065 (mt) cc_final: 0.7693 (mt) REVERT: S 82 ASP cc_start: 0.8376 (m-30) cc_final: 0.8100 (m-30) REVERT: S 87 THR cc_start: 0.8541 (t) cc_final: 0.8195 (t) REVERT: T 102 ARG cc_start: 0.8853 (tpt-90) cc_final: 0.7028 (mtm180) REVERT: T 104 GLU cc_start: 0.8552 (tp30) cc_final: 0.8316 (tt0) REVERT: T 108 ARG cc_start: 0.8776 (ttp80) cc_final: 0.8490 (ttt-90) REVERT: T 139 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8403 (ptt90) REVERT: U 75 TYR cc_start: 0.8878 (t80) cc_final: 0.8502 (t80) REVERT: W 5 LYS cc_start: 0.8979 (ptpp) cc_final: 0.8485 (tptt) REVERT: W 148 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7878 (mp10) REVERT: W 149 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7791 (tp) REVERT: X 67 ILE cc_start: 0.9335 (mt) cc_final: 0.9044 (mt) REVERT: X 71 THR cc_start: 0.9436 (t) cc_final: 0.9180 (m) REVERT: Y 32 SER cc_start: 0.9127 (t) cc_final: 0.8822 (p) REVERT: Y 76 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9184 (tp) REVERT: Z 49 TYR cc_start: 0.9043 (m-80) cc_final: 0.8826 (m-80) REVERT: Z 106 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8096 (tm-30) REVERT: Z 109 GLU cc_start: 0.8671 (mp0) cc_final: 0.8077 (mp0) REVERT: q 71 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7103 (ptm160) REVERT: q 97 LYS cc_start: 0.7011 (tppp) cc_final: 0.5958 (pttp) REVERT: o 52 LYS cc_start: 0.9273 (tptt) cc_final: 0.9017 (tptp) outliers start: 342 outliers final: 254 residues processed: 1380 average time/residue: 1.1292 time to fit residues: 2723.8490 Evaluate side-chains 1397 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1125 time to evaluate : 6.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 69 ILE Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 64 GLN Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain a residue 102 ILE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 175 TYR Chi-restraints excluded: chain b residue 224 ILE Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 342 SER Chi-restraints excluded: chain b residue 371 ASP Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 436 LEU Chi-restraints excluded: chain b residue 440 ASN Chi-restraints excluded: chain b residue 484 SER Chi-restraints excluded: chain b residue 531 MET Chi-restraints excluded: chain b residue 593 VAL Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain c residue 14 LEU Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 76 GLU Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain d residue 24 SER Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 48 ASP Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain e residue 3 SER Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain e residue 38 ILE Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 67 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain e residue 113 LYS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain g residue 107 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain H residue 5 GLN Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 3 VAL Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain i residue 64 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 56 ILE Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 25 LYS Chi-restraints excluded: chain m residue 41 MET Chi-restraints excluded: chain m residue 139 ASP Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 221 SER Chi-restraints excluded: chain m residue 224 VAL Chi-restraints excluded: chain m residue 226 ILE Chi-restraints excluded: chain m residue 235 LEU Chi-restraints excluded: chain m residue 242 VAL Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 318 VAL Chi-restraints excluded: chain m residue 350 THR Chi-restraints excluded: chain m residue 418 ILE Chi-restraints excluded: chain m residue 462 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 128 ARG Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain M residue 116 GLU Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain u residue 4 TYR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 11 SER Chi-restraints excluded: chain u residue 28 GLU Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 110 ASN Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 67 THR Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 136 VAL Chi-restraints excluded: chain r residue 237 VAL Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain T residue 139 ARG Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 199 GLN Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 8 VAL Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 185 THR Chi-restraints excluded: chain y residue 190 SER Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 89 VAL Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain q residue 6 LYS Chi-restraints excluded: chain q residue 71 ARG Chi-restraints excluded: chain o residue 13 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 348 optimal weight: 5.9990 chunk 934 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 608 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 chunk 1038 optimal weight: 10.0000 chunk 861 optimal weight: 10.0000 chunk 480 optimal weight: 6.9990 chunk 86 optimal weight: 0.3980 chunk 343 optimal weight: 0.0970 chunk 545 optimal weight: 9.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 20 ASN ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS b 413 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN c 12 GLN ** d 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN f 88 ASN f 106 ASN g 3 GLN I 99 ASN H 49 ASN H 157 ASN ** j 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 50 ASN N 86 ASN ** r 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 244 GLN ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN V 24 ASN V 81 GLN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS ** W 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 31 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 142085 Z= 0.180 Angle : 0.560 13.491 208074 Z= 0.289 Chirality : 0.035 0.263 25976 Planarity : 0.004 0.089 14023 Dihedral : 22.606 179.896 60058 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.07 % Favored : 92.85 % Rotamer: Outliers : 3.81 % Allowed : 17.99 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -1.43 (0.09), residues: 7557 helix: -0.04 (0.10), residues: 2626 sheet: -0.78 (0.16), residues: 975 loop : -1.64 (0.09), residues: 3956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 203 HIS 0.008 0.001 HIS A 19 PHE 0.019 0.001 PHE Z 136 TYR 0.033 0.001 TYR P 139 ARG 0.006 0.000 ARG b 599 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1493 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1247 time to evaluate : 6.306 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: D 15 ARG cc_start: 0.8089 (ptp-110) cc_final: 0.7883 (mtt180) REVERT: D 79 TYR cc_start: 0.8484 (m-80) cc_final: 0.8243 (m-10) REVERT: D 151 GLN cc_start: 0.8364 (tp-100) cc_final: 0.7747 (mp10) REVERT: D 177 GLU cc_start: 0.8646 (pm20) cc_final: 0.8336 (pm20) REVERT: D 264 GLN cc_start: 0.5192 (OUTLIER) cc_final: 0.4516 (pt0) REVERT: J 89 TYR cc_start: 0.7826 (m-80) cc_final: 0.7135 (m-10) REVERT: J 109 HIS cc_start: 0.7143 (p90) cc_final: 0.6896 (p-80) REVERT: J 125 MET cc_start: 0.7510 (mpp) cc_final: 0.7157 (mpp) REVERT: J 128 TYR cc_start: 0.6634 (OUTLIER) cc_final: 0.3354 (m-80) REVERT: J 132 ASN cc_start: 0.7448 (p0) cc_final: 0.7165 (m110) REVERT: A 36 GLU cc_start: 0.8737 (tt0) cc_final: 0.8280 (tt0) REVERT: A 221 LYS cc_start: 0.7604 (mmpt) cc_final: 0.7068 (mttt) REVERT: a 70 LYS cc_start: 0.9343 (ttmt) cc_final: 0.9077 (ttmm) REVERT: a 135 GLU cc_start: 0.8223 (pp20) cc_final: 0.7763 (tm-30) REVERT: B 7 GLU cc_start: 0.6712 (mp0) cc_final: 0.6119 (mp0) REVERT: B 345 ASN cc_start: 0.8995 (t0) cc_final: 0.8639 (t0) REVERT: b 62 GLU cc_start: 0.8873 (tp30) cc_final: 0.8499 (tp30) REVERT: b 152 GLN cc_start: 0.8106 (tp40) cc_final: 0.7896 (mm-40) REVERT: b 175 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7813 (m-10) REVERT: b 189 LYS cc_start: 0.7721 (ttmp) cc_final: 0.7232 (ttpp) REVERT: b 254 MET cc_start: 0.8147 (tmm) cc_final: 0.7863 (tmm) REVERT: b 330 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8560 (mt-10) REVERT: b 347 LYS cc_start: 0.5802 (OUTLIER) cc_final: 0.5512 (mptt) REVERT: b 468 PHE cc_start: 0.8915 (t80) cc_final: 0.8671 (t80) REVERT: b 521 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7879 (mtm-85) REVERT: b 547 ASP cc_start: 0.7336 (m-30) cc_final: 0.6865 (p0) REVERT: b 598 MET cc_start: 0.6266 (mmp) cc_final: 0.5780 (mtm) REVERT: C 179 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9111 (tp) REVERT: C 194 TYR cc_start: 0.9296 (OUTLIER) cc_final: 0.8432 (p90) REVERT: c 69 TYR cc_start: 0.8452 (m-80) cc_final: 0.8235 (m-80) REVERT: E 137 ASP cc_start: 0.8064 (m-30) cc_final: 0.7851 (m-30) REVERT: E 169 ASP cc_start: 0.8258 (m-30) cc_final: 0.7913 (m-30) REVERT: F 64 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8535 (mp10) REVERT: f 14 LEU cc_start: 0.9526 (mt) cc_final: 0.9216 (mt) REVERT: f 15 SER cc_start: 0.9341 (t) cc_final: 0.8963 (m) REVERT: f 70 LYS cc_start: 0.8799 (pttt) cc_final: 0.8584 (pttt) REVERT: f 92 LYS cc_start: 0.9030 (pttm) cc_final: 0.8639 (tttt) REVERT: G 124 ASP cc_start: 0.7332 (m-30) cc_final: 0.6677 (p0) REVERT: g 29 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8793 (pt) REVERT: H 1 MET cc_start: 0.8667 (ptm) cc_final: 0.8360 (ptt) REVERT: H 19 SER cc_start: 0.8811 (m) cc_final: 0.8450 (t) REVERT: H 51 GLN cc_start: 0.8412 (mp10) cc_final: 0.8087 (mp-120) REVERT: H 171 ASP cc_start: 0.7608 (t70) cc_final: 0.7075 (t0) REVERT: h 32 LYS cc_start: 0.9353 (mtmt) cc_final: 0.9062 (mttm) REVERT: h 64 GLU cc_start: 0.8881 (tp30) cc_final: 0.8422 (mm-30) REVERT: i 42 SER cc_start: 0.9545 (t) cc_final: 0.9140 (p) REVERT: j 54 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8511 (mttp) REVERT: k 12 LEU cc_start: 0.9045 (mm) cc_final: 0.8675 (mm) REVERT: m 139 ASP cc_start: 0.6601 (OUTLIER) cc_final: 0.5864 (m-30) REVERT: m 166 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7449 (tp30) REVERT: m 263 ASP cc_start: 0.6979 (m-30) cc_final: 0.6146 (t0) REVERT: m 325 ASN cc_start: 0.6728 (t0) cc_final: 0.6187 (m-40) REVERT: m 359 MET cc_start: 0.5632 (mmm) cc_final: 0.4641 (mmm) REVERT: m 360 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8159 (pttm) REVERT: m 452 GLN cc_start: 0.7459 (tp-100) cc_final: 0.7173 (tp40) REVERT: L 128 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.6103 (mtt90) REVERT: L 161 ASP cc_start: 0.8157 (t0) cc_final: 0.7837 (t0) REVERT: L 162 ASN cc_start: 0.8046 (p0) cc_final: 0.7581 (m-40) REVERT: N 46 ASP cc_start: 0.8585 (p0) cc_final: 0.8295 (p0) REVERT: u 28 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: u 104 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7907 (tm-30) REVERT: u 132 GLU cc_start: 0.8774 (mp0) cc_final: 0.8437 (mp0) REVERT: O 62 THR cc_start: 0.9202 (m) cc_final: 0.8980 (p) REVERT: O 84 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8732 (tt) REVERT: O 85 ARG cc_start: 0.8820 (ttp80) cc_final: 0.8486 (ttp80) REVERT: O 106 GLU cc_start: 0.8229 (mp0) cc_final: 0.7846 (mp0) REVERT: R 36 ASN cc_start: 0.8930 (p0) cc_final: 0.8660 (p0) REVERT: R 76 SER cc_start: 0.9379 (m) cc_final: 0.9103 (p) REVERT: R 86 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: R 99 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9228 (tm) REVERT: R 150 GLN cc_start: 0.8366 (tp-100) cc_final: 0.7988 (tm-30) REVERT: r 24 LYS cc_start: 0.8524 (ttmt) cc_final: 0.8019 (tppt) REVERT: r 41 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7420 (mmtt) REVERT: r 139 THR cc_start: 0.7923 (p) cc_final: 0.7686 (t) REVERT: r 175 SER cc_start: 0.7348 (t) cc_final: 0.7091 (p) REVERT: S 14 LEU cc_start: 0.8152 (mt) cc_final: 0.7775 (mt) REVERT: S 82 ASP cc_start: 0.8353 (m-30) cc_final: 0.8080 (m-30) REVERT: S 87 THR cc_start: 0.8212 (t) cc_final: 0.7745 (t) REVERT: T 102 ARG cc_start: 0.8692 (tpt-90) cc_final: 0.6945 (mtm180) REVERT: T 107 GLU cc_start: 0.7083 (pp20) cc_final: 0.6775 (pp20) REVERT: T 108 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8335 (ttt-90) REVERT: T 139 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8327 (ptt90) REVERT: U 33 TYR cc_start: 0.7996 (t80) cc_final: 0.7716 (t80) REVERT: U 75 TYR cc_start: 0.8745 (t80) cc_final: 0.8465 (t80) REVERT: W 5 LYS cc_start: 0.8977 (ptpp) cc_final: 0.8486 (tptt) REVERT: W 149 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7791 (tp) REVERT: X 67 ILE cc_start: 0.9317 (mt) cc_final: 0.8998 (mt) REVERT: X 71 THR cc_start: 0.9416 (t) cc_final: 0.9171 (m) REVERT: Y 32 SER cc_start: 0.9129 (t) cc_final: 0.8744 (p) REVERT: Y 76 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.9131 (tp) REVERT: y 209 ASP cc_start: 0.8688 (t0) cc_final: 0.8200 (t70) REVERT: Z 30 ASP cc_start: 0.7429 (t70) cc_final: 0.6606 (t0) REVERT: Z 31 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7362 (mm-30) REVERT: Z 47 GLU cc_start: 0.7706 (tt0) cc_final: 0.7486 (pt0) REVERT: Z 49 TYR cc_start: 0.8989 (m-80) cc_final: 0.8772 (m-80) REVERT: Z 65 ARG cc_start: 0.8849 (ttm-80) cc_final: 0.8542 (ttm170) REVERT: Z 105 SER cc_start: 0.9240 (p) cc_final: 0.8955 (p) REVERT: Z 106 GLN cc_start: 0.8244 (tm-30) cc_final: 0.8019 (tm-30) REVERT: Z 109 GLU cc_start: 0.8582 (mp0) cc_final: 0.8066 (mp0) REVERT: q 97 LYS cc_start: 0.6955 (tppp) cc_final: 0.5868 (pttp) REVERT: o 52 LYS cc_start: 0.9268 (tptt) cc_final: 0.9025 (tptp) outliers start: 246 outliers final: 171 residues processed: 1403 average time/residue: 1.2147 time to fit residues: 2972.3481 Evaluate side-chains 1338 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1149 time to evaluate : 6.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain a residue 102 ILE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 175 TYR Chi-restraints excluded: chain b residue 237 MET Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 347 LYS Chi-restraints excluded: chain b residue 371 ASP Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 436 LEU Chi-restraints excluded: chain b residue 531 MET Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain c residue 14 LEU Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain d residue 24 SER Chi-restraints excluded: chain d residue 48 ASP Chi-restraints excluded: chain d residue 51 LEU Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain e residue 3 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 67 SER Chi-restraints excluded: chain e residue 113 LYS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain f residue 89 LEU Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 77 GLN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 107 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain i residue 3 VAL Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain m residue 139 ASP Chi-restraints excluded: chain m residue 224 VAL Chi-restraints excluded: chain m residue 226 ILE Chi-restraints excluded: chain m residue 235 LEU Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 318 VAL Chi-restraints excluded: chain m residue 350 THR Chi-restraints excluded: chain m residue 360 LYS Chi-restraints excluded: chain m residue 462 ILE Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 128 ARG Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 38 ASP Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain u residue 4 TYR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 11 SER Chi-restraints excluded: chain u residue 28 GLU Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 136 VAL Chi-restraints excluded: chain r residue 155 THR Chi-restraints excluded: chain r residue 237 VAL Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain T residue 139 ARG Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain W residue 92 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 224 ASP Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 190 SER Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain K residue 82 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 1000 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 591 optimal weight: 30.0000 chunk 758 optimal weight: 20.0000 chunk 587 optimal weight: 8.9990 chunk 873 optimal weight: 10.0000 chunk 579 optimal weight: 7.9990 chunk 1034 optimal weight: 10.0000 chunk 647 optimal weight: 20.0000 chunk 630 optimal weight: 3.9990 chunk 477 optimal weight: 0.0370 overall best weight: 6.2068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN C 5 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN c 12 GLN E 167 ASN F 104 GLN f 17 GLN f 42 GLN f 106 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 HIS g 3 GLN I 53 HIS I 99 ASN H 157 ASN ** j 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 50 ASN Q 58 ASN R 7 GLN ** r 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 244 GLN ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 146 ASN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS W 199 GLN y 170 GLN ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 31 GLN ** z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 142085 Z= 0.386 Angle : 0.663 13.332 208074 Z= 0.337 Chirality : 0.040 0.268 25976 Planarity : 0.005 0.093 14023 Dihedral : 22.598 179.358 60058 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.51 % Favored : 91.39 % Rotamer: Outliers : 4.71 % Allowed : 17.89 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -1.54 (0.09), residues: 7557 helix: -0.11 (0.10), residues: 2637 sheet: -0.97 (0.16), residues: 993 loop : -1.69 (0.09), residues: 3927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 203 HIS 0.011 0.001 HIS m 395 PHE 0.021 0.002 PHE F 229 TYR 0.037 0.002 TYR P 139 ARG 0.009 0.001 ARG V 70 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1448 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1144 time to evaluate : 7.032 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: D 15 ARG cc_start: 0.8234 (ptp-110) cc_final: 0.7957 (mtt180) REVERT: D 79 TYR cc_start: 0.8534 (m-80) cc_final: 0.8269 (m-10) REVERT: D 151 GLN cc_start: 0.8451 (tp-100) cc_final: 0.7967 (mp10) REVERT: D 177 GLU cc_start: 0.8690 (pm20) cc_final: 0.8355 (pm20) REVERT: D 264 GLN cc_start: 0.5297 (OUTLIER) cc_final: 0.4592 (pt0) REVERT: J 89 TYR cc_start: 0.7919 (m-80) cc_final: 0.7190 (m-10) REVERT: J 109 HIS cc_start: 0.6909 (p90) cc_final: 0.6582 (p-80) REVERT: J 128 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.3002 (m-80) REVERT: J 131 MET cc_start: 0.7660 (mmm) cc_final: 0.7452 (mmm) REVERT: J 132 ASN cc_start: 0.7505 (p0) cc_final: 0.7109 (m110) REVERT: a 70 LYS cc_start: 0.9356 (ttmt) cc_final: 0.9109 (ttmm) REVERT: a 136 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: B 7 GLU cc_start: 0.6682 (mp0) cc_final: 0.6024 (mp0) REVERT: B 67 PHE cc_start: 0.8657 (m-10) cc_final: 0.8407 (m-10) REVERT: B 173 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.6654 (tm-30) REVERT: B 345 ASN cc_start: 0.9050 (t0) cc_final: 0.8683 (t0) REVERT: b 62 GLU cc_start: 0.8844 (tp30) cc_final: 0.8454 (tp30) REVERT: b 189 LYS cc_start: 0.7846 (ttmp) cc_final: 0.7171 (tttm) REVERT: b 254 MET cc_start: 0.8007 (tmm) cc_final: 0.7730 (tmm) REVERT: b 330 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8508 (mt-10) REVERT: b 347 LYS cc_start: 0.5796 (OUTLIER) cc_final: 0.5478 (mptt) REVERT: b 442 TYR cc_start: 0.8393 (m-10) cc_final: 0.8083 (m-80) REVERT: b 547 ASP cc_start: 0.7397 (m-30) cc_final: 0.6907 (p0) REVERT: b 598 MET cc_start: 0.6441 (mmp) cc_final: 0.5871 (mtm) REVERT: b 604 ARG cc_start: 0.6037 (ptp-110) cc_final: 0.5396 (ptt180) REVERT: C 179 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9120 (tp) REVERT: C 194 TYR cc_start: 0.9413 (OUTLIER) cc_final: 0.8773 (p90) REVERT: E 169 ASP cc_start: 0.8406 (m-30) cc_final: 0.8078 (m-30) REVERT: F 64 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8503 (mp10) REVERT: F 203 TRP cc_start: 0.8914 (t-100) cc_final: 0.8521 (t60) REVERT: f 92 LYS cc_start: 0.9108 (pttm) cc_final: 0.8640 (tttt) REVERT: G 123 GLN cc_start: 0.8075 (mt0) cc_final: 0.7822 (mt0) REVERT: G 124 ASP cc_start: 0.7441 (m-30) cc_final: 0.6831 (p0) REVERT: g 29 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8833 (pt) REVERT: I 76 ARG cc_start: 0.8692 (mmt90) cc_final: 0.8452 (mmm-85) REVERT: H 1 MET cc_start: 0.8757 (ptm) cc_final: 0.8465 (ptt) REVERT: H 19 SER cc_start: 0.8911 (m) cc_final: 0.8460 (t) REVERT: H 171 ASP cc_start: 0.7696 (t70) cc_final: 0.7084 (t0) REVERT: h 32 LYS cc_start: 0.9406 (mtmt) cc_final: 0.9082 (mttm) REVERT: h 64 GLU cc_start: 0.8913 (tp30) cc_final: 0.8440 (mm-30) REVERT: i 42 SER cc_start: 0.9577 (t) cc_final: 0.9190 (p) REVERT: j 54 LYS cc_start: 0.8870 (mtmt) cc_final: 0.8622 (mttp) REVERT: k 12 LEU cc_start: 0.9051 (mm) cc_final: 0.8672 (mm) REVERT: m 139 ASP cc_start: 0.6524 (OUTLIER) cc_final: 0.5797 (m-30) REVERT: m 166 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7399 (tp30) REVERT: m 263 ASP cc_start: 0.7080 (m-30) cc_final: 0.6282 (t0) REVERT: m 325 ASN cc_start: 0.6833 (t0) cc_final: 0.6318 (m-40) REVERT: m 359 MET cc_start: 0.5629 (mmm) cc_final: 0.4671 (mmm) REVERT: m 360 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8317 (pttm) REVERT: m 452 GLN cc_start: 0.7502 (tp-100) cc_final: 0.7216 (tp40) REVERT: L 34 SER cc_start: 0.9417 (p) cc_final: 0.9114 (t) REVERT: L 128 ARG cc_start: 0.6554 (OUTLIER) cc_final: 0.6154 (mtt90) REVERT: N 46 ASP cc_start: 0.8584 (p0) cc_final: 0.8349 (p0) REVERT: u 28 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: u 104 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7684 (tm-30) REVERT: u 132 GLU cc_start: 0.8793 (mp0) cc_final: 0.8478 (mp0) REVERT: O 84 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8801 (tt) REVERT: O 106 GLU cc_start: 0.8299 (mp0) cc_final: 0.7924 (mp0) REVERT: R 36 ASN cc_start: 0.8948 (p0) cc_final: 0.8670 (p0) REVERT: R 68 GLN cc_start: 0.8585 (tp40) cc_final: 0.8134 (tp40) REVERT: R 76 SER cc_start: 0.9404 (m) cc_final: 0.9097 (p) REVERT: R 86 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: R 99 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9248 (tm) REVERT: R 150 GLN cc_start: 0.8423 (tp-100) cc_final: 0.7997 (tm-30) REVERT: r 24 LYS cc_start: 0.8478 (ttmt) cc_final: 0.7979 (tppt) REVERT: r 41 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7445 (mmtt) REVERT: r 175 SER cc_start: 0.7443 (t) cc_final: 0.7164 (p) REVERT: S 14 LEU cc_start: 0.8107 (mt) cc_final: 0.7695 (mt) REVERT: S 82 ASP cc_start: 0.8421 (m-30) cc_final: 0.8179 (m-30) REVERT: S 87 THR cc_start: 0.8325 (t) cc_final: 0.7871 (t) REVERT: T 102 ARG cc_start: 0.8771 (tpt-90) cc_final: 0.7008 (mtm180) REVERT: T 108 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8537 (ttt-90) REVERT: T 139 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8405 (ptt90) REVERT: U 33 TYR cc_start: 0.8070 (t80) cc_final: 0.7708 (t80) REVERT: U 75 TYR cc_start: 0.8883 (t80) cc_final: 0.8466 (t80) REVERT: W 5 LYS cc_start: 0.8997 (ptpp) cc_final: 0.8486 (tptt) REVERT: W 148 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7510 (mp10) REVERT: W 149 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7799 (tp) REVERT: W 199 GLN cc_start: 0.8159 (pt0) cc_final: 0.7754 (pt0) REVERT: X 67 ILE cc_start: 0.9299 (mt) cc_final: 0.8979 (mt) REVERT: X 71 THR cc_start: 0.9432 (t) cc_final: 0.9195 (m) REVERT: Y 19 TYR cc_start: 0.9102 (t80) cc_final: 0.8868 (t80) REVERT: Y 32 SER cc_start: 0.9153 (t) cc_final: 0.8882 (p) REVERT: Y 76 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9164 (tp) REVERT: y 122 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7105 (p0) REVERT: Z 30 ASP cc_start: 0.7442 (t70) cc_final: 0.6803 (t70) REVERT: Z 31 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7582 (mm-30) REVERT: Z 47 GLU cc_start: 0.7879 (tt0) cc_final: 0.7576 (pt0) REVERT: Z 49 TYR cc_start: 0.9029 (m-80) cc_final: 0.8771 (m-80) REVERT: Z 65 ARG cc_start: 0.8844 (ttm-80) cc_final: 0.8566 (ttm170) REVERT: q 71 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7325 (ptm160) REVERT: q 97 LYS cc_start: 0.6981 (tppp) cc_final: 0.5889 (pttp) REVERT: o 52 LYS cc_start: 0.9305 (tptt) cc_final: 0.9063 (tptp) outliers start: 304 outliers final: 242 residues processed: 1339 average time/residue: 1.1441 time to fit residues: 2671.2777 Evaluate side-chains 1367 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1104 time to evaluate : 6.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 64 GLN Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain a residue 102 ILE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 237 MET Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 342 SER Chi-restraints excluded: chain b residue 347 LYS Chi-restraints excluded: chain b residue 371 ASP Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 436 LEU Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain c residue 14 LEU Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain d residue 48 ASP Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain e residue 3 SER Chi-restraints excluded: chain e residue 14 THR Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 38 ILE Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 67 SER Chi-restraints excluded: chain e residue 113 LYS Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 77 GLN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 71 THR Chi-restraints excluded: chain g residue 107 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 22 VAL Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 3 VAL Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 26 SER Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 56 ILE Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 25 LYS Chi-restraints excluded: chain m residue 41 MET Chi-restraints excluded: chain m residue 139 ASP Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 224 VAL Chi-restraints excluded: chain m residue 226 ILE Chi-restraints excluded: chain m residue 235 LEU Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 318 VAL Chi-restraints excluded: chain m residue 350 THR Chi-restraints excluded: chain m residue 360 LYS Chi-restraints excluded: chain m residue 462 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 63 VAL Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 128 ARG Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 38 ASP Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain u residue 4 TYR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 11 SER Chi-restraints excluded: chain u residue 28 GLU Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain u residue 110 ASN Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 64 LYS Chi-restraints excluded: chain r residue 136 VAL Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 155 THR Chi-restraints excluded: chain r residue 192 THR Chi-restraints excluded: chain S residue 88 HIS Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain T residue 139 ARG Chi-restraints excluded: chain T residue 142 SER Chi-restraints excluded: chain U residue 32 SER Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain W residue 92 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 224 ASP Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain X residue 87 SER Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 37 LYS Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 190 SER Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain q residue 6 LYS Chi-restraints excluded: chain q residue 54 THR Chi-restraints excluded: chain q residue 71 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 639 optimal weight: 5.9990 chunk 412 optimal weight: 10.0000 chunk 617 optimal weight: 9.9990 chunk 311 optimal weight: 0.0980 chunk 203 optimal weight: 9.9990 chunk 200 optimal weight: 1.9990 chunk 657 optimal weight: 3.9990 chunk 704 optimal weight: 0.0040 chunk 511 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 812 optimal weight: 10.0000 overall best weight: 2.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 20 ASN ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 614 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 12 GLN ** d 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN f 42 GLN f 106 ASN G 232 HIS g 3 GLN I 99 ASN I 106 GLN H 49 ASN H 58 HIS H 157 ASN ** j 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 50 ASN P 97 ASN Q 58 ASN R 7 GLN r 4 ASN r 244 GLN ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 GLN T 146 ASN V 81 GLN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS ** W 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 31 GLN ** q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 142085 Z= 0.172 Angle : 0.562 13.211 208074 Z= 0.290 Chirality : 0.035 0.265 25976 Planarity : 0.004 0.088 14023 Dihedral : 22.532 179.946 60058 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.93 % Favored : 92.99 % Rotamer: Outliers : 3.89 % Allowed : 18.92 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -1.22 (0.10), residues: 7557 helix: 0.21 (0.10), residues: 2646 sheet: -0.74 (0.17), residues: 950 loop : -1.55 (0.10), residues: 3961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP U 92 HIS 0.007 0.001 HIS e 88 PHE 0.031 0.001 PHE y 7 TYR 0.032 0.001 TYR P 139 ARG 0.012 0.000 ARG V 128 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1436 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1185 time to evaluate : 7.077 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: D 15 ARG cc_start: 0.8195 (ptp-110) cc_final: 0.7901 (mtt180) REVERT: D 79 TYR cc_start: 0.8428 (m-80) cc_final: 0.8201 (m-10) REVERT: D 151 GLN cc_start: 0.8371 (tp-100) cc_final: 0.7709 (mp10) REVERT: D 172 TYR cc_start: 0.8760 (t80) cc_final: 0.8530 (t80) REVERT: D 177 GLU cc_start: 0.8682 (pm20) cc_final: 0.8358 (pm20) REVERT: D 264 GLN cc_start: 0.5190 (OUTLIER) cc_final: 0.4507 (pt0) REVERT: J 89 TYR cc_start: 0.7778 (m-80) cc_final: 0.7049 (m-10) REVERT: J 109 HIS cc_start: 0.7149 (p90) cc_final: 0.6891 (p-80) REVERT: J 125 MET cc_start: 0.7390 (mpp) cc_final: 0.7130 (mpp) REVERT: J 128 TYR cc_start: 0.6629 (OUTLIER) cc_final: 0.3170 (m-80) REVERT: J 132 ASN cc_start: 0.7442 (p0) cc_final: 0.7127 (m110) REVERT: a 70 LYS cc_start: 0.9332 (ttmt) cc_final: 0.9073 (ttmm) REVERT: B 7 GLU cc_start: 0.6691 (mp0) cc_final: 0.6049 (mp0) REVERT: B 173 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.6662 (tm-30) REVERT: B 345 ASN cc_start: 0.8997 (t0) cc_final: 0.8658 (t0) REVERT: b 62 GLU cc_start: 0.8813 (tp30) cc_final: 0.8541 (tp30) REVERT: b 189 LYS cc_start: 0.7693 (ttmp) cc_final: 0.7093 (tttp) REVERT: b 232 MET cc_start: 0.4904 (tpp) cc_final: 0.4472 (tpp) REVERT: b 254 MET cc_start: 0.8100 (tmm) cc_final: 0.7744 (tmm) REVERT: b 329 MET cc_start: 0.7370 (tpt) cc_final: 0.6767 (tpt) REVERT: b 330 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8561 (mt-10) REVERT: b 347 LYS cc_start: 0.5794 (OUTLIER) cc_final: 0.5566 (mptt) REVERT: b 547 ASP cc_start: 0.7391 (m-30) cc_final: 0.6928 (p0) REVERT: b 598 MET cc_start: 0.6403 (mmp) cc_final: 0.5730 (mtm) REVERT: C 179 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9114 (tp) REVERT: C 194 TYR cc_start: 0.9248 (OUTLIER) cc_final: 0.8438 (p90) REVERT: c 57 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7841 (mt-10) REVERT: c 69 TYR cc_start: 0.8474 (m-80) cc_final: 0.8021 (m-80) REVERT: E 138 GLN cc_start: 0.8307 (tm-30) cc_final: 0.7996 (tm-30) REVERT: E 169 ASP cc_start: 0.8308 (m-30) cc_final: 0.7976 (m-30) REVERT: f 43 PHE cc_start: 0.9061 (t80) cc_final: 0.8829 (t80) REVERT: f 70 LYS cc_start: 0.8824 (pttt) cc_final: 0.8611 (pttt) REVERT: f 92 LYS cc_start: 0.8988 (pttm) cc_final: 0.8600 (tttt) REVERT: G 123 GLN cc_start: 0.7909 (mt0) cc_final: 0.7701 (mt0) REVERT: G 124 ASP cc_start: 0.7184 (m-30) cc_final: 0.6821 (p0) REVERT: G 173 MET cc_start: 0.8706 (mmt) cc_final: 0.8235 (mmt) REVERT: g 29 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8742 (pt) REVERT: I 107 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8167 (tt0) REVERT: I 124 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8482 (mtpp) REVERT: H 1 MET cc_start: 0.8714 (ptm) cc_final: 0.8419 (ptt) REVERT: H 19 SER cc_start: 0.8804 (m) cc_final: 0.8449 (t) REVERT: H 69 ARG cc_start: 0.8941 (tpt90) cc_final: 0.8692 (tpt90) REVERT: H 86 TYR cc_start: 0.8352 (m-80) cc_final: 0.7781 (m-80) REVERT: h 32 LYS cc_start: 0.9363 (mtmt) cc_final: 0.9063 (mttm) REVERT: h 64 GLU cc_start: 0.8834 (tp30) cc_final: 0.8413 (mm-30) REVERT: i 42 SER cc_start: 0.9560 (t) cc_final: 0.9149 (p) REVERT: j 54 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8503 (mttp) REVERT: k 12 LEU cc_start: 0.9040 (mm) cc_final: 0.8654 (mm) REVERT: m 139 ASP cc_start: 0.6513 (OUTLIER) cc_final: 0.5839 (m-30) REVERT: m 166 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7413 (tp30) REVERT: m 263 ASP cc_start: 0.7014 (m-30) cc_final: 0.6206 (t0) REVERT: m 280 GLU cc_start: 0.5542 (pt0) cc_final: 0.5286 (tp30) REVERT: m 351 LYS cc_start: 0.7366 (tptm) cc_final: 0.5802 (mmtt) REVERT: m 360 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8034 (pttm) REVERT: m 433 ARG cc_start: 0.7545 (mmt90) cc_final: 0.7222 (mmm-85) REVERT: m 452 GLN cc_start: 0.7489 (tp-100) cc_final: 0.7252 (tp40) REVERT: L 128 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.6050 (mtt90) REVERT: L 161 ASP cc_start: 0.7976 (t0) cc_final: 0.7644 (t0) REVERT: L 162 ASN cc_start: 0.8072 (p0) cc_final: 0.7646 (m-40) REVERT: l 8 ARG cc_start: 0.8771 (ttm-80) cc_final: 0.8478 (mtp85) REVERT: l 36 ARG cc_start: 0.8116 (mmm-85) cc_final: 0.7895 (mmm-85) REVERT: N 46 ASP cc_start: 0.8623 (p0) cc_final: 0.8331 (p0) REVERT: u 28 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: u 104 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7833 (tm-30) REVERT: u 132 GLU cc_start: 0.8765 (mp0) cc_final: 0.8460 (mp0) REVERT: O 84 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8709 (tt) REVERT: O 85 ARG cc_start: 0.8810 (ttp80) cc_final: 0.8499 (ttp80) REVERT: O 106 GLU cc_start: 0.8203 (mp0) cc_final: 0.7819 (mp0) REVERT: P 128 ARG cc_start: 0.7949 (ptm-80) cc_final: 0.7656 (ptt90) REVERT: R 7 GLN cc_start: 0.9017 (mp-120) cc_final: 0.8794 (mp10) REVERT: R 36 ASN cc_start: 0.8942 (p0) cc_final: 0.8632 (p0) REVERT: R 68 GLN cc_start: 0.8561 (tp40) cc_final: 0.8061 (tp40) REVERT: R 76 SER cc_start: 0.9385 (m) cc_final: 0.9090 (p) REVERT: R 86 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: R 99 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9202 (tm) REVERT: R 150 GLN cc_start: 0.8485 (tp-100) cc_final: 0.8065 (tm-30) REVERT: r 24 LYS cc_start: 0.8468 (ttmt) cc_final: 0.7707 (tppt) REVERT: r 41 LYS cc_start: 0.7826 (ttmt) cc_final: 0.7303 (mmtt) REVERT: r 169 GLU cc_start: 0.6704 (pt0) cc_final: 0.5687 (mt-10) REVERT: r 175 SER cc_start: 0.7515 (t) cc_final: 0.7214 (p) REVERT: S 14 LEU cc_start: 0.7978 (mt) cc_final: 0.7661 (mt) REVERT: S 82 ASP cc_start: 0.8372 (m-30) cc_final: 0.8112 (m-30) REVERT: S 87 THR cc_start: 0.8302 (t) cc_final: 0.7835 (t) REVERT: T 102 ARG cc_start: 0.8654 (tpt-90) cc_final: 0.6745 (mtm180) REVERT: T 108 ARG cc_start: 0.8706 (ttp80) cc_final: 0.8363 (ttt-90) REVERT: T 139 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8248 (ptt90) REVERT: U 33 TYR cc_start: 0.8013 (t80) cc_final: 0.7701 (t80) REVERT: U 75 TYR cc_start: 0.8684 (t80) cc_final: 0.8372 (t80) REVERT: V 109 MET cc_start: 0.7895 (mmm) cc_final: 0.7467 (mmm) REVERT: W 5 LYS cc_start: 0.8966 (ptpp) cc_final: 0.8460 (tptt) REVERT: W 148 GLN cc_start: 0.7813 (mm-40) cc_final: 0.7433 (mp10) REVERT: W 149 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7783 (tp) REVERT: X 67 ILE cc_start: 0.9297 (mt) cc_final: 0.8964 (mt) REVERT: X 71 THR cc_start: 0.9390 (t) cc_final: 0.9152 (m) REVERT: Y 32 SER cc_start: 0.9169 (t) cc_final: 0.8778 (p) REVERT: Y 76 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9275 (tp) REVERT: y 209 ASP cc_start: 0.8683 (t0) cc_final: 0.8192 (t70) REVERT: Z 30 ASP cc_start: 0.7314 (t70) cc_final: 0.6511 (t0) REVERT: Z 31 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7455 (mm-30) REVERT: Z 47 GLU cc_start: 0.7788 (tt0) cc_final: 0.7505 (pt0) REVERT: Z 49 TYR cc_start: 0.8998 (m-80) cc_final: 0.8773 (m-80) REVERT: Z 65 ARG cc_start: 0.8851 (ttm-80) cc_final: 0.8575 (ttm170) REVERT: Z 102 GLU cc_start: 0.8512 (mp0) cc_final: 0.8148 (mp0) REVERT: Z 103 GLN cc_start: 0.8427 (pm20) cc_final: 0.8111 (pm20) REVERT: q 71 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7573 (ptp-170) REVERT: q 97 LYS cc_start: 0.6967 (tppp) cc_final: 0.5882 (pttp) REVERT: o 52 LYS cc_start: 0.9287 (tptt) cc_final: 0.9047 (tptp) outliers start: 251 outliers final: 199 residues processed: 1341 average time/residue: 1.2475 time to fit residues: 2939.1814 Evaluate side-chains 1353 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1136 time to evaluate : 6.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 237 MET Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 347 LYS Chi-restraints excluded: chain b residue 371 ASP Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 436 LEU Chi-restraints excluded: chain b residue 531 MET Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain e residue 3 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 38 ILE Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 67 SER Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 77 GLN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain g residue 107 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 157 ASN Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain i residue 3 VAL Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain i residue 93 ILE Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 25 LYS Chi-restraints excluded: chain m residue 139 ASP Chi-restraints excluded: chain m residue 224 VAL Chi-restraints excluded: chain m residue 226 ILE Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 318 VAL Chi-restraints excluded: chain m residue 350 THR Chi-restraints excluded: chain m residue 360 LYS Chi-restraints excluded: chain m residue 462 ILE Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 128 ARG Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain p residue 38 ASP Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain u residue 4 TYR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 11 SER Chi-restraints excluded: chain u residue 28 GLU Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain r residue 136 VAL Chi-restraints excluded: chain r residue 155 THR Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain T residue 134 GLN Chi-restraints excluded: chain T residue 139 ARG Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain W residue 92 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 185 THR Chi-restraints excluded: chain y residue 190 SER Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain q residue 54 THR Chi-restraints excluded: chain q residue 71 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 940 optimal weight: 10.0000 chunk 990 optimal weight: 20.0000 chunk 903 optimal weight: 10.0000 chunk 963 optimal weight: 10.0000 chunk 580 optimal weight: 9.9990 chunk 419 optimal weight: 40.0000 chunk 756 optimal weight: 10.0000 chunk 295 optimal weight: 0.0980 chunk 870 optimal weight: 10.0000 chunk 911 optimal weight: 10.0000 chunk 960 optimal weight: 10.0000 overall best weight: 8.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 614 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN c 12 GLN d 21 HIS ** F 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN f 106 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** I 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 ASN H 157 ASN H 183 HIS ** j 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 50 ASN P 118 GLN Q 58 ASN r 244 GLN ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS ** W 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 31 GLN ** z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 142085 Z= 0.487 Angle : 0.731 13.240 208074 Z= 0.370 Chirality : 0.043 0.290 25976 Planarity : 0.005 0.094 14023 Dihedral : 22.594 179.778 60058 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.17 % Favored : 90.68 % Rotamer: Outliers : 4.52 % Allowed : 18.70 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.11 % 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: -1.56 (0.09), residues: 7557 helix: -0.10 (0.10), residues: 2662 sheet: -1.00 (0.16), residues: 979 loop : -1.72 (0.09), residues: 3916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP U 92 HIS 0.010 0.002 HIS y 118 PHE 0.028 0.002 PHE y 7 TYR 0.042 0.002 TYR P 139 ARG 0.011 0.001 ARG V 128 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1114 time to evaluate : 6.955 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: D 15 ARG cc_start: 0.8288 (ptp-110) cc_final: 0.8071 (mtt180) REVERT: D 79 TYR cc_start: 0.8554 (m-80) cc_final: 0.8256 (m-10) REVERT: D 151 GLN cc_start: 0.8339 (tp-100) cc_final: 0.8009 (mp10) REVERT: D 177 GLU cc_start: 0.8735 (pm20) cc_final: 0.8382 (pm20) REVERT: D 264 GLN cc_start: 0.5348 (OUTLIER) cc_final: 0.4610 (pt0) REVERT: J 89 TYR cc_start: 0.7934 (m-80) cc_final: 0.7164 (m-10) REVERT: J 128 TYR cc_start: 0.6415 (OUTLIER) cc_final: 0.2899 (m-80) REVERT: J 132 ASN cc_start: 0.7219 (p0) cc_final: 0.6901 (m110) REVERT: A 225 ILE cc_start: 0.8554 (mt) cc_final: 0.8277 (tp) REVERT: a 70 LYS cc_start: 0.9379 (ttmt) cc_final: 0.9127 (ttmm) REVERT: a 135 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: B 7 GLU cc_start: 0.6768 (mp0) cc_final: 0.6085 (mp0) REVERT: B 173 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: B 345 ASN cc_start: 0.9060 (t0) cc_final: 0.8687 (t0) REVERT: b 66 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7404 (mtpp) REVERT: b 189 LYS cc_start: 0.7904 (ttmp) cc_final: 0.7247 (tttm) REVERT: b 254 MET cc_start: 0.7969 (tmm) cc_final: 0.7682 (tmm) REVERT: b 330 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8515 (mt-10) REVERT: b 347 LYS cc_start: 0.5842 (OUTLIER) cc_final: 0.5549 (mptt) REVERT: b 547 ASP cc_start: 0.7325 (m-30) cc_final: 0.6846 (p0) REVERT: C 194 TYR cc_start: 0.9428 (OUTLIER) cc_final: 0.8855 (p90) REVERT: E 169 ASP cc_start: 0.8439 (m-30) cc_final: 0.8136 (m-30) REVERT: F 64 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8522 (mp10) REVERT: g 29 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8855 (pt) REVERT: I 107 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8187 (tt0) REVERT: H 1 MET cc_start: 0.8845 (ptm) cc_final: 0.8548 (ptt) REVERT: H 19 SER cc_start: 0.8929 (m) cc_final: 0.8401 (p) REVERT: H 23 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.7086 (mtp85) REVERT: H 113 GLU cc_start: 0.8518 (mp0) cc_final: 0.8003 (mp0) REVERT: H 171 ASP cc_start: 0.7739 (t0) cc_final: 0.7353 (t0) REVERT: h 32 LYS cc_start: 0.9454 (mtmt) cc_final: 0.9101 (mttm) REVERT: h 64 GLU cc_start: 0.8939 (tp30) cc_final: 0.8469 (mm-30) REVERT: i 42 SER cc_start: 0.9610 (t) cc_final: 0.9190 (p) REVERT: j 54 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8577 (mttp) REVERT: k 12 LEU cc_start: 0.9017 (mm) cc_final: 0.8604 (mm) REVERT: m 139 ASP cc_start: 0.6726 (OUTLIER) cc_final: 0.5990 (m-30) REVERT: m 166 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7521 (tp30) REVERT: m 263 ASP cc_start: 0.7121 (m-30) cc_final: 0.6385 (t0) REVERT: m 433 ARG cc_start: 0.7579 (mmt90) cc_final: 0.7265 (mmm-85) REVERT: m 443 GLU cc_start: 0.6554 (mm-30) cc_final: 0.5420 (mp0) REVERT: m 452 GLN cc_start: 0.7490 (tp-100) cc_final: 0.7209 (tp40) REVERT: L 34 SER cc_start: 0.9416 (p) cc_final: 0.9152 (t) REVERT: L 128 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.6192 (mtt90) REVERT: N 46 ASP cc_start: 0.8601 (p0) cc_final: 0.8375 (p0) REVERT: u 28 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: u 104 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7676 (tm-30) REVERT: u 132 GLU cc_start: 0.8783 (mp0) cc_final: 0.8479 (mp0) REVERT: O 84 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8753 (tt) REVERT: O 106 GLU cc_start: 0.8318 (mp0) cc_final: 0.7927 (mp0) REVERT: P 103 GLU cc_start: 0.8568 (tp30) cc_final: 0.8281 (tm-30) REVERT: R 36 ASN cc_start: 0.9027 (p0) cc_final: 0.8699 (p0) REVERT: R 68 GLN cc_start: 0.8666 (tp40) cc_final: 0.8183 (tp40) REVERT: R 76 SER cc_start: 0.9416 (m) cc_final: 0.9115 (p) REVERT: R 86 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: R 99 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9258 (tm) REVERT: r 24 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8008 (tppt) REVERT: r 41 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7424 (mmtt) REVERT: r 175 SER cc_start: 0.7404 (t) cc_final: 0.7127 (p) REVERT: r 252 ASP cc_start: 0.8743 (p0) cc_final: 0.7838 (p0) REVERT: S 14 LEU cc_start: 0.8210 (mt) cc_final: 0.7756 (mt) REVERT: S 70 THR cc_start: 0.9051 (p) cc_final: 0.8827 (p) REVERT: S 82 ASP cc_start: 0.8461 (m-30) cc_final: 0.8216 (m-30) REVERT: S 87 THR cc_start: 0.8458 (t) cc_final: 0.8046 (t) REVERT: S 142 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8688 (tt0) REVERT: S 171 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.5299 (t80) REVERT: T 102 ARG cc_start: 0.8820 (tpt-90) cc_final: 0.6932 (mtm180) REVERT: T 139 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8450 (ptt90) REVERT: U 33 TYR cc_start: 0.8077 (t80) cc_final: 0.7660 (t80) REVERT: W 5 LYS cc_start: 0.9006 (ptpp) cc_final: 0.8479 (tptt) REVERT: W 148 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7458 (mp10) REVERT: W 149 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7775 (tp) REVERT: W 165 MET cc_start: 0.7159 (ttm) cc_final: 0.6588 (tpp) REVERT: X 67 ILE cc_start: 0.9324 (mt) cc_final: 0.9033 (mt) REVERT: Y 32 SER cc_start: 0.9183 (t) cc_final: 0.8922 (p) REVERT: Y 76 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9151 (tp) REVERT: y 7 PHE cc_start: 0.8258 (t80) cc_final: 0.7960 (t80) REVERT: y 122 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7162 (p0) REVERT: y 197 MET cc_start: 0.9064 (ptm) cc_final: 0.8688 (ptm) REVERT: Z 30 ASP cc_start: 0.7487 (t70) cc_final: 0.6905 (t70) REVERT: Z 31 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7695 (mm-30) REVERT: Z 47 GLU cc_start: 0.7913 (tt0) cc_final: 0.7546 (pt0) REVERT: Z 49 TYR cc_start: 0.9076 (m-80) cc_final: 0.8762 (m-80) REVERT: Z 65 ARG cc_start: 0.8857 (ttm-80) cc_final: 0.8568 (ttm170) REVERT: q 71 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7277 (ptm160) REVERT: q 97 LYS cc_start: 0.6987 (tppp) cc_final: 0.5912 (pttp) REVERT: o 52 LYS cc_start: 0.9308 (tptt) cc_final: 0.9075 (tptp) outliers start: 292 outliers final: 237 residues processed: 1299 average time/residue: 1.1283 time to fit residues: 2565.9274 Evaluate side-chains 1341 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1082 time to evaluate : 6.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 64 GLN Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain a residue 102 ILE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 347 LYS Chi-restraints excluded: chain b residue 371 ASP Chi-restraints excluded: chain b residue 418 ASP Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 436 LEU Chi-restraints excluded: chain b residue 581 VAL Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain c residue 14 LEU Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain d residue 48 ASP Chi-restraints excluded: chain d residue 59 ILE Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain e residue 3 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 38 ILE Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 67 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 64 GLN Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 77 GLN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain g residue 107 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain h residue 93 THR Chi-restraints excluded: chain i residue 3 VAL Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 25 LYS Chi-restraints excluded: chain m residue 139 ASP Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 224 VAL Chi-restraints excluded: chain m residue 226 ILE Chi-restraints excluded: chain m residue 255 LEU Chi-restraints excluded: chain m residue 318 VAL Chi-restraints excluded: chain m residue 350 THR Chi-restraints excluded: chain m residue 360 LYS Chi-restraints excluded: chain m residue 462 ILE Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 128 ARG Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain p residue 5 THR Chi-restraints excluded: chain p residue 38 ASP Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 101 THR Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 167 THR Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain u residue 4 TYR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 11 SER Chi-restraints excluded: chain u residue 28 GLU Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 142 SER Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 188 SER Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 57 ILE Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 136 VAL Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 155 THR Chi-restraints excluded: chain r residue 192 THR Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 142 GLN Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 171 PHE Chi-restraints excluded: chain T residue 139 ARG Chi-restraints excluded: chain U residue 32 SER Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain U residue 91 ASP Chi-restraints excluded: chain V residue 23 MET Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 102 ILE Chi-restraints excluded: chain V residue 131 SER Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain W residue 92 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 175 ILE Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain W residue 217 VAL Chi-restraints excluded: chain W residue 224 ASP Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 45 ILE Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 185 THR Chi-restraints excluded: chain y residue 190 SER Chi-restraints excluded: chain y residue 206 THR Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain K residue 79 SER Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain q residue 6 LYS Chi-restraints excluded: chain q residue 54 THR Chi-restraints excluded: chain q residue 71 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 632 optimal weight: 7.9990 chunk 1019 optimal weight: 10.0000 chunk 622 optimal weight: 30.0000 chunk 483 optimal weight: 0.9990 chunk 708 optimal weight: 10.0000 chunk 1068 optimal weight: 6.9990 chunk 983 optimal weight: 20.0000 chunk 851 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 657 optimal weight: 2.9990 chunk 521 optimal weight: 0.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 ASN ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN b 614 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 12 GLN F 104 GLN f 42 GLN f 106 ASN I 99 ASN H 49 ASN H 157 ASN j 76 ASN P 45 GLN Q 58 ASN R 7 GLN r 244 GLN ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS ** W 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 31 GLN ** z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 142085 Z= 0.189 Angle : 0.583 13.188 208074 Z= 0.300 Chirality : 0.036 0.272 25976 Planarity : 0.004 0.088 14023 Dihedral : 22.543 179.900 60058 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.16 % Favored : 92.74 % Rotamer: Outliers : 3.62 % Allowed : 19.66 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -1.23 (0.10), residues: 7557 helix: 0.25 (0.10), residues: 2653 sheet: -0.81 (0.17), residues: 947 loop : -1.58 (0.10), residues: 3957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP U 92 HIS 0.008 0.001 HIS o 43 PHE 0.028 0.001 PHE y 7 TYR 0.037 0.001 TYR P 139 ARG 0.013 0.000 ARG T 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15114 Ramachandran restraints generated. 7557 Oldfield, 0 Emsley, 7557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1374 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1140 time to evaluate : 6.460 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: D 15 ARG cc_start: 0.8271 (ptp-110) cc_final: 0.8060 (mtt180) REVERT: D 79 TYR cc_start: 0.8453 (m-80) cc_final: 0.8207 (m-10) REVERT: D 151 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7695 (mp10) REVERT: D 177 GLU cc_start: 0.8717 (pm20) cc_final: 0.8386 (pm20) REVERT: D 264 GLN cc_start: 0.5210 (OUTLIER) cc_final: 0.4544 (pt0) REVERT: J 89 TYR cc_start: 0.7799 (m-80) cc_final: 0.7015 (m-10) REVERT: J 109 HIS cc_start: 0.7052 (p90) cc_final: 0.6762 (p-80) REVERT: J 128 TYR cc_start: 0.6355 (OUTLIER) cc_final: 0.2785 (m-80) REVERT: A 225 ILE cc_start: 0.8422 (mt) cc_final: 0.8211 (tp) REVERT: a 70 LYS cc_start: 0.9343 (ttmt) cc_final: 0.9090 (ttmm) REVERT: B 5 LYS cc_start: 0.9258 (tttt) cc_final: 0.9049 (ttmt) REVERT: B 7 GLU cc_start: 0.6821 (mp0) cc_final: 0.6145 (mp0) REVERT: B 173 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.6444 (tm-30) REVERT: B 345 ASN cc_start: 0.9009 (t0) cc_final: 0.8657 (t0) REVERT: b 189 LYS cc_start: 0.7706 (ttmp) cc_final: 0.7102 (tttp) REVERT: b 232 MET cc_start: 0.4955 (tpp) cc_final: 0.4482 (tpp) REVERT: b 234 ASN cc_start: 0.8230 (m110) cc_final: 0.8008 (m110) REVERT: b 254 MET cc_start: 0.7998 (tmm) cc_final: 0.7750 (tmm) REVERT: b 329 MET cc_start: 0.7420 (tpt) cc_final: 0.6819 (tpt) REVERT: b 330 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8477 (mt-10) REVERT: b 347 LYS cc_start: 0.5799 (OUTLIER) cc_final: 0.5505 (mptt) REVERT: b 547 ASP cc_start: 0.7381 (m-30) cc_final: 0.6915 (p0) REVERT: b 598 MET cc_start: 0.6521 (mmp) cc_final: 0.5656 (mtm) REVERT: C 194 TYR cc_start: 0.9317 (OUTLIER) cc_final: 0.8553 (p90) REVERT: c 57 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7880 (mt-10) REVERT: c 69 TYR cc_start: 0.8493 (m-80) cc_final: 0.8038 (m-80) REVERT: E 5 LYS cc_start: 0.8819 (tttt) cc_final: 0.8565 (tttm) REVERT: E 138 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7846 (tm-30) REVERT: E 169 ASP cc_start: 0.8363 (m-30) cc_final: 0.8049 (m-30) REVERT: f 43 PHE cc_start: 0.9088 (t80) cc_final: 0.8839 (t80) REVERT: f 92 LYS cc_start: 0.8963 (pttm) cc_final: 0.8516 (tttm) REVERT: G 124 ASP cc_start: 0.7164 (m-30) cc_final: 0.6638 (p0) REVERT: G 173 MET cc_start: 0.8664 (mmt) cc_final: 0.8187 (mmt) REVERT: g 29 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8749 (pt) REVERT: I 107 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8228 (tt0) REVERT: I 124 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8470 (mtpp) REVERT: H 1 MET cc_start: 0.8774 (ptm) cc_final: 0.8464 (ptt) REVERT: H 19 SER cc_start: 0.8827 (m) cc_final: 0.8474 (t) REVERT: H 94 TYR cc_start: 0.8957 (p90) cc_final: 0.8547 (p90) REVERT: H 113 GLU cc_start: 0.8521 (mp0) cc_final: 0.8175 (mp0) REVERT: h 32 LYS cc_start: 0.9415 (mtmt) cc_final: 0.9094 (mttm) REVERT: h 64 GLU cc_start: 0.8844 (tp30) cc_final: 0.8439 (mm-30) REVERT: i 42 SER cc_start: 0.9572 (t) cc_final: 0.9192 (p) REVERT: i 54 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7438 (mt-10) REVERT: k 12 LEU cc_start: 0.9029 (mm) cc_final: 0.8620 (mm) REVERT: m 139 ASP cc_start: 0.6488 (OUTLIER) cc_final: 0.5873 (m-30) REVERT: m 166 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7343 (tp30) REVERT: m 263 ASP cc_start: 0.7032 (m-30) cc_final: 0.6258 (t0) REVERT: m 323 TYR cc_start: 0.5409 (OUTLIER) cc_final: 0.4779 (m-80) REVERT: m 360 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8042 (pttm) REVERT: m 433 ARG cc_start: 0.7548 (mmt90) cc_final: 0.7231 (mmm-85) REVERT: m 452 GLN cc_start: 0.7540 (tp-100) cc_final: 0.7293 (tp40) REVERT: L 128 ARG cc_start: 0.6469 (OUTLIER) cc_final: 0.6058 (mtt90) REVERT: L 162 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7732 (m-40) REVERT: l 8 ARG cc_start: 0.8794 (ttm-80) cc_final: 0.8500 (mtp85) REVERT: M 47 ASP cc_start: 0.7258 (t0) cc_final: 0.7032 (m-30) REVERT: N 46 ASP cc_start: 0.8631 (p0) cc_final: 0.8317 (p0) REVERT: u 28 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: u 104 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7643 (tm-30) REVERT: u 130 ASN cc_start: 0.8507 (m-40) cc_final: 0.8194 (t0) REVERT: u 132 GLU cc_start: 0.8763 (mp0) cc_final: 0.8436 (mp0) REVERT: O 84 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8721 (tt) REVERT: O 85 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8508 (ttp80) REVERT: P 147 GLU cc_start: 0.7539 (pt0) cc_final: 0.7333 (pt0) REVERT: R 36 ASN cc_start: 0.8936 (p0) cc_final: 0.8634 (p0) REVERT: R 68 GLN cc_start: 0.8594 (tp40) cc_final: 0.8104 (tp40) REVERT: R 76 SER cc_start: 0.9382 (m) cc_final: 0.9085 (p) REVERT: R 86 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: R 99 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9241 (tm) REVERT: R 150 GLN cc_start: 0.8051 (tp40) cc_final: 0.7566 (tm-30) REVERT: r 24 LYS cc_start: 0.8467 (ttmt) cc_final: 0.8031 (tppt) REVERT: r 41 LYS cc_start: 0.7832 (ttmt) cc_final: 0.7275 (mmtt) REVERT: r 169 GLU cc_start: 0.6736 (pt0) cc_final: 0.5756 (mt-10) REVERT: r 175 SER cc_start: 0.7506 (t) cc_final: 0.7193 (p) REVERT: S 14 LEU cc_start: 0.8024 (mt) cc_final: 0.7616 (mt) REVERT: S 82 ASP cc_start: 0.8400 (m-30) cc_final: 0.8134 (m-30) REVERT: S 87 THR cc_start: 0.8324 (t) cc_final: 0.7842 (t) REVERT: T 102 ARG cc_start: 0.8664 (tpt-90) cc_final: 0.6886 (mtm180) REVERT: T 128 LEU cc_start: 0.9178 (mp) cc_final: 0.8952 (mm) REVERT: T 139 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8134 (ptt90) REVERT: U 33 TYR cc_start: 0.8031 (t80) cc_final: 0.7745 (t80) REVERT: U 75 TYR cc_start: 0.8724 (t80) cc_final: 0.8333 (t80) REVERT: W 5 LYS cc_start: 0.9002 (ptpp) cc_final: 0.8485 (tptt) REVERT: W 149 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7808 (tp) REVERT: X 67 ILE cc_start: 0.9314 (mt) cc_final: 0.9005 (mt) REVERT: X 71 THR cc_start: 0.9391 (t) cc_final: 0.9159 (m) REVERT: Y 32 SER cc_start: 0.9193 (t) cc_final: 0.8827 (p) REVERT: Y 76 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9296 (tp) REVERT: Y 120 GLN cc_start: 0.8398 (mm110) cc_final: 0.8194 (mp10) REVERT: y 7 PHE cc_start: 0.7909 (t80) cc_final: 0.7678 (t80) REVERT: y 122 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7073 (p0) REVERT: Z 30 ASP cc_start: 0.7383 (t70) cc_final: 0.6575 (t0) REVERT: Z 31 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7516 (mm-30) REVERT: Z 47 GLU cc_start: 0.7791 (tt0) cc_final: 0.7435 (pt0) REVERT: Z 49 TYR cc_start: 0.8961 (m-80) cc_final: 0.8728 (m-80) REVERT: Z 65 ARG cc_start: 0.8846 (ttm-80) cc_final: 0.8589 (ttm170) REVERT: Z 102 GLU cc_start: 0.8628 (mp0) cc_final: 0.8334 (mp0) REVERT: Z 103 GLN cc_start: 0.8395 (pm20) cc_final: 0.8080 (pm20) REVERT: q 71 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6995 (ptm160) REVERT: q 97 LYS cc_start: 0.6961 (tppp) cc_final: 0.5880 (pttp) REVERT: o 52 LYS cc_start: 0.9285 (tptt) cc_final: 0.9056 (tptp) outliers start: 234 outliers final: 197 residues processed: 1290 average time/residue: 1.1509 time to fit residues: 2594.0892 Evaluate side-chains 1324 residues out of total 6502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1107 time to evaluate : 7.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 41 LYS Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 264 GLN Chi-restraints excluded: chain J residue 20 ASN Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 152 HIS Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain a residue 78 LEU Chi-restraints excluded: chain a residue 96 LYS Chi-restraints excluded: chain a residue 101 VAL Chi-restraints excluded: chain a residue 102 ILE Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 173 GLN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain b residue 19 ASP Chi-restraints excluded: chain b residue 74 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 169 THR Chi-restraints excluded: chain b residue 237 MET Chi-restraints excluded: chain b residue 239 SER Chi-restraints excluded: chain b residue 298 LEU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 347 LYS Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain b residue 436 LEU Chi-restraints excluded: chain b residue 581 VAL Chi-restraints excluded: chain b residue 595 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain c residue 14 LEU Chi-restraints excluded: chain d residue 23 VAL Chi-restraints excluded: chain d residue 48 ASP Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 106 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 82 ARG Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain e residue 3 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 50 ILE Chi-restraints excluded: chain e residue 55 ILE Chi-restraints excluded: chain e residue 63 THR Chi-restraints excluded: chain e residue 67 SER Chi-restraints excluded: chain e residue 73 THR Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 109 THR Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain f residue 56 SER Chi-restraints excluded: chain f residue 62 SER Chi-restraints excluded: chain f residue 66 VAL Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 67 ILE Chi-restraints excluded: chain G residue 77 GLN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 216 SER Chi-restraints excluded: chain G residue 229 VAL Chi-restraints excluded: chain G residue 246 MET Chi-restraints excluded: chain G residue 249 ARG Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 23 VAL Chi-restraints excluded: chain g residue 29 ILE Chi-restraints excluded: chain g residue 40 THR Chi-restraints excluded: chain g residue 66 SER Chi-restraints excluded: chain g residue 104 VAL Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 THR Chi-restraints excluded: chain I residue 75 ARG Chi-restraints excluded: chain I residue 86 THR Chi-restraints excluded: chain H residue 23 ARG Chi-restraints excluded: chain H residue 49 ASN Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain h residue 19 SER Chi-restraints excluded: chain h residue 28 LEU Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain i residue 3 VAL Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain i residue 79 SER Chi-restraints excluded: chain j residue 5 THR Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain j residue 82 SER Chi-restraints excluded: chain j residue 84 SER Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 72 THR Chi-restraints excluded: chain m residue 25 LYS Chi-restraints excluded: chain m residue 139 ASP Chi-restraints excluded: chain m residue 159 ASP Chi-restraints excluded: chain m residue 224 VAL Chi-restraints excluded: chain m residue 226 ILE Chi-restraints excluded: chain m residue 318 VAL Chi-restraints excluded: chain m residue 323 TYR Chi-restraints excluded: chain m residue 350 THR Chi-restraints excluded: chain m residue 360 LYS Chi-restraints excluded: chain m residue 462 ILE Chi-restraints excluded: chain L residue 69 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 128 ARG Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain M residue 4 ASP Chi-restraints excluded: chain M residue 25 LYS Chi-restraints excluded: chain M residue 40 ASP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 114 ASP Chi-restraints excluded: chain p residue 38 ASP Chi-restraints excluded: chain p residue 56 THR Chi-restraints excluded: chain p residue 58 SER Chi-restraints excluded: chain p residue 59 CYS Chi-restraints excluded: chain p residue 89 MET Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 19 LEU Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain u residue 4 TYR Chi-restraints excluded: chain u residue 9 CYS Chi-restraints excluded: chain u residue 11 SER Chi-restraints excluded: chain u residue 28 GLU Chi-restraints excluded: chain u residue 32 CYS Chi-restraints excluded: chain u residue 73 GLN Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain O residue 41 LEU Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain O residue 118 VAL Chi-restraints excluded: chain O residue 129 LEU Chi-restraints excluded: chain O residue 151 ASP Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 169 THR Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain R residue 46 LYS Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 86 GLU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain r residue 136 VAL Chi-restraints excluded: chain r residue 152 THR Chi-restraints excluded: chain r residue 192 THR Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain T residue 139 ARG Chi-restraints excluded: chain U residue 37 LEU Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 68 THR Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain W residue 50 THR Chi-restraints excluded: chain W residue 92 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 181 THR Chi-restraints excluded: chain W residue 187 LEU Chi-restraints excluded: chain W residue 215 VAL Chi-restraints excluded: chain W residue 231 THR Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 76 LEU Chi-restraints excluded: chain y residue 5 THR Chi-restraints excluded: chain y residue 101 LEU Chi-restraints excluded: chain y residue 122 ASP Chi-restraints excluded: chain y residue 185 THR Chi-restraints excluded: chain y residue 190 SER Chi-restraints excluded: chain Z residue 33 SER Chi-restraints excluded: chain Z residue 96 VAL Chi-restraints excluded: chain Z residue 97 SER Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain q residue 54 THR Chi-restraints excluded: chain q residue 71 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 676 optimal weight: 0.8980 chunk 906 optimal weight: 10.0000 chunk 260 optimal weight: 8.9990 chunk 784 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 236 optimal weight: 10.0000 chunk 852 optimal weight: 20.0000 chunk 356 optimal weight: 6.9990 chunk 875 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 ASN A 24 GLN ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN b 509 ASN b 614 ASN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN c 12 GLN F 104 GLN f 42 GLN ** f 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 232 HIS I 99 ASN I 106 GLN H 49 ASN H 157 ASN Q 58 ASN R 7 GLN ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 GLN ** T 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 44 HIS ** W 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 199 GLN ** Z 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 31 GLN ** z 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.078441 restraints weight = 291428.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.081378 restraints weight = 115736.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.082239 restraints weight = 70586.992| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 142085 Z= 0.338 Angle : 0.642 13.223 208074 Z= 0.327 Chirality : 0.039 0.295 25976 Planarity : 0.005 0.092 14023 Dihedral : 22.536 179.656 60056 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.64 % Favored : 91.24 % Rotamer: Outliers : 4.01 % Allowed : 19.44 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.69 % 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: -1.33 (0.09), residues: 7557 helix: 0.18 (0.10), residues: 2654 sheet: -0.90 (0.16), residues: 977 loop : -1.65 (0.10), residues: 3926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP U 92 HIS 0.009 0.001 HIS o 43 PHE 0.028 0.002 PHE y 7 TYR 0.043 0.002 TYR P 139 ARG 0.013 0.001 ARG T 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38141.90 seconds wall clock time: 663 minutes 19.44 seconds (39799.44 seconds total)