Starting phenix.real_space_refine on Fri Mar 22 02:33:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o19_12693/03_2024/7o19_12693_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o19_12693/03_2024/7o19_12693.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o19_12693/03_2024/7o19_12693_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o19_12693/03_2024/7o19_12693_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o19_12693/03_2024/7o19_12693_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o19_12693/03_2024/7o19_12693.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o19_12693/03_2024/7o19_12693.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o19_12693/03_2024/7o19_12693_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o19_12693/03_2024/7o19_12693_updated.pdb" } resolution = 2.9 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 4635 5.49 5 Mg 170 5.21 5 S 148 5.16 5 C 72298 2.51 5 N 26852 2.21 5 O 40913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AB ASP 194": "OD1" <-> "OD2" Residue "AB PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB ARG 225": "NH1" <-> "NH2" Residue "AC PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC ASP 112": "OD1" <-> "OD2" Residue "AC ARG 131": "NH1" <-> "NH2" Residue "AC ASP 181": "OD1" <-> "OD2" Residue "AC TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AD GLU 160": "OE1" <-> "OE2" Residue "AE PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF ARG 2": "NH1" <-> "NH2" Residue "AF GLU 5": "OE1" <-> "OE2" Residue "AF PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF GLU 73": "OE1" <-> "OE2" Residue "AG PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG GLU 60": "OE1" <-> "OE2" Residue "AG GLU 67": "OE1" <-> "OE2" Residue "AH GLU 42": "OE1" <-> "OE2" Residue "AH GLU 43": "OE1" <-> "OE2" Residue "AH ASP 48": "OD1" <-> "OD2" Residue "AI TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI ASP 91": "OD1" <-> "OD2" Residue "AI ARG 119": "NH1" <-> "NH2" Residue "AI ARG 124": "NH1" <-> "NH2" Residue "AJ PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ ASP 63": "OD1" <-> "OD2" Residue "AJ ASP 91": "OD1" <-> "OD2" Residue "AK PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK GLU 68": "OE1" <-> "OE2" Residue "AL ARG 56": "NH1" <-> "NH2" Residue "AL TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AM GLU 41": "OE1" <-> "OE2" Residue "AN GLU 9": "OE1" <-> "OE2" Residue "AN ASP 32": "OD1" <-> "OD2" Residue "AP ARG 28": "NH1" <-> "NH2" Residue "AP PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AP GLU 48": "OE1" <-> "OE2" Residue "AP GLU 77": "OE1" <-> "OE2" Residue "AQ ASP 15": "OD1" <-> "OD2" Residue "AQ PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ GLU 63": "OE1" <-> "OE2" Residue "AS PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AT PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU GLU 10": "OE1" <-> "OE2" Residue "AU PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC ARG 52": "NH1" <-> "NH2" Residue "BC ARG 63": "NH1" <-> "NH2" Residue "BC ASP 66": "OD1" <-> "OD2" Residue "BC ARG 80": "NH1" <-> "NH2" Residue "BC ASP 121": "OD1" <-> "OD2" Residue "BC ARG 133": "NH1" <-> "NH2" Residue "BC TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC ARG 167": "NH1" <-> "NH2" Residue "BC ARG 177": "NH1" <-> "NH2" Residue "BC ARG 182": "NH1" <-> "NH2" Residue "BC ARG 189": "NH1" <-> "NH2" Residue "BC ARG 212": "NH1" <-> "NH2" Residue "BD ARG 13": "NH1" <-> "NH2" Residue "BD GLU 17": "OE1" <-> "OE2" Residue "BD ARG 33": "NH1" <-> "NH2" Residue "BD ASP 43": "OD1" <-> "OD2" Residue "BD ARG 59": "NH1" <-> "NH2" Residue "BD GLU 64": "OE1" <-> "OE2" Residue "BD GLU 74": "OE1" <-> "OE2" Residue "BD ARG 77": "NH1" <-> "NH2" Residue "BD ARG 83": "NH1" <-> "NH2" Residue "BD PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD GLU 168": "OE1" <-> "OE2" Residue "BD ARG 169": "NH1" <-> "NH2" Residue "BD ARG 184": "NH1" <-> "NH2" Residue "BE ARG 21": "NH1" <-> "NH2" Residue "BE TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE ARG 44": "NH1" <-> "NH2" Residue "BE ARG 49": "NH1" <-> "NH2" Residue "BE ARG 67": "NH1" <-> "NH2" Residue "BE ARG 88": "NH1" <-> "NH2" Residue "BE ARG 102": "NH1" <-> "NH2" Residue "BE PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BE ASP 154": "OD1" <-> "OD2" Residue "BE ARG 162": "NH1" <-> "NH2" Residue "BE ASP 168": "OD1" <-> "OD2" Residue "BE ARG 170": "NH1" <-> "NH2" Residue "BE ASP 184": "OD1" <-> "OD2" Residue "BF GLU 19": "OE1" <-> "OE2" Residue "BF PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF ASP 56": "OD1" <-> "OD2" Residue "BF ARG 71": "NH1" <-> "NH2" Residue "BF ARG 80": "NH1" <-> "NH2" Residue "BF ARG 92": "NH1" <-> "NH2" Residue "BF GLU 94": "OE1" <-> "OE2" Residue "BF ARG 102": "NH1" <-> "NH2" Residue "BF ARG 110": "NH1" <-> "NH2" Residue "BF ARG 112": "NH1" <-> "NH2" Residue "BF ARG 115": "NH1" <-> "NH2" Residue "BF ARG 133": "NH1" <-> "NH2" Residue "BF GLU 140": "OE1" <-> "OE2" Residue "BG ARG 3": "NH1" <-> "NH2" Residue "BG ARG 153": "NH1" <-> "NH2" Residue "BG ARG 163": "NH1" <-> "NH2" Residue "BG ARG 170": "NH1" <-> "NH2" Residue "BH ASP 17": "OD1" <-> "OD2" Residue "BH ARG 27": "NH1" <-> "NH2" Residue "BH GLU 60": "OE1" <-> "OE2" Residue "BH GLU 109": "OE1" <-> "OE2" Residue "BH GLU 114": "OE1" <-> "OE2" Residue "BH PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI ASP 4": "OD1" <-> "OD2" Residue "BI ARG 49": "NH1" <-> "NH2" Residue "BI ARG 56": "NH1" <-> "NH2" Residue "BJ PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ ARG 13": "NH1" <-> "NH2" Residue "BJ ASP 14": "OD1" <-> "OD2" Residue "BJ ARG 37": "NH1" <-> "NH2" Residue "BJ PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BJ ARG 96": "NH1" <-> "NH2" Residue "BJ ARG 120": "NH1" <-> "NH2" Residue "BK ASP 12": "OD1" <-> "OD2" Residue "BK ASP 56": "OD1" <-> "OD2" Residue "BL ARG 21": "NH1" <-> "NH2" Residue "BL ARG 33": "NH1" <-> "NH2" Residue "BL ARG 41": "NH1" <-> "NH2" Residue "BL ARG 47": "NH1" <-> "NH2" Residue "BL GLU 51": "OE1" <-> "OE2" Residue "BL ARG 60": "NH1" <-> "NH2" Residue "BL PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BL GLU 76": "OE1" <-> "OE2" Residue "BL GLU 86": "OE1" <-> "OE2" Residue "BL ARG 126": "NH1" <-> "NH2" Residue "BL GLU 136": "OE1" <-> "OE2" Residue "BM ARG 10": "NH1" <-> "NH2" Residue "BM ARG 18": "NH1" <-> "NH2" Residue "BM PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM ARG 40": "NH1" <-> "NH2" Residue "BM ARG 44": "NH1" <-> "NH2" Residue "BM ARG 50": "NH1" <-> "NH2" Residue "BM ARG 55": "NH1" <-> "NH2" Residue "BM ARG 59": "NH1" <-> "NH2" Residue "BM ASP 70": "OD1" <-> "OD2" Residue "BM GLU 75": "OE1" <-> "OE2" Residue "BM TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BM ARG 114": "NH1" <-> "NH2" Residue "BM PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BN ARG 8": "NH1" <-> "NH2" Residue "BN ARG 12": "NH1" <-> "NH2" Residue "BN ARG 17": "NH1" <-> "NH2" Residue "BN ARG 22": "NH1" <-> "NH2" Residue "BN GLU 32": "OE1" <-> "OE2" Residue "BN ARG 46": "NH1" <-> "NH2" Residue "BN ARG 63": "NH1" <-> "NH2" Residue "BN ARG 64": "NH1" <-> "NH2" Residue "BN ARG 69": "NH1" <-> "NH2" Residue "BN ARG 71": "NH1" <-> "NH2" Residue "BN ASP 72": "OD1" <-> "OD2" Residue "BN GLU 82": "OE1" <-> "OE2" Residue "BN ARG 96": "NH1" <-> "NH2" Residue "BN TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BN ARG 118": "NH1" <-> "NH2" Residue "BO ARG 10": "NH1" <-> "NH2" Residue "BO ARG 16": "NH1" <-> "NH2" Residue "BO GLU 20": "OE1" <-> "OE2" Residue "BO ARG 25": "NH1" <-> "NH2" Residue "BO ARG 81": "NH1" <-> "NH2" Residue "BO ARG 94": "NH1" <-> "NH2" Residue "BO ARG 102": "NH1" <-> "NH2" Residue "BO ASP 108": "OD1" <-> "OD2" Residue "BO ARG 111": "NH1" <-> "NH2" Residue "BP ARG 21": "NH1" <-> "NH2" Residue "BP GLU 27": "OE1" <-> "OE2" Residue "BP ARG 39": "NH1" <-> "NH2" Residue "BP ARG 62": "NH1" <-> "NH2" Residue "BP ARG 89": "NH1" <-> "NH2" Residue "BP ARG 101": "NH1" <-> "NH2" Residue "BP ARG 109": "NH1" <-> "NH2" Residue "BQ ARG 3": "NH1" <-> "NH2" Residue "BQ ARG 6": "NH1" <-> "NH2" Residue "BQ ARG 13": "NH1" <-> "NH2" Residue "BQ TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ ARG 33": "NH1" <-> "NH2" Residue "BQ ARG 48": "NH1" <-> "NH2" Residue "BQ ARG 70": "NH1" <-> "NH2" Residue "BQ TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ ASP 91": "OD1" <-> "OD2" Residue "BR PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BR ARG 21": "NH1" <-> "NH2" Residue "BR GLU 23": "OE1" <-> "OE2" Residue "BR GLU 37": "OE1" <-> "OE2" Residue "BR ARG 68": "NH1" <-> "NH2" Residue "BR ARG 78": "NH1" <-> "NH2" Residue "BR ARG 79": "NH1" <-> "NH2" Residue "BR ARG 84": "NH1" <-> "NH2" Residue "BS ASP 62": "OD1" <-> "OD2" Residue "BS PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BS ARG 84": "NH1" <-> "NH2" Residue "BS ARG 88": "NH1" <-> "NH2" Residue "BS ARG 95": "NH1" <-> "NH2" Residue "BS ARG 110": "NH1" <-> "NH2" Residue "BT GLU 25": "OE1" <-> "OE2" Residue "BT ARG 73": "NH1" <-> "NH2" Residue "BU ARG 6": "NH1" <-> "NH2" Residue "BU ARG 7": "NH1" <-> "NH2" Residue "BU ARG 82": "NH1" <-> "NH2" Residue "BU ARG 86": "NH1" <-> "NH2" Residue "BU ARG 94": "NH1" <-> "NH2" Residue "BV GLU 7": "OE1" <-> "OE2" Residue "BV GLU 41": "OE1" <-> "OE2" Residue "BV ASP 90": "OD1" <-> "OD2" Residue "BW ARG 11": "NH1" <-> "NH2" Residue "BW GLU 83": "OE1" <-> "OE2" Residue "BX ARG 3": "NH1" <-> "NH2" Residue "BX ARG 11": "NH1" <-> "NH2" Residue "BX ARG 18": "NH1" <-> "NH2" Residue "BX ARG 37": "NH1" <-> "NH2" Residue "BX ARG 50": "NH1" <-> "NH2" Residue "BX ARG 57": "NH1" <-> "NH2" Residue "BX ARG 74": "NH1" <-> "NH2" Residue "BY ARG 29": "NH1" <-> "NH2" Residue "BY ARG 47": "NH1" <-> "NH2" Residue "BY ARG 52": "NH1" <-> "NH2" Residue "BZ ARG 11": "NH1" <-> "NH2" Residue "BZ ARG 30": "NH1" <-> "NH2" Residue "BZ GLU 37": "OE1" <-> "OE2" Residue "BZ ASP 40": "OD1" <-> "OD2" Residue "BZ ARG 45": "NH1" <-> "NH2" Residue "BZ PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B0 ARG 10": "NH1" <-> "NH2" Residue "B0 ARG 16": "NH1" <-> "NH2" Residue "B0 ASP 46": "OD1" <-> "OD2" Residue "B0 ARG 52": "NH1" <-> "NH2" Residue "B1 ARG 44": "NH1" <-> "NH2" Residue "B2 ARG 12": "NH1" <-> "NH2" Residue "B2 ARG 14": "NH1" <-> "NH2" Residue "B2 ARG 19": "NH1" <-> "NH2" Residue "B2 ARG 21": "NH1" <-> "NH2" Residue "B2 ARG 33": "NH1" <-> "NH2" Residue "B2 ARG 41": "NH1" <-> "NH2" Residue "B3 ARG 13": "NH1" <-> "NH2" Residue "B3 ARG 30": "NH1" <-> "NH2" Residue "B3 ARG 40": "NH1" <-> "NH2" Residue "B3 ARG 42": "NH1" <-> "NH2" Residue "B4 ASP 20": "OD1" <-> "OD2" Residue "B4 ARG 24": "NH1" <-> "NH2" Residue "B5 PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 145019 Number of models: 1 Model: "" Number of chains: 74 Chain: "AA" Number of atoms: 32930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32930 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 121, 'rna2p_pyr': 94, 'rna3p': 10, 'rna3p_pur': 748, 'rna3p_pyr': 560} Link IDs: {'rna2p': 216, 'rna3p': 1317} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "AB" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "AC" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "AD" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "AE" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1144 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "AF" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "AG" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "AH" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "AI" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "AJ" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "AK" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "AL" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "AM" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "AN" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "AO" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "AP" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "AQ" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "AR" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "AS" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 656 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "AT" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "AU" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "BA" Number of atoms: 62209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62209 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 6, 'rna2p_pur': 280, 'rna2p_pyr': 159, 'rna3p': 17, 'rna3p_pur': 1384, 'rna3p_pyr': 1051} Link IDs: {'rna2p': 445, 'rna3p': 2451} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "BB" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 50} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "BC" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "BD" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "BE" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "BF" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "BG" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "BH" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "BI" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "BJ" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "BK" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "BL" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "BM" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "BN" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "BO" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "BP" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "BQ" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "BR" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "BS" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "BT" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "BU" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "BV" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "BW" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "BX" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "BY" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "BZ" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "B0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "B1" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "B3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "B4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "B5" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 146 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "B7" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 146 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "B8" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 13, 'rna3p': 63} Chain: "AA" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Unusual residues: {' MG': 35} Classifications: {'undetermined': 35} Link IDs: {None: 34} Chain: "AB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 147 Unusual residues: {' MG': 132} Classifications: {'peptide': 1, 'undetermined': 132} Modifications used: {'COO': 1} Link IDs: {None: 132} Chain: "BC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 168 Classifications: {'water': 168} Link IDs: {None: 167} Chain: "AK" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AN" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "BA" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 608 Classifications: {'water': 608} Link IDs: {None: 607} Chain: "BC" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "BD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BL" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "BN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0JSP SG CYSBI 16 119.790 160.289 231.655 1.00 70.53 S ATOM A0JT1 SG CYSBI 18 117.403 161.792 234.165 1.00 70.25 S ATOM A0JWZ SG CYSBI 37 116.091 159.460 231.545 1.00 69.05 S ATOM A0JXK SG CYSBI 40 117.257 162.918 230.580 1.00 70.55 S ATOM A0WBF SG CYSB4 11 54.411 167.753 139.589 1.00 40.73 S ATOM A0WC4 SG CYSB4 14 54.284 164.166 138.537 1.00 35.76 S ATOM A0WEZ SG CYSB4 27 53.761 166.891 136.042 1.00 37.85 S Residues with excluded nonbonded symmetry interactions: 27 residue: pdb=" P ABA 404 " occ=0.60 ... (20 atoms not shown) pdb=" C4 ABA 404 " occ=0.60 residue: pdb=" P UBA2884 " occ=0.47 ... (18 atoms not shown) pdb=" C6 UBA2884 " occ=0.47 residue: pdb=" P GBA2885 " occ=0.47 ... (21 atoms not shown) pdb=" C4 GBA2885 " occ=0.47 residue: pdb=" P ABA2886 " occ=0.47 ... (20 atoms not shown) pdb=" C4 ABA2886 " occ=0.47 residue: pdb=" P ABA2887 " occ=0.47 ... (20 atoms not shown) pdb=" C4 ABA2887 " occ=0.47 residue: pdb=" P CBA2888 " occ=0.47 ... (18 atoms not shown) pdb=" C6 CBA2888 " occ=0.47 residue: pdb=" N MEQBD 150 " occ=0.49 ... (8 atoms not shown) pdb=" NE2 MEQBD 150 " occ=0.49 residue: pdb=" N ARGBW 41 " occ=0.49 ... (9 atoms not shown) pdb=" NH2 ARGBW 41 " occ=0.49 residue: pdb=" N ALABZ 2 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALABZ 2 " occ=0.50 residue: pdb=" N LYSBZ 3 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYSBZ 3 " occ=0.50 residue: pdb=" N THRB5 9 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 THRB5 9 " occ=0.50 residue: pdb=" N SERB5 10 " occ=0.50 ... (4 atoms not shown) pdb=" OG SERB5 10 " occ=0.50 ... (remaining 15 not shown) Time building chain proxies: 57.06, per 1000 atoms: 0.39 Number of scatterers: 145019 At special positions: 0 Unit cell: (241.262, 269.379, 252.146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 148 16.00 P 4635 15.00 Mg 170 11.99 O 40913 8.00 N 26852 7.00 C 72298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 58.11 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNAB 301 " pdb="ZN ZNAB 301 " - pdb=" NE2 HISAB 18 " pdb=" ZNB4 101 " pdb="ZN ZNB4 101 " - pdb=" ND1 HISB4 33 " pdb="ZN ZNB4 101 " - pdb=" SG CYSB4 27 " pdb="ZN ZNB4 101 " - pdb=" SG CYSB4 11 " pdb="ZN ZNB4 101 " - pdb=" SG CYSB4 14 " pdb=" ZNBI 101 " pdb="ZN ZNBI 101 " - pdb=" SG CYSBI 18 " pdb="ZN ZNBI 101 " - pdb=" SG CYSBI 37 " pdb="ZN ZNBI 101 " - pdb=" SG CYSBI 40 " pdb="ZN ZNBI 101 " - pdb=" SG CYSBI 16 " Number of angles added : 9 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10464 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: 175 helices and 72 sheets defined 38.8% alpha, 19.1% beta 1623 base pairs and 2539 stacking pairs defined. Time for finding SS restraints: 74.14 Creating SS restraints... Processing helix chain 'AB' and resid 5 through 13 removed outlier: 4.129A pdb=" N METAB 9 " --> pdb=" O SERAB 5 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEUAB 10 " --> pdb=" O METAB 6 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYSAB 11 " --> pdb=" O ARGAB 7 " (cutoff:3.500A) Processing helix chain 'AB' and resid 27 through 32 removed outlier: 3.650A pdb=" N ILEAB 31 " --> pdb=" O METAB 27 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N PHEAB 32 " --> pdb=" O LYSAB 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'AB' and resid 27 through 32' Processing helix chain 'AB' and resid 42 through 64 removed outlier: 3.708A pdb=" N THRAB 46 " --> pdb=" O ASNAB 42 " (cutoff:3.500A) Proline residue: AB 48 - end of helix removed outlier: 3.650A pdb=" N ILEAB 60 " --> pdb=" O GLUAB 56 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYSAB 64 " --> pdb=" O ILEAB 60 " (cutoff:3.500A) Processing helix chain 'AB' and resid 76 through 88 removed outlier: 3.711A pdb=" N LYSAB 81 " --> pdb=" O SERAB 77 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALAAB 84 " --> pdb=" O VALAB 80 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SERAB 86 " --> pdb=" O ASPAB 82 " (cutoff:3.500A) Processing helix chain 'AB' and resid 103 through 123 removed outlier: 4.615A pdb=" N GLNAB 109 " --> pdb=" O LYSAB 105 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SERAB 110 " --> pdb=" O THRAB 106 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLNAB 122 " --> pdb=" O GLUAB 118 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASPAB 123 " --> pdb=" O THRAB 119 " (cutoff:3.500A) Processing helix chain 'AB' and resid 130 through 148 removed outlier: 6.868A pdb=" N ALAAB 134 " --> pdb=" O THRAB 130 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEUAB 135 " --> pdb=" O LYSAB 131 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARGAB 137 " --> pdb=" O GLUAB 133 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THRAB 138 " --> pdb=" O ALAAB 134 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLUAB 145 " --> pdb=" O LEUAB 141 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASNAB 146 " --> pdb=" O GLUAB 142 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SERAB 147 " --> pdb=" O LYSAB 143 " (cutoff:3.500A) Processing helix chain 'AB' and resid 165 through 170 Processing helix chain 'AB' and resid 171 through 180 removed outlier: 3.656A pdb=" N ASNAB 178 " --> pdb=" O LYSAB 174 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEUAB 179 " --> pdb=" O GLUAB 175 " (cutoff:3.500A) Processing helix chain 'AB' and resid 206 through 227 removed outlier: 4.273A pdb=" N GLNAB 227 " --> pdb=" O GLUAB 223 " (cutoff:3.500A) Processing helix chain 'AC' and resid 6 through 12 removed outlier: 4.119A pdb=" N ARGAC 11 " --> pdb=" O PROAC 7 " (cutoff:3.500A) Processing helix chain 'AC' and resid 28 through 48 removed outlier: 3.543A pdb=" N LYSAC 45 " --> pdb=" O GLNAC 41 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALAAC 48 " --> pdb=" O THRAC 44 " (cutoff:3.500A) Processing helix chain 'AC' and resid 72 through 78 removed outlier: 3.876A pdb=" N VALAC 76 " --> pdb=" O ARGAC 72 " (cutoff:3.500A) Processing helix chain 'AC' and resid 81 through 96 removed outlier: 3.786A pdb=" N GLUAC 85 " --> pdb=" O GLYAC 81 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYSAC 86 " --> pdb=" O GLUAC 82 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILEAC 94 " --> pdb=" O VALAC 90 " (cutoff:3.500A) Processing helix chain 'AC' and resid 108 through 113 removed outlier: 4.148A pdb=" N ASPAC 112 " --> pdb=" O LYSAC 108 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ALAAC 113 " --> pdb=" O PROAC 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 108 through 113' Processing helix chain 'AC' and resid 114 through 127 Processing helix chain 'AC' and resid 129 through 145 removed outlier: 3.731A pdb=" N GLYAC 145 " --> pdb=" O ALAAC 141 " (cutoff:3.500A) Processing helix chain 'AD' and resid 7 through 16 removed outlier: 4.653A pdb=" N LEUAD 11 " --> pdb=" O PROAD 7 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SERAD 12 " --> pdb=" O LYSAD 8 " (cutoff:3.500A) Processing helix chain 'AD' and resid 27 through 32 removed outlier: 3.730A pdb=" N LYSAD 31 " --> pdb=" O ALAAD 27 " (cutoff:3.500A) Processing helix chain 'AD' and resid 49 through 66 Processing helix chain 'AD' and resid 68 through 83 removed outlier: 3.548A pdb=" N ASNAD 74 " --> pdb=" O ARGAD 70 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYSAD 83 " --> pdb=" O ALAAD 79 " (cutoff:3.500A) Processing helix chain 'AD' and resid 85 through 97 removed outlier: 3.607A pdb=" N LEUAD 91 " --> pdb=" O GLYAD 87 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARGAD 97 " --> pdb=" O LEUAD 93 " (cutoff:3.500A) Processing helix chain 'AD' and resid 98 through 106 removed outlier: 3.836A pdb=" N TYRAD 103 " --> pdb=" O ASPAD 99 " (cutoff:3.500A) Processing helix chain 'AD' and resid 110 through 121 removed outlier: 3.619A pdb=" N LYSAD 121 " --> pdb=" O LEUAD 117 " (cutoff:3.500A) Processing helix chain 'AD' and resid 146 through 151 removed outlier: 4.363A pdb=" N LYSAD 151 " --> pdb=" O GLUAD 147 " (cutoff:3.500A) Processing helix chain 'AD' and resid 152 through 166 removed outlier: 3.800A pdb=" N LYSAD 156 " --> pdb=" O GLNAD 152 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALAAD 162 " --> pdb=" O ALAAD 158 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLUAD 163 " --> pdb=" O LEUAD 159 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLNAD 164 " --> pdb=" O GLUAD 160 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARGAD 165 " --> pdb=" O LEUAD 161 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLUAD 166 " --> pdb=" O ALAAD 162 " (cutoff:3.500A) Processing helix chain 'AD' and resid 187 through 192 removed outlier: 4.093A pdb=" N LEUAD 191 " --> pdb=" O GLUAD 187 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N SERAD 192 " --> pdb=" O ARGAD 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'AD' and resid 187 through 192' Processing helix chain 'AD' and resid 196 through 206 removed outlier: 3.963A pdb=" N ILEAD 200 " --> pdb=" O ASNAD 196 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLUAD 202 " --> pdb=" O HISAD 198 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYSAD 206 " --> pdb=" O GLUAD 202 " (cutoff:3.500A) Processing helix chain 'AD' and resid 39 through 44 removed outlier: 4.605A pdb=" N ALAAD 43 " --> pdb=" O GLNAD 40 " (cutoff:3.500A) Processing helix chain 'AE' and resid 55 through 71 removed outlier: 3.894A pdb=" N ARGAE 69 " --> pdb=" O GLUAE 65 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASNAE 70 " --> pdb=" O LYSAE 66 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N METAE 71 " --> pdb=" O ALAAE 67 " (cutoff:3.500A) Processing helix chain 'AE' and resid 109 through 119 removed outlier: 4.215A pdb=" N ALAAE 113 " --> pdb=" O GLYAE 109 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VALAE 114 " --> pdb=" O ALAAE 110 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLYAE 119 " --> pdb=" O LEUAE 115 " (cutoff:3.500A) Processing helix chain 'AE' and resid 132 through 148 removed outlier: 3.646A pdb=" N ARGAE 138 " --> pdb=" O ILEAE 134 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ASNAE 148 " --> pdb=" O LEUAE 144 " (cutoff:3.500A) Processing helix chain 'AE' and resid 149 through 158 Processing helix chain 'AF' and resid 11 through 16 removed outlier: 3.562A pdb=" N SERAF 15 " --> pdb=" O HISAF 11 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLUAF 16 " --> pdb=" O PROAF 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'AF' and resid 11 through 16' Processing helix chain 'AF' and resid 17 through 33 removed outlier: 4.445A pdb=" N GLUAF 23 " --> pdb=" O PROAF 19 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARGAF 24 " --> pdb=" O GLYAF 20 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALAAF 32 " --> pdb=" O ALAAF 28 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLUAF 33 " --> pdb=" O ILEAF 29 " (cutoff:3.500A) Processing helix chain 'AF' and resid 67 through 81 removed outlier: 3.740A pdb=" N ILEAF 71 " --> pdb=" O PROAF 67 " (cutoff:3.500A) Processing helix chain 'AF' and resid 100 through 106 removed outlier: 4.908A pdb=" N LYSAF 106 " --> pdb=" O METAF 102 " (cutoff:3.500A) Processing helix chain 'AG' and resid 20 through 31 Processing helix chain 'AG' and resid 35 through 53 removed outlier: 3.951A pdb=" N LEUAG 50 " --> pdb=" O ALAAG 46 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALAAG 51 " --> pdb=" O LEUAG 47 " (cutoff:3.500A) Processing helix chain 'AG' and resid 57 through 70 removed outlier: 3.679A pdb=" N PHEAG 62 " --> pdb=" O GLUAG 58 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VALAG 69 " --> pdb=" O ALAAG 65 " (cutoff:3.500A) Processing helix chain 'AG' and resid 92 through 111 removed outlier: 3.554A pdb=" N VALAG 105 " --> pdb=" O METAG 101 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYSAG 110 " --> pdb=" O GLUAG 106 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARGAG 111 " --> pdb=" O ALAAG 107 " (cutoff:3.500A) Processing helix chain 'AG' and resid 115 through 130 removed outlier: 3.771A pdb=" N GLUAG 129 " --> pdb=" O SERAG 125 " (cutoff:3.500A) Processing helix chain 'AG' and resid 132 through 149 removed outlier: 3.821A pdb=" N ARGAG 138 " --> pdb=" O ALAAG 134 " (cutoff:3.500A) Processing helix chain 'AH' and resid 5 through 21 Processing helix chain 'AH' and resid 30 through 44 Processing helix chain 'AH' and resid 112 through 120 removed outlier: 3.508A pdb=" N GLNAH 118 " --> pdb=" O ARGAH 114 " (cutoff:3.500A) Processing helix chain 'AI' and resid 34 through 40 removed outlier: 4.926A pdb=" N GLYAI 40 " --> pdb=" O GLUAI 36 " (cutoff:3.500A) Processing helix chain 'AI' and resid 41 through 56 removed outlier: 3.720A pdb=" N VALAI 47 " --> pdb=" O THRAI 43 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VALAI 48 " --> pdb=" O ALAAI 44 " (cutoff:3.500A) Proline residue: AI 51 - end of helix removed outlier: 3.667A pdb=" N LEUAI 54 " --> pdb=" O GLNAI 50 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VALAI 55 " --> pdb=" O PROAI 51 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASPAI 56 " --> pdb=" O LEUAI 52 " (cutoff:3.500A) Processing helix chain 'AI' and resid 71 through 92 removed outlier: 3.796A pdb=" N ASPAI 91 " --> pdb=" O LEUAI 87 " (cutoff:3.500A) Processing helix chain 'AI' and resid 94 through 102 Processing helix chain 'AJ' and resid 14 through 33 removed outlier: 4.951A pdb=" N GLNAJ 20 " --> pdb=" O ARGAJ 16 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLUAJ 27 " --> pdb=" O ALAAJ 23 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THRAJ 28 " --> pdb=" O GLUAJ 24 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 80 through 90 removed outlier: 4.968A pdb=" N VALAJ 84 " --> pdb=" O THRAJ 80 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASPAJ 85 " --> pdb=" O GLUAJ 81 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N METAJ 88 " --> pdb=" O VALAJ 84 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEUAJ 90 " --> pdb=" O ALAAJ 86 " (cutoff:3.500A) Processing helix chain 'AK' and resid 46 through 51 removed outlier: 4.413A pdb=" N GLYAK 51 " --> pdb=" O ALAAK 47 " (cutoff:3.500A) Processing helix chain 'AK' and resid 54 through 59 removed outlier: 3.901A pdb=" N SERAK 58 " --> pdb=" O GLYAK 54 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THRAK 59 " --> pdb=" O SERAK 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'AK' and resid 54 through 59' Processing helix chain 'AK' and resid 60 through 76 removed outlier: 3.538A pdb=" N VALAK 74 " --> pdb=" O CYSAK 70 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYSAK 75 " --> pdb=" O ALAAK 71 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLUAK 76 " --> pdb=" O ASPAK 72 " (cutoff:3.500A) Processing helix chain 'AK' and resid 92 through 104 removed outlier: 3.814A pdb=" N THRAK 96 " --> pdb=" O GLYAK 92 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILEAK 97 " --> pdb=" O ARGAK 93 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARGAK 98 " --> pdb=" O GLUAK 94 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALAAK 99 " --> pdb=" O SERAK 95 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEUAK 100 " --> pdb=" O THRAK 96 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLYAK 104 " --> pdb=" O LEUAK 100 " (cutoff:3.500A) Processing helix chain 'AL' and resid 3 through 11 Proline residue: AL 11 - end of helix Processing helix chain 'AL' and resid 113 through 118 removed outlier: 4.142A pdb=" N TYRAL 117 " --> pdb=" O ALAAL 113 " (cutoff:3.500A) Processing helix chain 'AM' and resid 14 through 22 removed outlier: 4.207A pdb=" N THRAM 20 " --> pdb=" O VALAM 16 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SERAM 21 " --> pdb=" O ILEAM 17 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILEAM 22 " --> pdb=" O ALAAM 18 " (cutoff:3.500A) Processing helix chain 'AM' and resid 26 through 38 Processing helix chain 'AM' and resid 49 through 64 removed outlier: 4.302A pdb=" N GLUAM 59 " --> pdb=" O THRAM 55 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYSAM 62 " --> pdb=" O ASPAM 58 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHEAM 63 " --> pdb=" O GLUAM 59 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VALAM 64 " --> pdb=" O VALAM 60 " (cutoff:3.500A) Processing helix chain 'AM' and resid 66 through 84 Processing helix chain 'AM' and resid 85 through 94 Processing helix chain 'AM' and resid 106 through 111 Processing helix chain 'AN' and resid 2 through 20 removed outlier: 3.879A pdb=" N LYSAN 6 " --> pdb=" O LYSAN 2 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASPAN 17 " --> pdb=" O VALAN 13 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYSAN 18 " --> pdb=" O ALAAN 14 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHEAN 20 " --> pdb=" O ALAAN 16 " (cutoff:3.500A) Processing helix chain 'AN' and resid 24 through 29 removed outlier: 3.657A pdb=" N ILEAN 29 " --> pdb=" O GLUAN 25 " (cutoff:3.500A) Processing helix chain 'AN' and resid 38 through 51 removed outlier: 4.048A pdb=" N GLNAN 49 " --> pdb=" O VALAN 45 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THRAN 50 " --> pdb=" O LEUAN 46 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEUAN 51 " --> pdb=" O LYSAN 47 " (cutoff:3.500A) Processing helix chain 'AN' and resid 80 through 91 removed outlier: 3.672A pdb=" N ARGAN 85 " --> pdb=" O ARGAN 81 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARGAN 90 " --> pdb=" O GLUAN 86 " (cutoff:3.500A) Processing helix chain 'AO' and resid 4 through 16 Processing helix chain 'AO' and resid 24 through 44 removed outlier: 4.525A pdb=" N GLYAO 41 " --> pdb=" O ASNAO 37 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N HISAO 42 " --> pdb=" O HISAO 38 " (cutoff:3.500A) Processing helix chain 'AO' and resid 50 through 74 removed outlier: 3.839A pdb=" N GLYAO 55 " --> pdb=" O HISAO 51 " (cutoff:3.500A) Processing helix chain 'AO' and resid 75 through 86 removed outlier: 3.734A pdb=" N GLNAO 80 " --> pdb=" O ALAAO 76 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEUAO 81 " --> pdb=" O ARGAO 77 " (cutoff:3.500A) Processing helix chain 'AP' and resid 53 through 64 Processing helix chain 'AP' and resid 68 through 82 Processing helix chain 'AR' and resid 25 through 34 removed outlier: 4.347A pdb=" N ASNAR 31 " --> pdb=" O ALAAR 27 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYRAR 32 " --> pdb=" O THRAR 28 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILEAR 33 " --> pdb=" O LEUAR 29 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N THRAR 34 " --> pdb=" O LYSAR 30 " (cutoff:3.500A) Processing helix chain 'AR' and resid 41 through 46 removed outlier: 3.664A pdb=" N THRAR 45 " --> pdb=" O PROAR 41 " (cutoff:3.500A) Processing helix chain 'AR' and resid 48 through 66 removed outlier: 3.567A pdb=" N TYRAR 64 " --> pdb=" O LYSAR 60 " (cutoff:3.500A) Processing helix chain 'AS' and resid 12 through 26 removed outlier: 4.835A pdb=" N GLUAS 24 " --> pdb=" O GLUAS 20 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SERAS 25 " --> pdb=" O LYSAS 21 " (cutoff:3.500A) Processing helix chain 'AS' and resid 70 through 76 removed outlier: 4.790A pdb=" N PHEAS 74 " --> pdb=" O LYSAS 70 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALAAS 75 " --> pdb=" O LEUAS 71 " (cutoff:3.500A) Proline residue: AS 76 - end of helix No H-bonds generated for 'chain 'AS' and resid 70 through 76' Processing helix chain 'AT' and resid 4 through 41 removed outlier: 3.543A pdb=" N VALAT 35 " --> pdb=" O PHEAT 31 " (cutoff:3.500A) Processing helix chain 'AT' and resid 44 through 65 Proline residue: AT 56 - end of helix Processing helix chain 'AT' and resid 68 through 87 Processing helix chain 'AU' and resid 11 through 27 Processing helix chain 'AU' and resid 28 through 37 removed outlier: 5.671A pdb=" N PHEAU 37 " --> pdb=" O ARGAU 33 " (cutoff:3.500A) Processing helix chain 'AU' and resid 40 through 56 removed outlier: 3.554A pdb=" N VALAU 53 " --> pdb=" O LYSAU 49 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N HISAU 56 " --> pdb=" O ALAAU 52 " (cutoff:3.500A) Processing helix chain 'BC' and resid 10 through 15 removed outlier: 5.285A pdb=" N HISBC 15 " --> pdb=" O PROBC 11 " (cutoff:3.500A) Processing helix chain 'BC' and resid 30 through 35 removed outlier: 3.947A pdb=" N LEUBC 34 " --> pdb=" O PHEBC 30 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLUBC 35 " --> pdb=" O ALABC 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 30 through 35' Processing helix chain 'BC' and resid 131 through 136 removed outlier: 3.769A pdb=" N ILEBC 135 " --> pdb=" O PROBC 131 " (cutoff:3.500A) Proline residue: BC 136 - end of helix No H-bonds generated for 'chain 'BC' and resid 131 through 136' Processing helix chain 'BC' and resid 207 through 215 removed outlier: 3.913A pdb=" N ALABC 211 " --> pdb=" O LYSBC 207 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARGBC 212 " --> pdb=" O ALABC 208 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARGBC 214 " --> pdb=" O ALABC 210 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLYBC 215 " --> pdb=" O ALABC 211 " (cutoff:3.500A) Processing helix chain 'BC' and resid 221 through 226 removed outlier: 4.080A pdb=" N METBC 225 " --> pdb=" O ARGBC 221 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ASNBC 226 " --> pdb=" O GLYBC 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 221 through 226' Processing helix chain 'BC' and resid 260 through 268 removed outlier: 3.781A pdb=" N ASPBC 264 " --> pdb=" O ASNBC 260 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LYSBC 265 " --> pdb=" O LYSBC 261 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N PHEBC 266 " --> pdb=" O ARGBC 262 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILEBC 267 " --> pdb=" O THRBC 263 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VALBC 268 " --> pdb=" O ASPBC 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 260 through 268' Processing helix chain 'BC' and resid 197 through 202 removed outlier: 4.258A pdb=" N METBC 201 " --> pdb=" O ALABC 198 " (cutoff:3.500A) Processing helix chain 'BD' and resid 56 through 61 removed outlier: 3.550A pdb=" N VALBD 60 " --> pdb=" O LYSBD 56 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N THRBD 61 " --> pdb=" O ALABD 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'BD' and resid 56 through 61' Processing helix chain 'BD' and resid 62 through 72 removed outlier: 3.548A pdb=" N HISBD 67 " --> pdb=" O PROBD 63 " (cutoff:3.500A) Processing helix chain 'BD' and resid 98 through 103 removed outlier: 4.259A pdb=" N ALABD 102 " --> pdb=" O VALBD 98 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASPBD 103 " --> pdb=" O GLUBD 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'BD' and resid 98 through 103' Processing helix chain 'BD' and resid 120 through 125 Processing helix chain 'BD' and resid 39 through 44 Processing helix chain 'BE' and resid 15 through 20 Processing helix chain 'BE' and resid 24 through 40 removed outlier: 3.510A pdb=" N GLNBE 30 " --> pdb=" O ALABE 26 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALABE 39 " --> pdb=" O TYRBE 35 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARGBE 40 " --> pdb=" O ALABE 36 " (cutoff:3.500A) Processing helix chain 'BE' and resid 97 through 116 Processing helix chain 'BE' and resid 130 through 142 removed outlier: 3.520A pdb=" N LEUBE 134 " --> pdb=" O LYSBE 130 " (cutoff:3.500A) Processing helix chain 'BE' and resid 154 through 163 removed outlier: 3.609A pdb=" N ARGBE 162 " --> pdb=" O PHEBE 158 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASNBE 163 " --> pdb=" O LEUBE 159 " (cutoff:3.500A) Processing helix chain 'BE' and resid 176 through 183 removed outlier: 3.540A pdb=" N LEUBE 180 " --> pdb=" O ASPBE 176 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILEBE 181 " --> pdb=" O PROBE 177 " (cutoff:3.500A) Processing helix chain 'BE' and resid 189 through 201 removed outlier: 3.855A pdb=" N GLUBE 197 " --> pdb=" O VALBE 193 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLUBE 198 " --> pdb=" O LYSBE 194 " (cutoff:3.500A) Processing helix chain 'BF' and resid 2 through 21 removed outlier: 3.608A pdb=" N ASPBF 6 " --> pdb=" O ALABF 2 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VALBF 13 " --> pdb=" O LYSBF 9 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYSBF 14 " --> pdb=" O ASPBF 10 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THRBF 18 " --> pdb=" O LYSBF 14 " (cutoff:3.500A) Processing helix chain 'BF' and resid 42 through 47 removed outlier: 3.805A pdb=" N ASPBF 46 " --> pdb=" O GLUBF 42 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYSBF 47 " --> pdb=" O ALABF 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'BF' and resid 42 through 47' Processing helix chain 'BF' and resid 48 through 62 removed outlier: 3.547A pdb=" N ASPBF 56 " --> pdb=" O ASNBF 52 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEUBF 57 " --> pdb=" O ALABF 53 " (cutoff:3.500A) Processing helix chain 'BF' and resid 93 through 111 removed outlier: 5.051A pdb=" N VALBF 108 " --> pdb=" O ILEBF 104 " (cutoff:3.500A) Proline residue: BF 109 - end of helix Processing helix chain 'BF' and resid 162 through 174 removed outlier: 3.820A pdb=" N PHEBF 173 " --> pdb=" O LEUBF 169 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASPBF 174 " --> pdb=" O LEUBF 170 " (cutoff:3.500A) Processing helix chain 'BF' and resid 134 through 139 removed outlier: 3.830A pdb=" N ILEBF 137 " --> pdb=" O GLUBF 134 " (cutoff:3.500A) Proline residue: BF 139 - end of helix Processing helix chain 'BG' and resid 2 through 8 removed outlier: 3.548A pdb=" N ALABG 7 " --> pdb=" O ARGBG 3 " (cutoff:3.500A) Proline residue: BG 8 - end of helix Processing helix chain 'BG' and resid 60 through 81 Processing helix chain 'BG' and resid 137 through 153 removed outlier: 3.722A pdb=" N TYRBG 151 " --> pdb=" O ASPBG 147 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ARGBG 152 " --> pdb=" O LEUBG 148 " (cutoff:3.500A) Processing helix chain 'BH' and resid 22 through 28 Processing helix chain 'BH' and resid 29 through 34 Processing helix chain 'BH' and resid 42 through 47 removed outlier: 3.837A pdb=" N PHEBH 46 " --> pdb=" O LYSBH 42 " (cutoff:3.500A) Processing helix chain 'BH' and resid 50 through 76 removed outlier: 3.687A pdb=" N ALABH 59 " --> pdb=" O GLUBH 55 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALABH 67 " --> pdb=" O ALABH 63 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARGBH 68 " --> pdb=" O ALABH 64 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLUBH 70 " --> pdb=" O ASNBH 66 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYSBH 71 " --> pdb=" O ALABH 67 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILEBH 72 " --> pdb=" O ARGBH 68 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASNBH 73 " --> pdb=" O ALABH 69 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALABH 74 " --> pdb=" O GLUBH 70 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEUBH 75 " --> pdb=" O LYSBH 71 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLUBH 76 " --> pdb=" O ILEBH 72 " (cutoff:3.500A) Processing helix chain 'BH' and resid 95 through 107 removed outlier: 4.033A pdb=" N ALABH 102 " --> pdb=" O ASPBH 98 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALABH 105 " --> pdb=" O ASPBH 101 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALABH 106 " --> pdb=" O ALABH 102 " (cutoff:3.500A) Processing helix chain 'BI' and resid 47 through 52 removed outlier: 4.499A pdb=" N VALBI 51 " --> pdb=" O LYSBI 47 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALABI 52 " --> pdb=" O GLNBI 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'BI' and resid 47 through 52' Processing helix chain 'BI' and resid 56 through 65 removed outlier: 3.635A pdb=" N PHEBI 60 " --> pdb=" O ARGBI 56 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYSBI 62 " --> pdb=" O ASPBI 58 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARGBI 63 " --> pdb=" O ARGBI 59 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHEBI 64 " --> pdb=" O PHEBI 60 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 24 through 38 removed outlier: 5.013A pdb=" N GLUBJ 31 " --> pdb=" O ARGBJ 27 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 88 through 96 Processing helix chain 'BJ' and resid 97 through 110 removed outlier: 4.198A pdb=" N ILEBJ 101 " --> pdb=" O PROBJ 97 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N METBJ 108 " --> pdb=" O ALABJ 104 " (cutoff:3.500A) Proline residue: BJ 110 - end of helix Processing helix chain 'BJ' and resid 112 through 122 removed outlier: 3.632A pdb=" N ARGBJ 120 " --> pdb=" O ARGBJ 116 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYSBJ 121 " --> pdb=" O ALABJ 117 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEUBJ 122 " --> pdb=" O METBJ 118 " (cutoff:3.500A) Processing helix chain 'BK' and resid 104 through 109 removed outlier: 4.891A pdb=" N ARGBK 108 " --> pdb=" O THRBK 104 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N SERBK 109 " --> pdb=" O ARGBK 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'BK' and resid 104 through 109' Processing helix chain 'BK' and resid 112 through 119 Processing helix chain 'BL' and resid 56 through 62 removed outlier: 3.617A pdb=" N LEUBL 61 " --> pdb=" O LEUBL 57 " (cutoff:3.500A) Proline residue: BL 62 - end of helix Processing helix chain 'BL' and resid 68 through 75 removed outlier: 4.247A pdb=" N ALABL 72 " --> pdb=" O SERBL 68 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILEBL 73 " --> pdb=" O ARGBL 69 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THRBL 74 " --> pdb=" O LYSBL 70 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALABL 75 " --> pdb=" O ALABL 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'BL' and resid 68 through 75' Processing helix chain 'BL' and resid 78 through 85 removed outlier: 4.005A pdb=" N LEUBL 82 " --> pdb=" O ARGBL 78 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALABL 83 " --> pdb=" O LEUBL 79 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LYSBL 84 " --> pdb=" O SERBL 80 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VALBL 85 " --> pdb=" O ASPBL 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'BL' and resid 78 through 85' Processing helix chain 'BL' and resid 91 through 99 removed outlier: 3.574A pdb=" N ASNBL 99 " --> pdb=" O LEUBL 95 " (cutoff:3.500A) Processing helix chain 'BL' and resid 128 through 139 removed outlier: 3.574A pdb=" N ALABL 138 " --> pdb=" O ALABL 134 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLYBL 139 " --> pdb=" O ILEBL 135 " (cutoff:3.500A) Processing helix chain 'BM' and resid 42 through 58 removed outlier: 3.502A pdb=" N LYSBM 58 " --> pdb=" O THRBM 54 " (cutoff:3.500A) Processing helix chain 'BM' and resid 109 through 125 removed outlier: 3.654A pdb=" N ALABM 122 " --> pdb=" O LYSBM 118 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYSBM 123 " --> pdb=" O LEUBM 119 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEUBM 124 " --> pdb=" O ALABM 120 " (cutoff:3.500A) Proline residue: BM 125 - end of helix Processing helix chain 'BN' and resid 13 through 32 Processing helix chain 'BN' and resid 37 through 57 removed outlier: 3.678A pdb=" N ARGBN 45 " --> pdb=" O ALABN 41 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARGBN 46 " --> pdb=" O LYSBN 42 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VALBN 47 " --> pdb=" O GLUBN 43 " (cutoff:3.500A) Proline residue: BN 50 - end of helix removed outlier: 3.516A pdb=" N LYSBN 56 " --> pdb=" O ILEBN 52 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THRBN 57 " --> pdb=" O THRBN 53 " (cutoff:3.500A) Processing helix chain 'BN' and resid 59 through 71 Processing helix chain 'BN' and resid 72 through 88 removed outlier: 3.546A pdb=" N LEUBN 83 " --> pdb=" O LEUBN 79 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLYBN 84 " --> pdb=" O PHEBN 80 " (cutoff:3.500A) Proline residue: BN 85 - end of helix Processing helix chain 'BO' and resid 2 through 22 removed outlier: 4.739A pdb=" N ARGBO 13 " --> pdb=" O ARGBO 9 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ALABO 14 " --> pdb=" O ARGBO 10 " (cutoff:3.500A) Processing helix chain 'BO' and resid 55 through 63 removed outlier: 3.578A pdb=" N ALABO 59 " --> pdb=" O GLUBO 55 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLUBO 60 " --> pdb=" O LYSBO 56 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLNBO 61 " --> pdb=" O ALABO 57 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEUBO 62 " --> pdb=" O ILEBO 58 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LYSBO 63 " --> pdb=" O ALABO 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'BO' and resid 55 through 63' Processing helix chain 'BO' and resid 67 through 86 removed outlier: 3.627A pdb=" N ALABO 73 " --> pdb=" O ASPBO 69 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLUBO 84 " --> pdb=" O GLUBO 80 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYSBO 85 " --> pdb=" O ARGBO 81 " (cutoff:3.500A) Processing helix chain 'BO' and resid 101 through 114 removed outlier: 3.511A pdb=" N GLUBO 112 " --> pdb=" O ASPBO 108 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALABO 113 " --> pdb=" O ALABO 109 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLYBO 114 " --> pdb=" O ALABO 110 " (cutoff:3.500A) Processing helix chain 'BP' and resid 2 through 13 removed outlier: 3.879A pdb=" N GLUBP 11 " --> pdb=" O GLNBP 7 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLNBP 12 " --> pdb=" O LEUBP 8 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N METBP 13 " --> pdb=" O GLUBP 9 " (cutoff:3.500A) Processing helix chain 'BP' and resid 97 through 104 removed outlier: 4.551A pdb=" N ARGBP 101 " --> pdb=" O LEUBP 97 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLUBP 102 " --> pdb=" O TYRBP 98 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARGBP 103 " --> pdb=" O TYRBP 99 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THRBP 104 " --> pdb=" O LEUBP 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP' and resid 97 through 104' Processing helix chain 'BQ' and resid 6 through 22 removed outlier: 3.632A pdb=" N ILEBQ 17 " --> pdb=" O ARGBQ 13 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLNBQ 20 " --> pdb=" O LYSBQ 16 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYSBQ 22 " --> pdb=" O LEUBQ 18 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 26 through 31 removed outlier: 3.882A pdb=" N ARGBQ 30 " --> pdb=" O GLYBQ 26 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 32 through 37 removed outlier: 4.058A pdb=" N GLNBQ 37 " --> pdb=" O ARGBQ 33 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 39 through 73 removed outlier: 3.936A pdb=" N ARGBQ 51 " --> pdb=" O TYRBQ 47 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLNBQ 52 " --> pdb=" O ARGBQ 48 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYSBQ 54 " --> pdb=" O ARGBQ 50 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARGBQ 55 " --> pdb=" O ARGBQ 51 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARGBQ 58 " --> pdb=" O LYSBQ 54 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASNBQ 72 " --> pdb=" O ALABQ 68 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 75 through 87 removed outlier: 3.568A pdb=" N ASNBQ 81 " --> pdb=" O SERBQ 77 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 91 through 102 removed outlier: 3.541A pdb=" N ASPBQ 97 " --> pdb=" O LYSBQ 93 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VALBQ 100 " --> pdb=" O ALABQ 96 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 103 through 118 Processing helix chain 'BS' and resid 13 through 25 removed outlier: 3.870A pdb=" N LEUBS 19 " --> pdb=" O GLNBS 15 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VALBS 20 " --> pdb=" O LYSBS 16 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEUBS 23 " --> pdb=" O LEUBS 19 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILEBS 24 " --> pdb=" O VALBS 20 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARGBS 25 " --> pdb=" O ALABS 21 " (cutoff:3.500A) Processing helix chain 'BS' and resid 28 through 40 removed outlier: 3.573A pdb=" N ASPBS 34 " --> pdb=" O SERBS 30 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYRBS 38 " --> pdb=" O ASPBS 34 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THRBS 39 " --> pdb=" O ILEBS 35 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASNBS 40 " --> pdb=" O LEUBS 36 " (cutoff:3.500A) Processing helix chain 'BS' and resid 41 through 61 removed outlier: 3.821A pdb=" N VALBS 45 " --> pdb=" O LYSBS 41 " (cutoff:3.500A) Processing helix chain 'BT' and resid 3 through 11 removed outlier: 4.021A pdb=" N LYSBT 9 " --> pdb=" O GLUBT 5 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VALBT 10 " --> pdb=" O ARGBT 6 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEUBT 11 " --> pdb=" O LEUBT 7 " (cutoff:3.500A) Processing helix chain 'BT' and resid 17 through 27 Processing helix chain 'BT' and resid 39 through 51 Processing helix chain 'BU' and resid 66 through 71 removed outlier: 3.945A pdb=" N VALBU 70 " --> pdb=" O GLNBU 66 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ALABU 71 " --> pdb=" O VALBU 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'BU' and resid 66 through 71' Processing helix chain 'BV' and resid 13 through 24 removed outlier: 3.510A pdb=" N ASNBV 24 " --> pdb=" O LEUBV 20 " (cutoff:3.500A) Processing helix chain 'BV' and resid 43 through 53 removed outlier: 3.831A pdb=" N ALABV 52 " --> pdb=" O METBV 48 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYSBV 53 " --> pdb=" O ASNBV 49 " (cutoff:3.500A) Processing helix chain 'BV' and resid 54 through 59 removed outlier: 4.108A pdb=" N SERBV 58 " --> pdb=" O ALABV 54 " (cutoff:3.500A) Processing helix chain 'BX' and resid 52 through 63 removed outlier: 3.733A pdb=" N ARGBX 57 " --> pdb=" O ALABX 53 " (cutoff:3.500A) Processing helix chain 'BX' and resid 64 through 75 Processing helix chain 'BY' and resid 2 through 10 removed outlier: 5.879A pdb=" N LEUBY 6 " --> pdb=" O LYSBY 2 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARGBY 7 " --> pdb=" O ALABY 3 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLUBY 8 " --> pdb=" O LYSBY 4 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYSBY 9 " --> pdb=" O GLUBY 5 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SERBY 10 " --> pdb=" O LEUBY 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'BY' and resid 2 through 10' Processing helix chain 'BY' and resid 11 through 35 Processing helix chain 'BY' and resid 39 through 62 removed outlier: 4.640A pdb=" N LEUBY 43 " --> pdb=" O GLNBY 39 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYSBY 44 " --> pdb=" O SERBY 40 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 17 through 28 Processing helix chain 'BZ' and resid 41 through 52 removed outlier: 3.569A pdb=" N METBZ 47 " --> pdb=" O ALABZ 43 " (cutoff:3.500A) Processing helix chain 'B0' and resid 9 through 19 removed outlier: 3.604A pdb=" N ARGB0 17 " --> pdb=" O ARGB0 13 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N HISB0 19 " --> pdb=" O METB0 15 " (cutoff:3.500A) Processing helix chain 'B2' and resid 8 through 16 Processing helix chain 'B2' and resid 17 through 25 removed outlier: 4.411A pdb=" N THRB2 24 " --> pdb=" O ALAB2 20 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LYSB2 25 " --> pdb=" O ARGB2 21 " (cutoff:3.500A) Processing helix chain 'B2' and resid 26 through 38 Processing helix chain 'B3' and resid 7 through 14 removed outlier: 3.714A pdb=" N LYSB3 12 " --> pdb=" O ARGB3 8 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARGB3 13 " --> pdb=" O GLYB3 9 " (cutoff:3.500A) Processing helix chain 'B3' and resid 32 through 37 removed outlier: 4.392A pdb=" N LYSB3 36 " --> pdb=" O ILEB3 32 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ALAB3 37 " --> pdb=" O LEUB3 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 32 through 37' Processing helix chain 'B3' and resid 38 through 46 removed outlier: 3.599A pdb=" N ARGB3 45 " --> pdb=" O LYSB3 41 " (cutoff:3.500A) Proline residue: B3 46 - end of helix Processing helix chain 'B3' and resid 51 through 63 removed outlier: 4.600A pdb=" N GLYB3 56 " --> pdb=" O LYSB3 52 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEUB3 57 " --> pdb=" O GLYB3 53 " (cutoff:3.500A) Proline residue: B3 63 - end of helix Processing helix chain 'B5' and resid 11 through 17 removed outlier: 5.995A pdb=" N ASNB5 17 " --> pdb=" O PHEB5 13 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'AB' and resid 15 through 18 removed outlier: 5.298A pdb=" N HISAB 15 " --> pdb=" O ILEAB 41 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N HISAB 39 " --> pdb=" O GLYAB 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'AB' and resid 90 through 93 removed outlier: 3.576A pdb=" N PHEAB 198 " --> pdb=" O VALAB 183 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALAAB 185 " --> pdb=" O PHEAB 198 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'AC' and resid 53 through 59 removed outlier: 3.855A pdb=" N THRAC 70 " --> pdb=" O ALAAC 104 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'AC' and resid 164 through 169 removed outlier: 5.706A pdb=" N ARGAC 164 " --> pdb=" O GLYAC 155 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLYAC 148 " --> pdb=" O PHEAC 203 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'AD' and resid 141 through 144 removed outlier: 3.902A pdb=" N ASPAD 141 " --> pdb=" O PHEAD 182 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLUAD 179 " --> pdb=" O ASPAD 174 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'AE' and resid 12 through 16 removed outlier: 6.592A pdb=" N LEUAE 36 " --> pdb=" O ILEAE 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'AE' and resid 83 through 88 removed outlier: 7.197A pdb=" N HISAE 83 " --> pdb=" O PROAE 98 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALAAE 99 " --> pdb=" O ASNAE 122 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASNAE 122 " --> pdb=" O ALAAE 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'AE' and resid 33 through 40 Processing sheet with id= 9, first strand: chain 'AF' and resid 38 through 42 removed outlier: 3.688A pdb=" N ARGAF 38 " --> pdb=" O ASNAF 63 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TYRAF 59 " --> pdb=" O TRPAF 42 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N HISAF 3 " --> pdb=" O THRAF 92 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARGAF 86 " --> pdb=" O METAF 9 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'AF' and resid 43 through 47 removed outlier: 3.632A pdb=" N GLYAF 43 " --> pdb=" O TYRAF 59 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEUAF 47 " --> pdb=" O HISAF 55 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N HISAF 55 " --> pdb=" O LEUAF 47 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'AG' and resid 73 through 79 Processing sheet with id= 12, first strand: chain 'AH' and resid 23 through 29 removed outlier: 6.662A pdb=" N ALAAH 23 " --> pdb=" O LEUAH 63 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASPAH 48 " --> pdb=" O THRAH 62 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'AH' and resid 74 through 77 removed outlier: 3.678A pdb=" N CYSAH 127 " --> pdb=" O VALAH 103 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VALAH 103 " --> pdb=" O ILEAH 126 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'AI' and resid 5 through 11 Processing sheet with id= 15, first strand: chain 'AJ' and resid 6 through 12 Processing sheet with id= 16, first strand: chain 'AJ' and resid 39 through 42 removed outlier: 4.510A pdb=" N LEUAJ 71 " --> pdb=" O LEUAJ 42 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'AK' and resid 42 through 45 Processing sheet with id= 18, first strand: chain 'AL' and resid 29 through 33 removed outlier: 5.022A pdb=" N LEUAL 81 " --> pdb=" O VALAL 98 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'AL' and resid 36 through 41 removed outlier: 5.323A pdb=" N LYSAL 51 " --> pdb=" O ILEAL 67 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'AP' and resid 4 through 10 Processing sheet with id= 21, first strand: chain 'AQ' and resid 7 through 11 removed outlier: 7.289A pdb=" N GLUAQ 60 " --> pdb=" O VALAQ 76 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'AQ' and resid 19 through 30 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'AS' and resid 30 through 34 removed outlier: 4.318A pdb=" N LEUAS 47 " --> pdb=" O VALAS 62 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'BC' and resid 2 through 6 removed outlier: 4.088A pdb=" N ALABC 2 " --> pdb=" O VALBC 20 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VALBC 16 " --> pdb=" O CYSBC 6 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'BC' and resid 80 through 83 removed outlier: 6.748A pdb=" N LEUBC 93 " --> pdb=" O GLUBC 79 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ILEBC 74 " --> pdb=" O SERBC 118 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SERBC 118 " --> pdb=" O ILEBC 74 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASPBC 114 " --> pdb=" O VALBC 78 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLYBC 127 " --> pdb=" O GLNBC 115 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLNBC 117 " --> pdb=" O GLYBC 127 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'BC' and resid 138 through 142 removed outlier: 4.304A pdb=" N SERBC 139 " --> pdb=" O ILEBC 164 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THRBC 173 " --> pdb=" O VALBC 165 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLUBC 180 " --> pdb=" O LEUBC 176 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'BC' and resid 90 through 96 removed outlier: 5.442A pdb=" N ASNBC 90 " --> pdb=" O ALABC 106 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLUBC 100 " --> pdb=" O TYRBC 96 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'BD' and resid 3 through 6 removed outlier: 4.229A pdb=" N GLUBD 168 " --> pdb=" O SERBD 113 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'BD' and resid 10 through 16 removed outlier: 3.674A pdb=" N GLYBD 10 " --> pdb=" O VALBD 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VALBD 20 " --> pdb=" O THRBD 16 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'BD' and resid 79 through 84 removed outlier: 5.798A pdb=" N ARGBD 46 " --> pdb=" O LEUBD 84 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLNBD 49 " --> pdb=" O THRBD 35 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLNBD 94 " --> pdb=" O VALBD 34 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'BD' and resid 105 through 108 removed outlier: 6.543A pdb=" N LYSBD 105 " --> pdb=" O VALBD 177 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'BE' and resid 2 through 6 removed outlier: 4.938A pdb=" N SERBE 10 " --> pdb=" O LEUBE 5 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'BE' and resid 117 through 120 removed outlier: 5.755A pdb=" N ARGBE 117 " --> pdb=" O ASPBE 184 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'BF' and resid 65 through 70 removed outlier: 6.486A pdb=" N LEUBF 66 " --> pdb=" O CYSBF 87 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N CYSBF 87 " --> pdb=" O LEUBF 66 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THRBF 68 " --> pdb=" O ILEBF 85 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TYRBF 83 " --> pdb=" O ALABF 70 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLYBF 39 " --> pdb=" O GLYBF 151 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLYBF 151 " --> pdb=" O GLYBF 39 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'BF' and resid 72 through 75 removed outlier: 5.173A pdb=" N SERBF 73 " --> pdb=" O ARGBF 80 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARGBF 80 " --> pdb=" O SERBF 73 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ALABF 75 " --> pdb=" O LYSBF 78 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'BG' and resid 15 through 20 removed outlier: 6.518A pdb=" N GLNBG 22 " --> pdb=" O LEUBG 37 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLYBG 31 " --> pdb=" O GLYBG 28 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'BG' and resid 40 through 43 removed outlier: 6.973A pdb=" N ALABG 40 " --> pdb=" O ARGBG 55 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'BG' and resid 94 through 99 removed outlier: 3.570A pdb=" N VALBG 102 " --> pdb=" O LYSBG 99 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASNBG 101 " --> pdb=" O LEUBG 117 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VALBG 113 " --> pdb=" O LEUBG 105 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'BG' and resid 121 through 125 removed outlier: 5.837A pdb=" N THRBG 129 " --> pdb=" O LEUBG 89 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'BH' and resid 17 through 21 removed outlier: 4.796A pdb=" N ASPBH 17 " --> pdb=" O LEUBH 5 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLNBH 2 " --> pdb=" O ALABH 39 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'BH' and resid 77 through 83 removed outlier: 3.531A pdb=" N VALBH 78 " --> pdb=" O ILEBH 143 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILEBH 80 " --> pdb=" O ASNBH 145 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VALBH 147 " --> pdb=" O ILEBH 80 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N SERBH 82 " --> pdb=" O VALBH 147 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLUBH 149 " --> pdb=" O SERBH 82 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VALBH 144 " --> pdb=" O HISBH 128 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N HISBH 128 " --> pdb=" O VALBH 144 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLUBH 114 " --> pdb=" O GLNBH 133 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'BI' and resid 12 through 15 No H-bonds generated for sheet with id= 42 Processing sheet with id= 43, first strand: chain 'BJ' and resid 52 through 57 removed outlier: 5.135A pdb=" N ASPBJ 19 " --> pdb=" O LEUBJ 140 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'BJ' and resid 74 through 78 removed outlier: 7.417A pdb=" N GLYBJ 83 " --> pdb=" O THRBJ 78 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'BK' and resid 18 through 21 removed outlier: 4.256A pdb=" N THRBK 6 " --> pdb=" O CYSBK 21 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ASNBK 82 " --> pdb=" O METBK 7 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'BM' and resid 62 through 65 removed outlier: 3.583A pdb=" N TYRBM 103 " --> pdb=" O LEUBM 33 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEUBM 33 " --> pdb=" O LEUBM 102 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYSBM 100 " --> pdb=" O ALABM 35 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'BM' and resid 73 through 76 removed outlier: 6.797A pdb=" N ILEBM 73 " --> pdb=" O GLUBM 90 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASNBM 88 " --> pdb=" O GLUBM 75 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'BM' and resid 30 through 36 removed outlier: 7.575A pdb=" N SERBM 30 " --> pdb=" O LYSBM 133 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYSBM 127 " --> pdb=" O VALBM 36 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'BN' and resid 33 through 36 removed outlier: 4.324A pdb=" N METBN 110 " --> pdb=" O CYSBN 100 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'BO' and resid 49 through 52 removed outlier: 3.701A pdb=" N VALBO 49 " --> pdb=" O VALBO 39 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'BP' and resid 38 through 45 removed outlier: 6.469A pdb=" N THRBP 25 " --> pdb=" O LYSBP 87 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SERBP 83 " --> pdb=" O LYSBP 29 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'BP' and resid 49 through 53 removed outlier: 3.862A pdb=" N ALABP 49 " --> pdb=" O THRBP 60 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARGBP 53 " --> pdb=" O HISBP 56 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HISBP 56 " --> pdb=" O ARGBP 53 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N SERBP 57 " --> pdb=" O THRBP 76 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'BR' and resid 11 through 15 removed outlier: 3.769A pdb=" N METBR 40 " --> pdb=" O VALBR 4 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'BR' and resid 18 through 21 removed outlier: 4.342A pdb=" N GLNBR 18 " --> pdb=" O ILEBR 98 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASPBR 95 " --> pdb=" O VALBR 64 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYSBR 60 " --> pdb=" O THRBR 99 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLUBR 31 " --> pdb=" O VALBR 63 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'BR' and resid 57 through 60 Processing sheet with id= 56, first strand: chain 'BR' and resid 65 through 68 Processing sheet with id= 57, first strand: chain 'BR' and resid 71 through 78 removed outlier: 4.181A pdb=" N TYRBR 83 " --> pdb=" O ARGBR 78 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'BS' and resid 2 through 8 removed outlier: 6.732A pdb=" N VALBS 106 " --> pdb=" O THRBS 72 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'BS' and resid 73 through 79 removed outlier: 4.704A pdb=" N THRBS 100 " --> pdb=" O GLYBS 79 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'BS' and resid 81 through 88 removed outlier: 4.183A pdb=" N ARGBS 92 " --> pdb=" O ARGBS 88 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'BT' and resid 28 through 33 removed outlier: 6.063A pdb=" N ASNBT 28 " --> pdb=" O LEUBT 87 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYSBT 66 " --> pdb=" O ARGBT 77 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASPBT 79 " --> pdb=" O LYSBT 64 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LYSBT 64 " --> pdb=" O ASPBT 79 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYSBT 81 " --> pdb=" O VALBT 62 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VALBT 62 " --> pdb=" O LYSBT 81 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALABT 83 " --> pdb=" O THRBT 60 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THRBT 60 " --> pdb=" O ALABT 83 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VALBT 85 " --> pdb=" O VALBT 58 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VALBT 58 " --> pdb=" O VALBT 85 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'BU' and resid 40 through 45 removed outlier: 5.619A pdb=" N ASNBU 40 " --> pdb=" O ALABU 63 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'BU' and resid 83 through 86 Processing sheet with id= 64, first strand: chain 'BV' and resid 69 through 72 removed outlier: 3.813A pdb=" N ILEBV 89 " --> pdb=" O PROBV 27 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASPBV 76 " --> pdb=" O ASPBV 90 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'BW' and resid 66 through 71 Processing sheet with id= 66, first strand: chain 'BX' and resid 12 through 19 removed outlier: 3.542A pdb=" N GLYBX 15 " --> pdb=" O ARGBX 27 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASNBX 23 " --> pdb=" O SERBX 19 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'BX' and resid 35 through 41 removed outlier: 3.559A pdb=" N ARGBX 45 " --> pdb=" O VALBX 40 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'BZ' and resid 34 through 39 removed outlier: 4.467A pdb=" N HISBZ 34 " --> pdb=" O GLNBZ 9 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N METBZ 54 " --> pdb=" O THRBZ 10 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'B0' and resid 29 through 32 removed outlier: 4.301A pdb=" N GLUB0 36 " --> pdb=" O ASPB0 31 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'B1' and resid 20 through 26 removed outlier: 7.226A pdb=" N ILEB1 48 " --> pdb=" O SERB1 14 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEUB1 34 " --> pdb=" O GLUB1 51 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'B3' and resid 22 through 25 removed outlier: 5.725A pdb=" N PHEB3 22 " --> pdb=" O VALB3 50 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'B4' and resid 14 through 19 1753 hydrogen bonds defined for protein. 5160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4065 hydrogen bonds 6278 hydrogen bond angles 0 basepair planarities 1623 basepair parallelities 2539 stacking parallelities Total time for adding SS restraints: 390.86 Time building geometry restraints manager: 63.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 11650 1.28 - 1.42: 63837 1.42 - 1.55: 71373 1.55 - 1.69: 9467 1.69 - 1.83: 265 Bond restraints: 156592 Sorted by residual: bond pdb=" C4 5MUBA1939 " pdb=" C5 5MUBA1939 " ideal model delta sigma weight residual 1.802 1.420 0.382 2.00e-02 2.50e+03 3.65e+02 bond pdb=" C4 5MUBA 747 " pdb=" C5 5MUBA 747 " ideal model delta sigma weight residual 1.802 1.421 0.381 2.00e-02 2.50e+03 3.63e+02 bond pdb=" C2' ABA 892 " pdb=" C1' ABA 892 " ideal model delta sigma weight residual 1.529 1.288 0.241 1.50e-02 4.44e+03 2.59e+02 bond pdb=" O4' ABA 892 " pdb=" C1' ABA 892 " ideal model delta sigma weight residual 1.412 1.624 -0.212 1.50e-02 4.44e+03 2.00e+02 bond pdb=" N PROB5 24 " pdb=" CD PROB5 24 " ideal model delta sigma weight residual 1.473 1.664 -0.191 1.40e-02 5.10e+03 1.86e+02 ... (remaining 156587 not shown) Histogram of bond angle deviations from ideal: 95.08 - 105.45: 21510 105.45 - 115.82: 113592 115.82 - 126.19: 86210 126.19 - 136.55: 13058 136.55 - 146.92: 6 Bond angle restraints: 234376 Sorted by residual: angle pdb=" C1' OMGBA2251 " pdb=" N9 OMGBA2251 " pdb=" C8 OMGBA2251 " ideal model delta sigma weight residual 142.82 117.24 25.58 3.00e+00 1.11e-01 7.27e+01 angle pdb=" C1' OMGBA2251 " pdb=" N9 OMGBA2251 " pdb=" C4 OMGBA2251 " ideal model delta sigma weight residual 108.29 133.80 -25.51 3.00e+00 1.11e-01 7.23e+01 angle pdb=" CA PROBK 102 " pdb=" N PROBK 102 " pdb=" CD PROBK 102 " ideal model delta sigma weight residual 112.00 101.40 10.60 1.40e+00 5.10e-01 5.73e+01 angle pdb=" C3' OMGBA2251 " pdb=" O3' OMGBA2251 " pdb=" P GBA2252 " ideal model delta sigma weight residual 120.20 129.40 -9.20 1.50e+00 4.44e-01 3.76e+01 angle pdb=" CA PROAU 2 " pdb=" N PROAU 2 " pdb=" CD PROAU 2 " ideal model delta sigma weight residual 112.00 103.66 8.34 1.40e+00 5.10e-01 3.55e+01 ... (remaining 234371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 89069 35.82 - 71.64: 10010 71.64 - 107.46: 1123 107.46 - 143.28: 16 143.28 - 179.10: 14 Dihedral angle restraints: 100232 sinusoidal: 84016 harmonic: 16216 Sorted by residual: dihedral pdb=" CA HISB3 31 " pdb=" C HISB3 31 " pdb=" N ILEB3 32 " pdb=" CA ILEB3 32 " ideal model delta harmonic sigma weight residual -180.00 -127.51 -52.49 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" O4' CAA 489 " pdb=" C1' CAA 489 " pdb=" N1 CAA 489 " pdb=" C2 CAA 489 " ideal model delta sinusoidal sigma weight residual -160.00 12.80 -172.80 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' UB8 55 " pdb=" C1' UB8 55 " pdb=" N1 UB8 55 " pdb=" C2 UB8 55 " ideal model delta sinusoidal sigma weight residual 200.00 35.91 164.09 1 1.50e+01 4.44e-03 8.37e+01 ... (remaining 100229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 26333 0.079 - 0.159: 3106 0.159 - 0.238: 395 0.238 - 0.318: 42 0.318 - 0.397: 5 Chirality restraints: 29881 Sorted by residual: chirality pdb=" P CB8 75 " pdb=" OP1 CB8 75 " pdb=" OP2 CB8 75 " pdb=" O5' CB8 75 " both_signs ideal model delta sigma weight residual True 2.41 -2.01 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C2' ABA 892 " pdb=" C3' ABA 892 " pdb=" O2' ABA 892 " pdb=" C1' ABA 892 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" P ABA2051 " pdb=" OP1 ABA2051 " pdb=" OP2 ABA2051 " pdb=" O5' ABA2051 " both_signs ideal model delta sigma weight residual True 2.41 -2.07 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 29878 not shown) Planarity restraints: 12470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGBA2251 " -0.158 2.00e-02 2.50e+03 6.56e-01 9.68e+03 pdb=" C4' OMGBA2251 " -0.475 2.00e-02 2.50e+03 pdb=" O4' OMGBA2251 " -0.611 2.00e-02 2.50e+03 pdb=" C3' OMGBA2251 " 0.577 2.00e-02 2.50e+03 pdb=" O3' OMGBA2251 " 0.786 2.00e-02 2.50e+03 pdb=" C2' OMGBA2251 " 0.126 2.00e-02 2.50e+03 pdb=" O2' OMGBA2251 " -1.096 2.00e-02 2.50e+03 pdb=" C1' OMGBA2251 " -0.175 2.00e-02 2.50e+03 pdb=" N9 OMGBA2251 " 1.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MGAA1516 " 0.078 2.00e-02 2.50e+03 6.02e-01 8.16e+03 pdb=" C4' 2MGAA1516 " 0.432 2.00e-02 2.50e+03 pdb=" O4' 2MGAA1516 " 0.580 2.00e-02 2.50e+03 pdb=" C3' 2MGAA1516 " -0.596 2.00e-02 2.50e+03 pdb=" O3' 2MGAA1516 " -0.666 2.00e-02 2.50e+03 pdb=" C2' 2MGAA1516 " -0.152 2.00e-02 2.50e+03 pdb=" O2' 2MGAA1516 " 1.012 2.00e-02 2.50e+03 pdb=" C1' 2MGAA1516 " 0.228 2.00e-02 2.50e+03 pdb=" N9 2MGAA1516 " -0.916 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MCAA1407 " -0.061 2.00e-02 2.50e+03 5.91e-01 7.86e+03 pdb=" C4' 5MCAA1407 " -0.438 2.00e-02 2.50e+03 pdb=" O4' 5MCAA1407 " -0.610 2.00e-02 2.50e+03 pdb=" C3' 5MCAA1407 " 0.596 2.00e-02 2.50e+03 pdb=" O3' 5MCAA1407 " 0.636 2.00e-02 2.50e+03 pdb=" C2' 5MCAA1407 " 0.180 2.00e-02 2.50e+03 pdb=" O2' 5MCAA1407 " -0.970 2.00e-02 2.50e+03 pdb=" C1' 5MCAA1407 " -0.224 2.00e-02 2.50e+03 pdb=" N1 5MCAA1407 " 0.891 2.00e-02 2.50e+03 ... (remaining 12467 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 965 2.12 - 2.82: 42608 2.82 - 3.51: 184573 3.51 - 4.21: 473100 4.21 - 4.90: 631595 Nonbonded interactions: 1332841 Sorted by model distance: nonbonded pdb=" C PROB5 24 " pdb=" O3' AB8 76 " model vdw 1.430 3.270 nonbonded pdb=" OP1 GBA 962 " pdb="MG MGBA3083 " model vdw 1.434 2.170 nonbonded pdb=" OP1 GAA 588 " pdb=" O HOHAA1701 " model vdw 1.472 2.440 nonbonded pdb=" OP1 UAA1224 " pdb="MG MGAA1607 " model vdw 1.540 2.170 nonbonded pdb=" OP2 ABA2821 " pdb="MG MGBA3107 " model vdw 1.552 2.170 ... (remaining 1332836 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.610 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: 0.180 Extract box with map and model: 19.550 Check model and map are aligned: 1.610 Set scattering table: 1.060 Process input model: 705.570 Find NCS groups from input model: 3.170 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:11.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 746.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 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 : 0.016 0.382 156592 Z= 0.946 Angle : 1.840 25.585 234376 Z= 0.698 Chirality : 0.053 0.397 29881 Planarity : 0.018 0.656 12470 Dihedral : 22.503 179.101 89768 Min Nonbonded Distance : 1.430 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.22 % Rotamer: Outliers : 0.04 % Allowed : 0.45 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.50 (0.10), residues: 5584 helix: -1.69 (0.11), residues: 1771 sheet: -0.08 (0.15), residues: 1141 loop : -0.76 (0.11), residues: 2672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPAB 23 HIS 0.037 0.002 HISAF 3 PHE 0.029 0.003 PHEBM 31 TYR 0.038 0.002 TYRBN 112 ARG 0.029 0.001 ARGBD 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 855 time to evaluate : 6.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AE 72 ILE cc_start: 0.8452 (pt) cc_final: 0.7601 (mm) REVERT: AO 89 ARG cc_start: 0.4361 (ptt180) cc_final: 0.1243 (pmt170) REVERT: AQ 48 ASP cc_start: 0.7550 (t0) cc_final: 0.7296 (t0) REVERT: BG 26 ILE cc_start: 0.8399 (mt) cc_final: 0.8166 (tt) outliers start: 2 outliers final: 1 residues processed: 857 average time/residue: 2.1606 time to fit residues: 2641.2607 Evaluate side-chains 636 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 635 time to evaluate : 6.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BO residue 89 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1006 random chunks: chunk 849 optimal weight: 3.9990 chunk 762 optimal weight: 7.9990 chunk 423 optimal weight: 2.9990 chunk 260 optimal weight: 7.9990 chunk 514 optimal weight: 1.9990 chunk 407 optimal weight: 0.9990 chunk 788 optimal weight: 0.2980 chunk 305 optimal weight: 8.9990 chunk 479 optimal weight: 0.9990 chunk 586 optimal weight: 0.9990 chunk 913 optimal weight: 6.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 19 GLN AB 146 ASN AC 8 ASN AC 123 GLN ** AC 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 61 GLN ** AE 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AO 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 239 ASN ** BE 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 52 ASN BG 38 ASN BI 20 ASN BI 33 ASN BJ 128 ASN BJ 138 GLN BO 38 GLN BO 43 ASN ** BP 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 10 GLN BT 92 ASN BV 12 GLN BY 20 ASN B1 26 ASN B5 14 ASN B5 17 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 156592 Z= 0.132 Angle : 0.612 14.270 234376 Z= 0.334 Chirality : 0.035 0.452 29881 Planarity : 0.006 0.126 12470 Dihedral : 22.930 178.891 78570 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 2.21 % Allowed : 10.47 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.11), residues: 5584 helix: -0.00 (0.12), residues: 1802 sheet: 0.20 (0.15), residues: 1127 loop : -0.47 (0.11), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPBX 39 HIS 0.010 0.001 HISAB 18 PHE 0.017 0.001 PHEAC 130 TYR 0.015 0.001 TYRAB 22 ARG 0.010 0.000 ARGAE 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 692 time to evaluate : 6.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AC 142 MET cc_start: 0.6276 (mmm) cc_final: 0.6022 (mmm) REVERT: AD 65 TYR cc_start: 0.7714 (m-80) cc_final: 0.7330 (m-10) REVERT: AG 38 THR cc_start: 0.7247 (m) cc_final: 0.6800 (t) REVERT: AG 86 GLN cc_start: 0.7447 (mm-40) cc_final: 0.7038 (mm-40) REVERT: AK 68 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6667 (mt-10) REVERT: AO 89 ARG cc_start: 0.3702 (ptt180) cc_final: 0.0622 (pmt-80) REVERT: AR 48 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.6038 (mmt-90) REVERT: BJ 19 ASP cc_start: 0.7881 (t0) cc_final: 0.7680 (t0) REVERT: BR 99 THR cc_start: 0.8150 (p) cc_final: 0.7916 (m) REVERT: B0 32 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8315 (ptpp) outliers start: 103 outliers final: 30 residues processed: 715 average time/residue: 2.1068 time to fit residues: 2171.8435 Evaluate side-chains 648 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 616 time to evaluate : 6.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 208 ARG Chi-restraints excluded: chain AF residue 92 THR Chi-restraints excluded: chain AH residue 42 GLU Chi-restraints excluded: chain AH residue 90 ASP Chi-restraints excluded: chain AI residue 35 LEU Chi-restraints excluded: chain AI residue 47 VAL Chi-restraints excluded: chain AI residue 66 THR Chi-restraints excluded: chain AK residue 113 VAL Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AN residue 48 LEU Chi-restraints excluded: chain AO residue 35 GLN Chi-restraints excluded: chain AO residue 68 ASP Chi-restraints excluded: chain AR residue 29 LEU Chi-restraints excluded: chain AR residue 48 ARG Chi-restraints excluded: chain AS residue 79 THR Chi-restraints excluded: chain AT residue 86 LEU Chi-restraints excluded: chain BG residue 39 ASP Chi-restraints excluded: chain BG residue 48 ASN Chi-restraints excluded: chain BJ residue 91 GLU Chi-restraints excluded: chain BL residue 91 ASP Chi-restraints excluded: chain BM residue 7 THR Chi-restraints excluded: chain BM residue 110 GLU Chi-restraints excluded: chain BN residue 57 THR Chi-restraints excluded: chain BO residue 69 ASP Chi-restraints excluded: chain BR residue 22 LEU Chi-restraints excluded: chain BR residue 48 LYS Chi-restraints excluded: chain BS residue 68 ASP Chi-restraints excluded: chain BW residue 41 ARG Chi-restraints excluded: chain B0 residue 31 ASP Chi-restraints excluded: chain B0 residue 32 LYS Chi-restraints excluded: chain B0 residue 52 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1006 random chunks: chunk 507 optimal weight: 10.0000 chunk 283 optimal weight: 50.0000 chunk 760 optimal weight: 30.0000 chunk 622 optimal weight: 10.0000 chunk 252 optimal weight: 30.0000 chunk 915 optimal weight: 1.9990 chunk 988 optimal weight: 8.9990 chunk 815 optimal weight: 10.0000 chunk 907 optimal weight: 7.9990 chunk 312 optimal weight: 40.0000 chunk 734 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AC 8 ASN ** AC 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 123 GLN ** AE 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 38 ASN AH 67 GLN ** AI 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 75 GLN AM 14 HIS ** AO 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 79 ASN BH 11 ASN BI 33 ASN BJ 138 GLN BO 38 GLN ** BP 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 10 GLN BP 66 ASN BT 92 ASN BX 34 HIS BY 20 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 156592 Z= 0.285 Angle : 0.622 13.661 234376 Z= 0.336 Chirality : 0.037 0.445 29881 Planarity : 0.006 0.138 12470 Dihedral : 22.786 178.469 78568 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.72 % Rotamer: Outliers : 2.60 % Allowed : 12.90 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.11), residues: 5584 helix: 0.48 (0.12), residues: 1813 sheet: 0.31 (0.15), residues: 1141 loop : -0.39 (0.12), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAN 42 HIS 0.006 0.001 HISAF 3 PHE 0.016 0.001 PHEAJ 49 TYR 0.019 0.001 TYRAI 6 ARG 0.009 0.000 ARGBD 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 654 time to evaluate : 6.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 131 LYS cc_start: 0.6468 (tptp) cc_final: 0.5601 (tmtt) REVERT: AC 142 MET cc_start: 0.6405 (mmm) cc_final: 0.6109 (mmm) REVERT: AD 65 TYR cc_start: 0.7779 (m-80) cc_final: 0.7357 (m-10) REVERT: AE 147 MET cc_start: 0.6838 (ttm) cc_final: 0.6569 (ttm) REVERT: AG 31 MET cc_start: 0.7820 (ttp) cc_final: 0.7508 (ttt) REVERT: AG 38 THR cc_start: 0.7246 (m) cc_final: 0.6806 (t) REVERT: AG 86 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7044 (mm-40) REVERT: AH 10 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8014 (ttm) REVERT: AH 38 ASN cc_start: 0.7131 (t0) cc_final: 0.6887 (t0) REVERT: AI 32 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7321 (mt0) REVERT: AK 82 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7204 (pp) REVERT: AO 89 ARG cc_start: 0.3918 (ptt180) cc_final: 0.0514 (pmt170) REVERT: AP 76 LYS cc_start: 0.7871 (tmmm) cc_final: 0.7637 (ptpt) REVERT: BD 165 MET cc_start: 0.8249 (ttt) cc_final: 0.7988 (ttt) REVERT: BI 40 CYS cc_start: 0.6898 (OUTLIER) cc_final: 0.6570 (p) REVERT: BJ 12 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7306 (tttp) REVERT: BL 1 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7927 (ptp) REVERT: BN 74 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: BP 102 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7220 (pt0) REVERT: BS 86 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.7024 (ttt) REVERT: BV 43 ASP cc_start: 0.7640 (t0) cc_final: 0.7420 (t0) outliers start: 121 outliers final: 48 residues processed: 692 average time/residue: 2.1408 time to fit residues: 2136.9282 Evaluate side-chains 676 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 619 time to evaluate : 6.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AD residue 191 LEU Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 100 SER Chi-restraints excluded: chain AF residue 30 THR Chi-restraints excluded: chain AF residue 92 THR Chi-restraints excluded: chain AG residue 125 SER Chi-restraints excluded: chain AH residue 10 MET Chi-restraints excluded: chain AI residue 32 GLN Chi-restraints excluded: chain AI residue 35 LEU Chi-restraints excluded: chain AI residue 47 VAL Chi-restraints excluded: chain AJ residue 69 THR Chi-restraints excluded: chain AK residue 81 ASN Chi-restraints excluded: chain AK residue 82 LEU Chi-restraints excluded: chain AL residue 103 ASP Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 20 THR Chi-restraints excluded: chain AN residue 48 LEU Chi-restraints excluded: chain AO residue 18 ASP Chi-restraints excluded: chain AO residue 35 GLN Chi-restraints excluded: chain AR residue 29 LEU Chi-restraints excluded: chain AR residue 31 ASN Chi-restraints excluded: chain AS residue 79 THR Chi-restraints excluded: chain AT residue 86 LEU Chi-restraints excluded: chain AU residue 3 VAL Chi-restraints excluded: chain AU residue 43 THR Chi-restraints excluded: chain BC residue 97 LYS Chi-restraints excluded: chain BE residue 13 THR Chi-restraints excluded: chain BF residue 175 PHE Chi-restraints excluded: chain BG residue 2 SER Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 30 ASN Chi-restraints excluded: chain BG residue 39 ASP Chi-restraints excluded: chain BG residue 162 VAL Chi-restraints excluded: chain BI residue 40 CYS Chi-restraints excluded: chain BJ residue 12 LYS Chi-restraints excluded: chain BJ residue 91 GLU Chi-restraints excluded: chain BL residue 1 MET Chi-restraints excluded: chain BL residue 91 ASP Chi-restraints excluded: chain BM residue 7 THR Chi-restraints excluded: chain BN residue 57 THR Chi-restraints excluded: chain BN residue 74 GLU Chi-restraints excluded: chain BO residue 69 ASP Chi-restraints excluded: chain BP residue 102 GLU Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 22 LEU Chi-restraints excluded: chain BR residue 48 LYS Chi-restraints excluded: chain BS residue 86 MET Chi-restraints excluded: chain BU residue 81 ASP Chi-restraints excluded: chain BU residue 89 ASP Chi-restraints excluded: chain BV residue 7 GLU Chi-restraints excluded: chain BV residue 41 GLU Chi-restraints excluded: chain BW residue 70 GLU Chi-restraints excluded: chain BY residue 30 MET Chi-restraints excluded: chain B0 residue 31 ASP Chi-restraints excluded: chain B0 residue 52 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1006 random chunks: chunk 904 optimal weight: 5.9990 chunk 688 optimal weight: 10.0000 chunk 474 optimal weight: 20.0000 chunk 101 optimal weight: 50.0000 chunk 436 optimal weight: 20.0000 chunk 614 optimal weight: 10.0000 chunk 918 optimal weight: 10.0000 chunk 972 optimal weight: 0.9980 chunk 479 optimal weight: 10.0000 chunk 870 optimal weight: 20.0000 chunk 262 optimal weight: 4.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 8 ASN ** AC 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 123 GLN AC 185 ASN ** AE 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 67 GLN AH 76 GLN ** AO 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 79 ASN ** AQ 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 33 ASN BJ 128 ASN BJ 138 GLN BP 7 GLN BP 10 GLN BT 92 ASN BY 20 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 156592 Z= 0.233 Angle : 0.593 13.719 234376 Z= 0.323 Chirality : 0.036 0.422 29881 Planarity : 0.006 0.133 12470 Dihedral : 22.743 178.098 78568 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 2.77 % Allowed : 14.51 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.11), residues: 5584 helix: 0.75 (0.12), residues: 1825 sheet: 0.37 (0.15), residues: 1130 loop : -0.35 (0.12), residues: 2629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPAF 42 HIS 0.005 0.001 HISBN 16 PHE 0.018 0.001 PHEAJ 49 TYR 0.020 0.001 TYRBN 112 ARG 0.008 0.000 ARGAE 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 659 time to evaluate : 5.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 131 LYS cc_start: 0.6374 (tptp) cc_final: 0.5604 (tmtt) REVERT: AF 90 MET cc_start: 0.6418 (mtt) cc_final: 0.6193 (mtp) REVERT: AG 31 MET cc_start: 0.7833 (ttp) cc_final: 0.7489 (ttt) REVERT: AG 38 THR cc_start: 0.7219 (m) cc_final: 0.6823 (t) REVERT: AG 86 GLN cc_start: 0.7429 (mm-40) cc_final: 0.6999 (mm-40) REVERT: AH 10 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7874 (ttm) REVERT: AH 38 ASN cc_start: 0.7491 (t0) cc_final: 0.7257 (t0) REVERT: AH 76 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7467 (pp30) REVERT: AI 32 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: AI 89 GLU cc_start: 0.5531 (OUTLIER) cc_final: 0.5081 (pt0) REVERT: AO 89 ARG cc_start: 0.3529 (ptt180) cc_final: 0.0122 (pmt170) REVERT: AP 76 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7609 (ptpt) REVERT: AQ 50 ASN cc_start: 0.8130 (p0) cc_final: 0.7766 (p0) REVERT: AS 13 LEU cc_start: 0.6939 (mm) cc_final: 0.6339 (mt) REVERT: BD 165 MET cc_start: 0.8236 (ttt) cc_final: 0.7968 (ttt) REVERT: BI 40 CYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6627 (p) REVERT: BJ 12 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7318 (tttp) REVERT: BN 74 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: BP 102 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7155 (pt0) REVERT: BS 86 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.7009 (ttt) REVERT: BU 52 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7552 (pt) REVERT: BW 17 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.6925 (tp30) REVERT: B1 33 LYS cc_start: 0.8291 (mmtp) cc_final: 0.8071 (mptm) outliers start: 129 outliers final: 56 residues processed: 704 average time/residue: 2.0850 time to fit residues: 2120.3856 Evaluate side-chains 681 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 613 time to evaluate : 6.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 136 MET Chi-restraints excluded: chain AC residue 168 TYR Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 100 SER Chi-restraints excluded: chain AF residue 30 THR Chi-restraints excluded: chain AF residue 36 ILE Chi-restraints excluded: chain AF residue 71 ILE Chi-restraints excluded: chain AF residue 92 THR Chi-restraints excluded: chain AH residue 10 MET Chi-restraints excluded: chain AH residue 76 GLN Chi-restraints excluded: chain AI residue 32 GLN Chi-restraints excluded: chain AI residue 35 LEU Chi-restraints excluded: chain AI residue 47 VAL Chi-restraints excluded: chain AI residue 89 GLU Chi-restraints excluded: chain AJ residue 69 THR Chi-restraints excluded: chain AJ residue 98 VAL Chi-restraints excluded: chain AK residue 75 LYS Chi-restraints excluded: chain AK residue 81 ASN Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 20 THR Chi-restraints excluded: chain AN residue 66 GLN Chi-restraints excluded: chain AO residue 35 GLN Chi-restraints excluded: chain AO residue 68 ASP Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AP residue 76 LYS Chi-restraints excluded: chain AR residue 29 LEU Chi-restraints excluded: chain AR residue 71 THR Chi-restraints excluded: chain AS residue 79 THR Chi-restraints excluded: chain AT residue 86 LEU Chi-restraints excluded: chain AU residue 3 VAL Chi-restraints excluded: chain BC residue 97 LYS Chi-restraints excluded: chain BD residue 110 THR Chi-restraints excluded: chain BE residue 13 THR Chi-restraints excluded: chain BE residue 22 ASP Chi-restraints excluded: chain BF residue 13 VAL Chi-restraints excluded: chain BF residue 130 MET Chi-restraints excluded: chain BF residue 175 PHE Chi-restraints excluded: chain BG residue 2 SER Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 162 VAL Chi-restraints excluded: chain BI residue 40 CYS Chi-restraints excluded: chain BJ residue 12 LYS Chi-restraints excluded: chain BL residue 91 ASP Chi-restraints excluded: chain BM residue 7 THR Chi-restraints excluded: chain BM residue 135 VAL Chi-restraints excluded: chain BN residue 57 THR Chi-restraints excluded: chain BN residue 74 GLU Chi-restraints excluded: chain BO residue 69 ASP Chi-restraints excluded: chain BP residue 102 GLU Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 22 LEU Chi-restraints excluded: chain BR residue 48 LYS Chi-restraints excluded: chain BR residue 54 VAL Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BS residue 59 GLU Chi-restraints excluded: chain BS residue 86 MET Chi-restraints excluded: chain BU residue 52 LEU Chi-restraints excluded: chain BU residue 89 ASP Chi-restraints excluded: chain BV residue 7 GLU Chi-restraints excluded: chain BV residue 41 GLU Chi-restraints excluded: chain BV residue 90 ASP Chi-restraints excluded: chain BW residue 17 GLU Chi-restraints excluded: chain BW residue 70 GLU Chi-restraints excluded: chain BX residue 56 MET Chi-restraints excluded: chain B0 residue 31 ASP Chi-restraints excluded: chain B0 residue 52 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1006 random chunks: chunk 809 optimal weight: 9.9990 chunk 551 optimal weight: 10.0000 chunk 14 optimal weight: 40.0000 chunk 724 optimal weight: 20.0000 chunk 401 optimal weight: 10.0000 chunk 829 optimal weight: 0.6980 chunk 672 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 496 optimal weight: 10.0000 chunk 872 optimal weight: 7.9990 chunk 245 optimal weight: 10.0000 overall best weight: 7.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 8 ASN ** AC 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 123 GLN ** AC 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 18 GLN AH 67 GLN AP 79 ASN BH 11 ASN BI 33 ASN BJ 128 ASN BJ 138 GLN BP 7 GLN BT 92 ASN BV 12 GLN BY 20 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 156592 Z= 0.275 Angle : 0.611 13.713 234376 Z= 0.331 Chirality : 0.037 0.421 29881 Planarity : 0.006 0.135 12470 Dihedral : 22.723 178.467 78568 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.22 % Favored : 96.72 % Rotamer: Outliers : 2.92 % Allowed : 16.06 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.11), residues: 5584 helix: 0.85 (0.12), residues: 1819 sheet: 0.40 (0.15), residues: 1140 loop : -0.35 (0.12), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRPAC 22 HIS 0.005 0.001 HISBN 16 PHE 0.017 0.001 PHEAJ 49 TYR 0.020 0.001 TYRBH 25 ARG 0.006 0.000 ARGBG 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 639 time to evaluate : 5.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 131 LYS cc_start: 0.6202 (tptp) cc_final: 0.5348 (tmtt) REVERT: AD 65 TYR cc_start: 0.7881 (m-80) cc_final: 0.7619 (m-10) REVERT: AG 38 THR cc_start: 0.7215 (m) cc_final: 0.6835 (t) REVERT: AG 86 GLN cc_start: 0.7445 (mm-40) cc_final: 0.6984 (mm-40) REVERT: AH 10 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8030 (ttm) REVERT: AK 82 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7065 (pp) REVERT: AO 89 ARG cc_start: 0.3492 (ptt180) cc_final: 0.0152 (pmt170) REVERT: AQ 50 ASN cc_start: 0.8095 (p0) cc_final: 0.7788 (p0) REVERT: BE 1 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.5090 (ptp) REVERT: BG 2 SER cc_start: 0.6631 (OUTLIER) cc_final: 0.6369 (t) REVERT: BI 40 CYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6657 (p) REVERT: BJ 12 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7324 (tttp) REVERT: BL 1 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7708 (ptp) REVERT: BN 74 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: BP 102 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7202 (pt0) REVERT: BX 41 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7318 (mp0) outliers start: 136 outliers final: 60 residues processed: 689 average time/residue: 2.1401 time to fit residues: 2125.8325 Evaluate side-chains 671 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 601 time to evaluate : 6.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 136 MET Chi-restraints excluded: chain AC residue 84 VAL Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 100 SER Chi-restraints excluded: chain AF residue 14 GLN Chi-restraints excluded: chain AF residue 30 THR Chi-restraints excluded: chain AF residue 92 THR Chi-restraints excluded: chain AG residue 49 THR Chi-restraints excluded: chain AG residue 125 SER Chi-restraints excluded: chain AH residue 10 MET Chi-restraints excluded: chain AH residue 90 ASP Chi-restraints excluded: chain AI residue 35 LEU Chi-restraints excluded: chain AI residue 47 VAL Chi-restraints excluded: chain AI residue 48 VAL Chi-restraints excluded: chain AI residue 88 MET Chi-restraints excluded: chain AJ residue 17 LEU Chi-restraints excluded: chain AJ residue 69 THR Chi-restraints excluded: chain AJ residue 74 VAL Chi-restraints excluded: chain AK residue 81 ASN Chi-restraints excluded: chain AK residue 82 LEU Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 20 THR Chi-restraints excluded: chain AO residue 35 GLN Chi-restraints excluded: chain AO residue 68 ASP Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AR residue 29 LEU Chi-restraints excluded: chain AR residue 31 ASN Chi-restraints excluded: chain AR residue 71 THR Chi-restraints excluded: chain AS residue 79 THR Chi-restraints excluded: chain AT residue 86 LEU Chi-restraints excluded: chain AU residue 3 VAL Chi-restraints excluded: chain BD residue 110 THR Chi-restraints excluded: chain BE residue 1 MET Chi-restraints excluded: chain BE residue 13 THR Chi-restraints excluded: chain BE residue 84 THR Chi-restraints excluded: chain BF residue 13 VAL Chi-restraints excluded: chain BG residue 2 SER Chi-restraints excluded: chain BG residue 30 ASN Chi-restraints excluded: chain BG residue 162 VAL Chi-restraints excluded: chain BG residue 168 VAL Chi-restraints excluded: chain BI residue 40 CYS Chi-restraints excluded: chain BJ residue 12 LYS Chi-restraints excluded: chain BL residue 1 MET Chi-restraints excluded: chain BL residue 91 ASP Chi-restraints excluded: chain BM residue 7 THR Chi-restraints excluded: chain BM residue 135 VAL Chi-restraints excluded: chain BN residue 57 THR Chi-restraints excluded: chain BN residue 74 GLU Chi-restraints excluded: chain BO residue 20 GLU Chi-restraints excluded: chain BO residue 69 ASP Chi-restraints excluded: chain BP residue 7 GLN Chi-restraints excluded: chain BP residue 102 GLU Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 22 LEU Chi-restraints excluded: chain BR residue 48 LYS Chi-restraints excluded: chain BR residue 54 VAL Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BS residue 59 GLU Chi-restraints excluded: chain BS residue 68 ASP Chi-restraints excluded: chain BU residue 89 ASP Chi-restraints excluded: chain BV residue 7 GLU Chi-restraints excluded: chain BV residue 41 GLU Chi-restraints excluded: chain BV residue 90 ASP Chi-restraints excluded: chain BW residue 41 ARG Chi-restraints excluded: chain BW residue 70 GLU Chi-restraints excluded: chain BX residue 41 GLU Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B1 residue 37 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1006 random chunks: chunk 327 optimal weight: 8.9990 chunk 875 optimal weight: 20.0000 chunk 192 optimal weight: 10.0000 chunk 570 optimal weight: 20.0000 chunk 240 optimal weight: 40.0000 chunk 973 optimal weight: 20.0000 chunk 807 optimal weight: 4.9990 chunk 450 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 321 optimal weight: 40.0000 chunk 510 optimal weight: 10.0000 overall best weight: 8.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 8 ASN ** AC 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 123 GLN ** AC 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 17 GLN ** AF 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 67 GLN AP 79 ASN AQ 9 GLN BI 33 ASN BJ 128 ASN BJ 138 GLN BP 10 GLN BT 92 ASN BY 20 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 156592 Z= 0.310 Angle : 0.631 13.740 234376 Z= 0.340 Chirality : 0.038 0.411 29881 Planarity : 0.006 0.137 12470 Dihedral : 22.722 179.064 78568 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.35 % Favored : 96.60 % Rotamer: Outliers : 3.18 % Allowed : 16.71 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.11), residues: 5584 helix: 0.77 (0.12), residues: 1832 sheet: 0.35 (0.15), residues: 1145 loop : -0.39 (0.12), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRPAN 42 HIS 0.005 0.001 HISBN 16 PHE 0.018 0.001 PHEAJ 49 TYR 0.022 0.002 TYRBH 25 ARG 0.011 0.000 ARGAE 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 634 time to evaluate : 6.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 131 LYS cc_start: 0.6210 (tptp) cc_final: 0.5320 (tmtt) REVERT: AD 65 TYR cc_start: 0.7941 (m-80) cc_final: 0.7492 (m-10) REVERT: AH 10 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8032 (ttm) REVERT: AH 38 ASN cc_start: 0.7689 (t0) cc_final: 0.7414 (t160) REVERT: AJ 66 GLU cc_start: 0.7417 (pp20) cc_final: 0.7161 (pm20) REVERT: AK 82 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7037 (pp) REVERT: AO 89 ARG cc_start: 0.3623 (ptt180) cc_final: 0.0236 (pmt170) REVERT: AQ 77 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7581 (ptt-90) REVERT: AS 14 HIS cc_start: 0.6650 (OUTLIER) cc_final: 0.5181 (p-80) REVERT: BE 1 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.5132 (ptp) REVERT: BE 100 MET cc_start: 0.8625 (mtp) cc_final: 0.8384 (mtp) REVERT: BG 2 SER cc_start: 0.6711 (OUTLIER) cc_final: 0.6497 (t) REVERT: BG 130 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7172 (pm20) REVERT: BI 40 CYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6677 (p) REVERT: BJ 12 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7336 (tttp) REVERT: BL 1 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7907 (ptp) REVERT: BN 74 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7125 (tt0) REVERT: BP 7 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7414 (tm-30) REVERT: BU 10 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7137 (tm-30) outliers start: 148 outliers final: 69 residues processed: 699 average time/residue: 2.1211 time to fit residues: 2154.9631 Evaluate side-chains 685 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 604 time to evaluate : 6.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 136 MET Chi-restraints excluded: chain AB residue 205 ASP Chi-restraints excluded: chain AC residue 79 LYS Chi-restraints excluded: chain AC residue 84 VAL Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 100 SER Chi-restraints excluded: chain AE residue 145 GLU Chi-restraints excluded: chain AF residue 30 THR Chi-restraints excluded: chain AF residue 92 THR Chi-restraints excluded: chain AG residue 49 THR Chi-restraints excluded: chain AG residue 125 SER Chi-restraints excluded: chain AH residue 10 MET Chi-restraints excluded: chain AI residue 30 ILE Chi-restraints excluded: chain AI residue 35 LEU Chi-restraints excluded: chain AI residue 47 VAL Chi-restraints excluded: chain AI residue 48 VAL Chi-restraints excluded: chain AJ residue 51 VAL Chi-restraints excluded: chain AJ residue 69 THR Chi-restraints excluded: chain AJ residue 74 VAL Chi-restraints excluded: chain AJ residue 98 VAL Chi-restraints excluded: chain AK residue 82 LEU Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 20 THR Chi-restraints excluded: chain AN residue 33 VAL Chi-restraints excluded: chain AO residue 68 ASP Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AQ residue 77 ARG Chi-restraints excluded: chain AR residue 29 LEU Chi-restraints excluded: chain AR residue 71 THR Chi-restraints excluded: chain AS residue 14 HIS Chi-restraints excluded: chain AT residue 86 LEU Chi-restraints excluded: chain AU residue 3 VAL Chi-restraints excluded: chain AU residue 43 THR Chi-restraints excluded: chain BD residue 110 THR Chi-restraints excluded: chain BE residue 1 MET Chi-restraints excluded: chain BE residue 13 THR Chi-restraints excluded: chain BE residue 84 THR Chi-restraints excluded: chain BF residue 13 VAL Chi-restraints excluded: chain BF residue 175 PHE Chi-restraints excluded: chain BG residue 2 SER Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 30 ASN Chi-restraints excluded: chain BG residue 36 THR Chi-restraints excluded: chain BG residue 130 GLU Chi-restraints excluded: chain BG residue 162 VAL Chi-restraints excluded: chain BG residue 168 VAL Chi-restraints excluded: chain BH residue 18 GLN Chi-restraints excluded: chain BI residue 39 LYS Chi-restraints excluded: chain BI residue 40 CYS Chi-restraints excluded: chain BJ residue 12 LYS Chi-restraints excluded: chain BK residue 91 SER Chi-restraints excluded: chain BK residue 121 GLU Chi-restraints excluded: chain BL residue 1 MET Chi-restraints excluded: chain BL residue 91 ASP Chi-restraints excluded: chain BL residue 116 VAL Chi-restraints excluded: chain BM residue 7 THR Chi-restraints excluded: chain BM residue 135 VAL Chi-restraints excluded: chain BN residue 57 THR Chi-restraints excluded: chain BN residue 74 GLU Chi-restraints excluded: chain BO residue 20 GLU Chi-restraints excluded: chain BO residue 49 VAL Chi-restraints excluded: chain BO residue 69 ASP Chi-restraints excluded: chain BO residue 83 LEU Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 22 LEU Chi-restraints excluded: chain BR residue 48 LYS Chi-restraints excluded: chain BR residue 54 VAL Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BU residue 10 GLU Chi-restraints excluded: chain BU residue 89 ASP Chi-restraints excluded: chain BV residue 7 GLU Chi-restraints excluded: chain BV residue 41 GLU Chi-restraints excluded: chain BV residue 90 ASP Chi-restraints excluded: chain BW residue 41 ARG Chi-restraints excluded: chain BW residue 70 GLU Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B0 residue 33 THR Chi-restraints excluded: chain B0 residue 52 ARG Chi-restraints excluded: chain B1 residue 37 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1006 random chunks: chunk 938 optimal weight: 6.9990 chunk 109 optimal weight: 40.0000 chunk 554 optimal weight: 40.0000 chunk 710 optimal weight: 1.9990 chunk 550 optimal weight: 10.0000 chunk 819 optimal weight: 6.9990 chunk 543 optimal weight: 10.0000 chunk 969 optimal weight: 10.0000 chunk 606 optimal weight: 10.0000 chunk 591 optimal weight: 50.0000 chunk 447 optimal weight: 20.0000 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 8 ASN ** AC 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 123 GLN ** AC 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AP 79 ASN AQ 9 GLN BI 33 ASN BJ 128 ASN BJ 138 GLN BP 7 GLN BT 92 ASN BY 20 ASN ** B1 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 156592 Z= 0.262 Angle : 0.616 14.170 234376 Z= 0.333 Chirality : 0.037 0.419 29881 Planarity : 0.006 0.135 12470 Dihedral : 22.730 178.827 78568 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.54 % Rotamer: Outliers : 2.80 % Allowed : 17.95 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 5584 helix: 0.81 (0.12), residues: 1827 sheet: 0.32 (0.15), residues: 1144 loop : -0.39 (0.12), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRPAN 42 HIS 0.006 0.001 HISAF 3 PHE 0.018 0.001 PHEAJ 49 TYR 0.034 0.002 TYRAI 38 ARG 0.010 0.000 ARGAE 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 621 time to evaluate : 6.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 131 LYS cc_start: 0.6181 (tptp) cc_final: 0.5295 (tmtt) REVERT: AD 65 TYR cc_start: 0.7927 (m-80) cc_final: 0.7432 (m-10) REVERT: AE 147 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6649 (ttm) REVERT: AH 10 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8075 (ttm) REVERT: AH 38 ASN cc_start: 0.7645 (t0) cc_final: 0.7327 (t160) REVERT: AI 83 ILE cc_start: 0.8395 (mt) cc_final: 0.8122 (mm) REVERT: AK 82 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7045 (pp) REVERT: AO 89 ARG cc_start: 0.3618 (ptt180) cc_final: 0.0260 (pmt170) REVERT: AS 14 HIS cc_start: 0.6596 (OUTLIER) cc_final: 0.5122 (p-80) REVERT: BE 1 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.5128 (ptp) REVERT: BG 2 SER cc_start: 0.6700 (OUTLIER) cc_final: 0.6500 (t) REVERT: BG 130 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7174 (pm20) REVERT: BJ 12 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7327 (tttp) REVERT: BL 1 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7890 (ptp) REVERT: BN 74 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: BP 102 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7041 (pt0) REVERT: BW 17 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6985 (tp30) outliers start: 130 outliers final: 74 residues processed: 674 average time/residue: 2.1023 time to fit residues: 2047.5405 Evaluate side-chains 688 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 602 time to evaluate : 6.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 136 MET Chi-restraints excluded: chain AB residue 205 ASP Chi-restraints excluded: chain AC residue 79 LYS Chi-restraints excluded: chain AC residue 84 VAL Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 100 SER Chi-restraints excluded: chain AE residue 147 MET Chi-restraints excluded: chain AF residue 14 GLN Chi-restraints excluded: chain AF residue 30 THR Chi-restraints excluded: chain AF residue 92 THR Chi-restraints excluded: chain AG residue 49 THR Chi-restraints excluded: chain AG residue 125 SER Chi-restraints excluded: chain AH residue 10 MET Chi-restraints excluded: chain AI residue 35 LEU Chi-restraints excluded: chain AI residue 47 VAL Chi-restraints excluded: chain AI residue 48 VAL Chi-restraints excluded: chain AI residue 66 THR Chi-restraints excluded: chain AJ residue 51 VAL Chi-restraints excluded: chain AJ residue 69 THR Chi-restraints excluded: chain AJ residue 74 VAL Chi-restraints excluded: chain AK residue 82 LEU Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 20 THR Chi-restraints excluded: chain AM residue 81 MET Chi-restraints excluded: chain AN residue 33 VAL Chi-restraints excluded: chain AO residue 68 ASP Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AP residue 76 LYS Chi-restraints excluded: chain AR residue 29 LEU Chi-restraints excluded: chain AR residue 31 ASN Chi-restraints excluded: chain AR residue 71 THR Chi-restraints excluded: chain AS residue 14 HIS Chi-restraints excluded: chain AS residue 79 THR Chi-restraints excluded: chain AT residue 86 LEU Chi-restraints excluded: chain AU residue 3 VAL Chi-restraints excluded: chain AU residue 43 THR Chi-restraints excluded: chain BC residue 97 LYS Chi-restraints excluded: chain BD residue 110 THR Chi-restraints excluded: chain BE residue 1 MET Chi-restraints excluded: chain BE residue 13 THR Chi-restraints excluded: chain BE residue 22 ASP Chi-restraints excluded: chain BE residue 84 THR Chi-restraints excluded: chain BF residue 13 VAL Chi-restraints excluded: chain BF residue 175 PHE Chi-restraints excluded: chain BG residue 2 SER Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 30 ASN Chi-restraints excluded: chain BG residue 36 THR Chi-restraints excluded: chain BG residue 39 ASP Chi-restraints excluded: chain BG residue 130 GLU Chi-restraints excluded: chain BG residue 162 VAL Chi-restraints excluded: chain BG residue 168 VAL Chi-restraints excluded: chain BI residue 39 LYS Chi-restraints excluded: chain BJ residue 12 LYS Chi-restraints excluded: chain BK residue 91 SER Chi-restraints excluded: chain BL residue 1 MET Chi-restraints excluded: chain BL residue 91 ASP Chi-restraints excluded: chain BM residue 7 THR Chi-restraints excluded: chain BM residue 135 VAL Chi-restraints excluded: chain BN residue 57 THR Chi-restraints excluded: chain BN residue 74 GLU Chi-restraints excluded: chain BO residue 20 GLU Chi-restraints excluded: chain BO residue 24 THR Chi-restraints excluded: chain BO residue 49 VAL Chi-restraints excluded: chain BO residue 69 ASP Chi-restraints excluded: chain BP residue 26 VAL Chi-restraints excluded: chain BP residue 102 GLU Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 22 LEU Chi-restraints excluded: chain BR residue 48 LYS Chi-restraints excluded: chain BR residue 54 VAL Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BU residue 60 GLU Chi-restraints excluded: chain BV residue 7 GLU Chi-restraints excluded: chain BV residue 62 THR Chi-restraints excluded: chain BV residue 90 ASP Chi-restraints excluded: chain BW residue 17 GLU Chi-restraints excluded: chain BW residue 41 ARG Chi-restraints excluded: chain BW residue 70 GLU Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B0 residue 31 ASP Chi-restraints excluded: chain B0 residue 52 ARG Chi-restraints excluded: chain B1 residue 37 LYS Chi-restraints excluded: chain B3 residue 32 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1006 random chunks: chunk 599 optimal weight: 50.0000 chunk 387 optimal weight: 10.0000 chunk 579 optimal weight: 10.0000 chunk 292 optimal weight: 7.9990 chunk 190 optimal weight: 50.0000 chunk 187 optimal weight: 0.0870 chunk 616 optimal weight: 10.0000 chunk 660 optimal weight: 30.0000 chunk 479 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 762 optimal weight: 20.0000 overall best weight: 7.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 8 ASN ** AC 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 123 GLN ** AC 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 17 GLN ** AF 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 67 GLN AI 75 GLN AP 79 ASN BI 33 ASN BJ 128 ASN BJ 138 GLN BP 10 GLN BT 92 ASN BV 12 GLN BY 20 ASN ** B1 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 156592 Z= 0.272 Angle : 0.615 13.744 234376 Z= 0.332 Chirality : 0.037 0.420 29881 Planarity : 0.006 0.134 12470 Dihedral : 22.707 178.567 78568 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.56 % Rotamer: Outliers : 2.67 % Allowed : 18.43 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.11), residues: 5584 helix: 0.85 (0.12), residues: 1832 sheet: 0.33 (0.15), residues: 1147 loop : -0.40 (0.12), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRPAN 42 HIS 0.006 0.001 HISAS 57 PHE 0.018 0.001 PHEAJ 49 TYR 0.020 0.002 TYRAI 38 ARG 0.011 0.000 ARGAR 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 624 time to evaluate : 6.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AC 154 SER cc_start: 0.8037 (p) cc_final: 0.7611 (m) REVERT: AE 101 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6817 (tm-30) REVERT: AF 93 LYS cc_start: 0.7983 (pptt) cc_final: 0.7595 (pptt) REVERT: AF 94 HIS cc_start: 0.6990 (m-70) cc_final: 0.6719 (m90) REVERT: AH 10 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8092 (ttm) REVERT: AJ 66 GLU cc_start: 0.7448 (pp20) cc_final: 0.7142 (pm20) REVERT: AO 89 ARG cc_start: 0.3716 (ptt180) cc_final: 0.0258 (pmt170) REVERT: AQ 15 ASP cc_start: 0.6186 (t0) cc_final: 0.5923 (t0) REVERT: AQ 50 ASN cc_start: 0.7992 (p0) cc_final: 0.7648 (p0) REVERT: AR 35 GLU cc_start: 0.7217 (pm20) cc_final: 0.6994 (pm20) REVERT: AS 14 HIS cc_start: 0.6496 (OUTLIER) cc_final: 0.5091 (p-80) REVERT: BC 115 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7540 (mp10) REVERT: BE 1 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.5154 (ptp) REVERT: BI 40 CYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6659 (p) REVERT: BJ 12 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7338 (tttp) REVERT: BL 1 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7883 (ptp) REVERT: BN 74 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7145 (tt0) REVERT: BW 17 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7000 (tp30) REVERT: BX 41 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7306 (mp0) outliers start: 124 outliers final: 75 residues processed: 682 average time/residue: 2.1300 time to fit residues: 2108.0471 Evaluate side-chains 689 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 604 time to evaluate : 6.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 10 LEU Chi-restraints excluded: chain AB residue 106 THR Chi-restraints excluded: chain AB residue 136 MET Chi-restraints excluded: chain AB residue 205 ASP Chi-restraints excluded: chain AC residue 79 LYS Chi-restraints excluded: chain AC residue 84 VAL Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 100 SER Chi-restraints excluded: chain AE residue 123 VAL Chi-restraints excluded: chain AE residue 145 GLU Chi-restraints excluded: chain AF residue 30 THR Chi-restraints excluded: chain AF residue 92 THR Chi-restraints excluded: chain AG residue 49 THR Chi-restraints excluded: chain AG residue 125 SER Chi-restraints excluded: chain AH residue 10 MET Chi-restraints excluded: chain AI residue 35 LEU Chi-restraints excluded: chain AI residue 47 VAL Chi-restraints excluded: chain AI residue 48 VAL Chi-restraints excluded: chain AJ residue 51 VAL Chi-restraints excluded: chain AJ residue 69 THR Chi-restraints excluded: chain AJ residue 74 VAL Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 20 THR Chi-restraints excluded: chain AM residue 81 MET Chi-restraints excluded: chain AN residue 33 VAL Chi-restraints excluded: chain AO residue 68 ASP Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AP residue 76 LYS Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AR residue 29 LEU Chi-restraints excluded: chain AR residue 71 THR Chi-restraints excluded: chain AS residue 14 HIS Chi-restraints excluded: chain AS residue 79 THR Chi-restraints excluded: chain AT residue 86 LEU Chi-restraints excluded: chain AU residue 3 VAL Chi-restraints excluded: chain AU residue 43 THR Chi-restraints excluded: chain BC residue 97 LYS Chi-restraints excluded: chain BC residue 115 GLN Chi-restraints excluded: chain BD residue 110 THR Chi-restraints excluded: chain BE residue 1 MET Chi-restraints excluded: chain BE residue 13 THR Chi-restraints excluded: chain BE residue 84 THR Chi-restraints excluded: chain BF residue 13 VAL Chi-restraints excluded: chain BF residue 175 PHE Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 30 ASN Chi-restraints excluded: chain BG residue 36 THR Chi-restraints excluded: chain BG residue 162 VAL Chi-restraints excluded: chain BG residue 168 VAL Chi-restraints excluded: chain BI residue 40 CYS Chi-restraints excluded: chain BJ residue 12 LYS Chi-restraints excluded: chain BK residue 91 SER Chi-restraints excluded: chain BK residue 121 GLU Chi-restraints excluded: chain BL residue 1 MET Chi-restraints excluded: chain BL residue 91 ASP Chi-restraints excluded: chain BM residue 7 THR Chi-restraints excluded: chain BM residue 135 VAL Chi-restraints excluded: chain BN residue 57 THR Chi-restraints excluded: chain BN residue 74 GLU Chi-restraints excluded: chain BO residue 20 GLU Chi-restraints excluded: chain BO residue 24 THR Chi-restraints excluded: chain BO residue 49 VAL Chi-restraints excluded: chain BO residue 69 ASP Chi-restraints excluded: chain BO residue 83 LEU Chi-restraints excluded: chain BP residue 26 VAL Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 22 LEU Chi-restraints excluded: chain BR residue 48 LYS Chi-restraints excluded: chain BR residue 54 VAL Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BS residue 59 GLU Chi-restraints excluded: chain BU residue 60 GLU Chi-restraints excluded: chain BV residue 7 GLU Chi-restraints excluded: chain BV residue 41 GLU Chi-restraints excluded: chain BV residue 90 ASP Chi-restraints excluded: chain BW residue 17 GLU Chi-restraints excluded: chain BW residue 41 ARG Chi-restraints excluded: chain BW residue 43 THR Chi-restraints excluded: chain BW residue 70 GLU Chi-restraints excluded: chain BX residue 41 GLU Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B0 residue 52 ARG Chi-restraints excluded: chain B1 residue 37 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1006 random chunks: chunk 882 optimal weight: 2.9990 chunk 928 optimal weight: 6.9990 chunk 847 optimal weight: 20.0000 chunk 903 optimal weight: 30.0000 chunk 543 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 709 optimal weight: 9.9990 chunk 277 optimal weight: 0.0070 chunk 816 optimal weight: 10.0000 chunk 854 optimal weight: 5.9990 chunk 900 optimal weight: 5.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 19 GLN ** AB 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 8 ASN AC 100 GLN AC 102 ASN AC 123 GLN ** AC 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 17 GLN ** AF 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AP 79 ASN BH 11 ASN BI 33 ASN BJ 128 ASN BJ 138 GLN BP 10 GLN BT 92 ASN BY 20 ASN BY 38 GLN ** B1 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 156592 Z= 0.180 Angle : 0.595 13.846 234376 Z= 0.325 Chirality : 0.035 0.426 29881 Planarity : 0.006 0.130 12470 Dihedral : 22.731 178.319 78568 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 2.24 % Allowed : 19.05 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.11), residues: 5584 helix: 0.86 (0.13), residues: 1830 sheet: 0.33 (0.15), residues: 1129 loop : -0.37 (0.12), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRPAB 104 HIS 0.009 0.001 HISAE 83 PHE 0.020 0.001 PHEAJ 49 TYR 0.024 0.001 TYRAI 38 ARG 0.019 0.000 ARGAE 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 621 time to evaluate : 6.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AC 154 SER cc_start: 0.8032 (p) cc_final: 0.7611 (m) REVERT: AD 65 TYR cc_start: 0.7864 (m-80) cc_final: 0.7441 (m-10) REVERT: AE 101 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6856 (tm-30) REVERT: AF 93 LYS cc_start: 0.7988 (pptt) cc_final: 0.7570 (pptt) REVERT: AF 94 HIS cc_start: 0.6975 (m-70) cc_final: 0.6680 (m90) REVERT: AH 10 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8044 (ttm) REVERT: AH 96 MET cc_start: 0.7541 (tpt) cc_final: 0.6978 (tpt) REVERT: AJ 66 GLU cc_start: 0.7416 (pp20) cc_final: 0.7120 (pm20) REVERT: AO 22 THR cc_start: 0.8559 (p) cc_final: 0.8298 (t) REVERT: AO 89 ARG cc_start: 0.3691 (ptt180) cc_final: 0.0232 (pmt170) REVERT: AQ 15 ASP cc_start: 0.6182 (t0) cc_final: 0.5920 (t0) REVERT: AQ 50 ASN cc_start: 0.8054 (p0) cc_final: 0.7729 (p0) REVERT: AS 14 HIS cc_start: 0.6402 (OUTLIER) cc_final: 0.4991 (p-80) REVERT: BC 115 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7542 (mp10) REVERT: BD 165 MET cc_start: 0.8235 (ttt) cc_final: 0.7993 (ttt) REVERT: BE 1 MET cc_start: 0.6526 (OUTLIER) cc_final: 0.5134 (ptp) REVERT: BI 40 CYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6631 (p) REVERT: BN 74 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: BW 17 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6991 (tp30) REVERT: BX 41 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7305 (mp0) outliers start: 104 outliers final: 74 residues processed: 672 average time/residue: 2.1252 time to fit residues: 2068.1493 Evaluate side-chains 687 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 605 time to evaluate : 6.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 136 MET Chi-restraints excluded: chain AB residue 205 ASP Chi-restraints excluded: chain AC residue 79 LYS Chi-restraints excluded: chain AC residue 84 VAL Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 100 SER Chi-restraints excluded: chain AF residue 30 THR Chi-restraints excluded: chain AF residue 74 LEU Chi-restraints excluded: chain AF residue 92 THR Chi-restraints excluded: chain AG residue 49 THR Chi-restraints excluded: chain AG residue 125 SER Chi-restraints excluded: chain AH residue 10 MET Chi-restraints excluded: chain AI residue 35 LEU Chi-restraints excluded: chain AI residue 47 VAL Chi-restraints excluded: chain AI residue 48 VAL Chi-restraints excluded: chain AI residue 88 MET Chi-restraints excluded: chain AJ residue 51 VAL Chi-restraints excluded: chain AJ residue 69 THR Chi-restraints excluded: chain AJ residue 74 VAL Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 20 THR Chi-restraints excluded: chain AM residue 81 MET Chi-restraints excluded: chain AN residue 33 VAL Chi-restraints excluded: chain AO residue 68 ASP Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AP residue 76 LYS Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AR residue 29 LEU Chi-restraints excluded: chain AR residue 71 THR Chi-restraints excluded: chain AS residue 14 HIS Chi-restraints excluded: chain AS residue 79 THR Chi-restraints excluded: chain AT residue 86 LEU Chi-restraints excluded: chain AU residue 3 VAL Chi-restraints excluded: chain AU residue 43 THR Chi-restraints excluded: chain BC residue 97 LYS Chi-restraints excluded: chain BC residue 115 GLN Chi-restraints excluded: chain BD residue 110 THR Chi-restraints excluded: chain BE residue 1 MET Chi-restraints excluded: chain BE residue 13 THR Chi-restraints excluded: chain BE residue 84 THR Chi-restraints excluded: chain BF residue 13 VAL Chi-restraints excluded: chain BF residue 175 PHE Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 36 THR Chi-restraints excluded: chain BG residue 39 ASP Chi-restraints excluded: chain BG residue 162 VAL Chi-restraints excluded: chain BG residue 168 VAL Chi-restraints excluded: chain BI residue 39 LYS Chi-restraints excluded: chain BI residue 40 CYS Chi-restraints excluded: chain BK residue 121 GLU Chi-restraints excluded: chain BL residue 91 ASP Chi-restraints excluded: chain BM residue 7 THR Chi-restraints excluded: chain BM residue 135 VAL Chi-restraints excluded: chain BN residue 57 THR Chi-restraints excluded: chain BN residue 74 GLU Chi-restraints excluded: chain BO residue 20 GLU Chi-restraints excluded: chain BO residue 24 THR Chi-restraints excluded: chain BO residue 49 VAL Chi-restraints excluded: chain BO residue 69 ASP Chi-restraints excluded: chain BO residue 83 LEU Chi-restraints excluded: chain BP residue 26 VAL Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 20 VAL Chi-restraints excluded: chain BR residue 22 LEU Chi-restraints excluded: chain BR residue 48 LYS Chi-restraints excluded: chain BR residue 54 VAL Chi-restraints excluded: chain BS residue 59 GLU Chi-restraints excluded: chain BU residue 60 GLU Chi-restraints excluded: chain BV residue 7 GLU Chi-restraints excluded: chain BV residue 41 GLU Chi-restraints excluded: chain BV residue 90 ASP Chi-restraints excluded: chain BW residue 17 GLU Chi-restraints excluded: chain BW residue 43 THR Chi-restraints excluded: chain BW residue 70 GLU Chi-restraints excluded: chain BX residue 41 GLU Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B0 residue 31 ASP Chi-restraints excluded: chain B0 residue 52 ARG Chi-restraints excluded: chain B1 residue 37 LYS Chi-restraints excluded: chain B3 residue 32 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1006 random chunks: chunk 593 optimal weight: 50.0000 chunk 955 optimal weight: 9.9990 chunk 583 optimal weight: 10.0000 chunk 453 optimal weight: 30.0000 chunk 664 optimal weight: 20.0000 chunk 1002 optimal weight: 40.0000 chunk 922 optimal weight: 5.9990 chunk 798 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 616 optimal weight: 20.0000 chunk 489 optimal weight: 50.0000 overall best weight: 13.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 19 GLN ** AB 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 8 ASN AC 123 GLN ** AC 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 17 GLN ** AF 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AH 38 ASN AH 67 GLN AP 79 ASN BC 239 ASN BH 133 GLN BI 33 ASN BJ 128 ASN BJ 138 GLN BP 10 GLN BT 92 ASN BY 20 ASN ** B1 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 156592 Z= 0.449 Angle : 0.711 13.819 234376 Z= 0.374 Chirality : 0.042 0.400 29881 Planarity : 0.007 0.145 12470 Dihedral : 22.736 179.744 78568 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 2.06 % Allowed : 19.35 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 5584 helix: 0.60 (0.12), residues: 1841 sheet: 0.27 (0.15), residues: 1140 loop : -0.53 (0.12), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRPAB 104 HIS 0.010 0.001 HISBN 16 PHE 0.020 0.002 PHEBD 118 TYR 0.026 0.002 TYRBH 25 ARG 0.012 0.001 ARGAR 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11168 Ramachandran restraints generated. 5584 Oldfield, 0 Emsley, 5584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 614 time to evaluate : 6.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AE 101 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6878 (tm-30) REVERT: AH 10 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8109 (ttm) REVERT: AH 96 MET cc_start: 0.7640 (tpt) cc_final: 0.7047 (tpt) REVERT: AJ 66 GLU cc_start: 0.7452 (pp20) cc_final: 0.7234 (pm20) REVERT: AO 89 ARG cc_start: 0.3791 (ptt180) cc_final: 0.0645 (pmt170) REVERT: AQ 15 ASP cc_start: 0.6200 (t0) cc_final: 0.5874 (t0) REVERT: AQ 50 ASN cc_start: 0.8160 (p0) cc_final: 0.7815 (p0) REVERT: AS 14 HIS cc_start: 0.6620 (OUTLIER) cc_final: 0.5159 (p-80) REVERT: BC 115 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: BI 40 CYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6866 (p) REVERT: BN 74 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: BP 102 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7122 (pt0) REVERT: BW 17 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7027 (tp30) REVERT: BX 41 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7397 (mp0) outliers start: 96 outliers final: 74 residues processed: 666 average time/residue: 2.3153 time to fit residues: 2254.9532 Evaluate side-chains 677 residues out of total 4657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 595 time to evaluate : 5.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 136 MET Chi-restraints excluded: chain AB residue 205 ASP Chi-restraints excluded: chain AC residue 79 LYS Chi-restraints excluded: chain AC residue 84 VAL Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 100 SER Chi-restraints excluded: chain AF residue 30 THR Chi-restraints excluded: chain AF residue 92 THR Chi-restraints excluded: chain AG residue 6 VAL Chi-restraints excluded: chain AG residue 49 THR Chi-restraints excluded: chain AG residue 125 SER Chi-restraints excluded: chain AH residue 10 MET Chi-restraints excluded: chain AI residue 35 LEU Chi-restraints excluded: chain AI residue 47 VAL Chi-restraints excluded: chain AI residue 48 VAL Chi-restraints excluded: chain AJ residue 51 VAL Chi-restraints excluded: chain AJ residue 69 THR Chi-restraints excluded: chain AJ residue 74 VAL Chi-restraints excluded: chain AL residue 109 ASP Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 20 THR Chi-restraints excluded: chain AM residue 81 MET Chi-restraints excluded: chain AN residue 33 VAL Chi-restraints excluded: chain AO residue 68 ASP Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AP residue 76 LYS Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AR residue 29 LEU Chi-restraints excluded: chain AR residue 45 THR Chi-restraints excluded: chain AR residue 71 THR Chi-restraints excluded: chain AS residue 14 HIS Chi-restraints excluded: chain AS residue 79 THR Chi-restraints excluded: chain AT residue 86 LEU Chi-restraints excluded: chain AU residue 3 VAL Chi-restraints excluded: chain AU residue 43 THR Chi-restraints excluded: chain BC residue 97 LYS Chi-restraints excluded: chain BC residue 115 GLN Chi-restraints excluded: chain BD residue 110 THR Chi-restraints excluded: chain BE residue 13 THR Chi-restraints excluded: chain BE residue 84 THR Chi-restraints excluded: chain BF residue 13 VAL Chi-restraints excluded: chain BF residue 130 MET Chi-restraints excluded: chain BF residue 175 PHE Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 36 THR Chi-restraints excluded: chain BG residue 162 VAL Chi-restraints excluded: chain BG residue 168 VAL Chi-restraints excluded: chain BI residue 39 LYS Chi-restraints excluded: chain BI residue 40 CYS Chi-restraints excluded: chain BK residue 121 GLU Chi-restraints excluded: chain BL residue 91 ASP Chi-restraints excluded: chain BM residue 7 THR Chi-restraints excluded: chain BM residue 135 VAL Chi-restraints excluded: chain BN residue 57 THR Chi-restraints excluded: chain BN residue 74 GLU Chi-restraints excluded: chain BO residue 20 GLU Chi-restraints excluded: chain BO residue 24 THR Chi-restraints excluded: chain BO residue 49 VAL Chi-restraints excluded: chain BO residue 69 ASP Chi-restraints excluded: chain BO residue 83 LEU Chi-restraints excluded: chain BP residue 26 VAL Chi-restraints excluded: chain BP residue 102 GLU Chi-restraints excluded: chain BP residue 104 THR Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 20 VAL Chi-restraints excluded: chain BR residue 22 LEU Chi-restraints excluded: chain BR residue 48 LYS Chi-restraints excluded: chain BR residue 54 VAL Chi-restraints excluded: chain BS residue 4 ILE Chi-restraints excluded: chain BS residue 59 GLU Chi-restraints excluded: chain BU residue 60 GLU Chi-restraints excluded: chain BV residue 7 GLU Chi-restraints excluded: chain BV residue 45 ASP Chi-restraints excluded: chain BW residue 17 GLU Chi-restraints excluded: chain BW residue 43 THR Chi-restraints excluded: chain BW residue 70 GLU Chi-restraints excluded: chain BX residue 41 GLU Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B0 residue 31 ASP Chi-restraints excluded: chain B0 residue 52 ARG Chi-restraints excluded: chain B1 residue 37 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1006 random chunks: chunk 633 optimal weight: 8.9990 chunk 850 optimal weight: 6.9990 chunk 244 optimal weight: 30.0000 chunk 735 optimal weight: 4.9990 chunk 117 optimal weight: 50.0000 chunk 221 optimal weight: 30.0000 chunk 799 optimal weight: 40.0000 chunk 334 optimal weight: 8.9990 chunk 820 optimal weight: 40.0000 chunk 101 optimal weight: 50.0000 chunk 147 optimal weight: 20.0000 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 8 ASN AC 123 GLN ** AC 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 17 GLN ** AF 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AP 79 ASN BH 11 ASN BI 33 ASN BJ 128 ASN BJ 138 GLN BP 10 GLN BT 92 ASN BY 20 ASN ** B1 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.070228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.048676 restraints weight = 523749.770| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.10 r_work: 0.2845 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 156592 Z= 0.346 Angle : 0.667 13.813 234376 Z= 0.357 Chirality : 0.040 0.416 29881 Planarity : 0.006 0.140 12470 Dihedral : 22.757 179.983 78568 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 2.13 % Allowed : 19.67 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.11), residues: 5584 helix: 0.62 (0.12), residues: 1841 sheet: 0.23 (0.15), residues: 1136 loop : -0.53 (0.12), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRPAB 104 HIS 0.007 0.001 HISAO 46 PHE 0.020 0.002 PHEAS 10 TYR 0.022 0.002 TYRBH 25 ARG 0.014 0.000 ARGAR 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35898.44 seconds wall clock time: 627 minutes 16.84 seconds (37636.84 seconds total)