Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 21 17:49:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4k_13805/07_2023/7q4k_13805_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4k_13805/07_2023/7q4k_13805.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4k_13805/07_2023/7q4k_13805_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4k_13805/07_2023/7q4k_13805_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4k_13805/07_2023/7q4k_13805_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4k_13805/07_2023/7q4k_13805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4k_13805/07_2023/7q4k_13805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4k_13805/07_2023/7q4k_13805_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q4k_13805/07_2023/7q4k_13805_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4711 5.49 5 Mg 172 5.21 5 S 152 5.16 5 C 73006 2.51 5 N 27120 2.21 5 O 41446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AB GLU 44": "OE1" <-> "OE2" Residue "AB GLU 140": "OE1" <-> "OE2" Residue "AB ARG 225": "NH1" <-> "NH2" Residue "AC PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC ARG 131": "NH1" <-> "NH2" Residue "AC GLU 161": "OE1" <-> "OE2" Residue "AD GLU 57": "OE1" <-> "OE2" Residue "AD GLU 88": "OE1" <-> "OE2" Residue "AD GLU 163": "OE1" <-> "OE2" Residue "AE GLU 116": "OE1" <-> "OE2" Residue "AF ARG 2": "NH1" <-> "NH2" Residue "AG GLU 21": "OE1" <-> "OE2" Residue "AG ARG 79": "NH1" <-> "NH2" Residue "AH GLU 43": "OE1" <-> "OE2" Residue "AI ARG 119": "NH1" <-> "NH2" Residue "AI ARG 124": "NH1" <-> "NH2" Residue "AL ARG 56": "NH1" <-> "NH2" Residue "AL GLU 76": "OE1" <-> "OE2" Residue "AN GLU 92": "OE1" <-> "OE2" Residue "AO PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AO GLU 83": "OE1" <-> "OE2" Residue "AP PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AP ARG 28": "NH1" <-> "NH2" Residue "AP PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ GLU 80": "OE1" <-> "OE2" Residue "AT ARG 10": "NH1" <-> "NH2" Residue "AT GLU 15": "OE1" <-> "OE2" Residue "AU GLU 8": "OE1" <-> "OE2" Residue "AU GLU 39": "OE1" <-> "OE2" Residue "BC ARG 52": "NH1" <-> "NH2" Residue "BC ARG 63": "NH1" <-> "NH2" Residue "BC ARG 80": "NH1" <-> "NH2" Residue "BC TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC ARG 133": "NH1" <-> "NH2" 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 GLU 199": "OE1" <-> "OE2" Residue "BC ARG 212": "NH1" <-> "NH2" Residue "BD ARG 13": "NH1" <-> "NH2" Residue "BD ARG 33": "NH1" <-> "NH2" Residue "BD ARG 59": "NH1" <-> "NH2" Residue "BD GLU 74": "OE1" <-> "OE2" Residue "BD ARG 77": "NH1" <-> "NH2" Residue "BD ARG 83": "NH1" <-> "NH2" Residue "BD ARG 169": "NH1" <-> "NH2" Residue "BD ARG 184": "NH1" <-> "NH2" Residue "BE ARG 21": "NH1" <-> "NH2" 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 ARG 162": "NH1" <-> "NH2" Residue "BE ARG 170": "NH1" <-> "NH2" Residue "BF ARG 71": "NH1" <-> "NH2" Residue "BF ARG 80": "NH1" <-> "NH2" Residue "BF ARG 92": "NH1" <-> "NH2" 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 "BG ARG 3": "NH1" <-> "NH2" Residue "BG ARG 153": "NH1" <-> "NH2" Residue "BG GLU 155": "OE1" <-> "OE2" Residue "BG ARG 163": "NH1" <-> "NH2" Residue "BG ARG 170": "NH1" <-> "NH2" Residue "BH ARG 27": "NH1" <-> "NH2" Residue "BH GLU 109": "OE1" <-> "OE2" Residue "BH GLU 129": "OE1" <-> "OE2" Residue "BI PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI ARG 49": "NH1" <-> "NH2" Residue "BI ARG 56": "NH1" <-> "NH2" Residue "BJ ARG 13": "NH1" <-> "NH2" Residue "BJ ARG 37": "NH1" <-> "NH2" Residue "BJ ARG 96": "NH1" <-> "NH2" Residue "BJ ARG 120": "NH1" <-> "NH2" 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 ARG 60": "NH1" <-> "NH2" Residue "BL ARG 126": "NH1" <-> "NH2" Residue "BM ARG 10": "NH1" <-> "NH2" Residue "BM ARG 18": "NH1" <-> "NH2" 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 GLU 111": "OE1" <-> "OE2" Residue "BM ARG 114": "NH1" <-> "NH2" 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 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 ARG 96": "NH1" <-> "NH2" Residue "BN ARG 118": "NH1" <-> "NH2" Residue "BO ARG 10": "NH1" <-> "NH2" Residue "BO ARG 16": "NH1" <-> "NH2" 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 ARG 111": "NH1" <-> "NH2" Residue "BP GLU 9": "OE1" <-> "OE2" Residue "BP ARG 21": "NH1" <-> "NH2" 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 ARG 33": "NH1" <-> "NH2" Residue "BQ ARG 48": "NH1" <-> "NH2" Residue "BQ ARG 70": "NH1" <-> "NH2" Residue "BR ARG 21": "NH1" <-> "NH2" Residue "BR GLU 31": "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 ARG 11": "NH1" <-> "NH2" 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 ARG 69": "NH1" <-> "NH2" Residue "BT ARG 73": "NH1" <-> "NH2" Residue "BT GLU 89": "OE1" <-> "OE2" 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 35": "OE1" <-> "OE2" Residue "BW ARG 11": "NH1" <-> "NH2" Residue "BW GLU 17": "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 ARG 45": "NH1" <-> "NH2" Residue "BZ GLU 58": "OE1" <-> "OE2" Residue "B0 ARG 10": "NH1" <-> "NH2" Residue "B0 ARG 16": "NH1" <-> "NH2" 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 ARG 24": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 146607 Number of models: 1 Model: "" Number of chains: 73 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': 123, 'rna2p_pyr': 94, 'rna3p': 10, 'rna3p_pur': 746, 'rna3p_pyr': 560} Link IDs: {'rna2p': 218, 'rna3p': 1315} 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': 7, 'rna2p_pur': 282, 'rna2p_pyr': 160, 'rna3p': 17, 'rna3p_pur': 1382, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 449, 'rna3p': 2447} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 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: "D1" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D2" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1634 Classifications: {'RNA': 76} Modifications used: {'rna2p': 6, 'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p': 6, 'rna3p_pur': 31, 'rna3p_pyr': 26} Link IDs: {'rna2p': 12, 'rna3p': 63} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 6 Chain: "D3" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1604 Classifications: {'RNA': 75} Modifications used: {'p5*END': 1, 'rna2p': 3, 'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p': 4, 'rna3p_pur': 32, 'rna3p_pyr': 25} Link IDs: {'rna2p': 13, 'rna3p': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "D4" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 189 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna3p': 8} 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: "BA" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 185 Unusual residues: {' MG': 134, 'ERY': 1} Classifications: {'undetermined': 135} Link IDs: {None: 134} 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: "D2" 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: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 166 Classifications: {'water': 166} Link IDs: {None: 165} Chain: "AK" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 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: "AQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BA" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 614 Classifications: {'water': 614} Link IDs: {None: 613} Chain: "BC" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "BD" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "BE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "BN" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 52.06, per 1000 atoms: 0.36 Number of scatterers: 146607 At special positions: 0 Unit cell: (236.9, 271.4, 251.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 152 16.00 P 4711 15.00 Mg 172 11.99 O 41446 8.00 N 27120 7.00 C 73006 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYSBI 18 " - pdb=" SG CYSBI 40 " distance=2.03 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: 57.79 Conformation dependent library (CDL) restraints added in 6.2 seconds 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10440 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 176 helices and 74 sheets defined 39.1% alpha, 19.6% beta 1618 base pairs and 2534 stacking pairs defined. Time for finding SS restraints: 60.93 Creating SS restraints... Processing helix chain 'AB' and resid 5 through 13 removed outlier: 4.003A pdb=" N ALAAB 12 " --> pdb=" O ASPAB 8 " (cutoff:3.500A) Processing helix chain 'AB' and resid 27 through 32 removed outlier: 3.518A pdb=" N ILEAB 31 " --> pdb=" O METAB 27 " (cutoff:3.500A) removed outlier: 5.957A 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 Proline residue: AB 48 - end of helix removed outlier: 3.556A pdb=" N GLUAB 52 " --> pdb=" O PROAB 48 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARGAB 63 " --> pdb=" O LYSAB 59 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYSAB 64 " --> pdb=" O ILEAB 60 " (cutoff:3.500A) Processing helix chain 'AB' and resid 73 through 88 removed outlier: 5.625A pdb=" N GLUAB 78 " --> pdb=" O ARGAB 74 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ALAAB 79 " --> pdb=" O ALAAB 75 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYSAB 87 " --> pdb=" O ALAAB 83 " (cutoff:3.500A) Processing helix chain 'AB' and resid 103 through 122 removed outlier: 3.628A pdb=" N VALAB 107 " --> pdb=" O ASNAB 103 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLNAB 109 " --> pdb=" O LYSAB 105 " (cutoff:3.500A) Processing helix chain 'AB' and resid 130 through 148 removed outlier: 6.241A pdb=" N ALAAB 134 " --> pdb=" O THRAB 130 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEUAB 135 " --> pdb=" O LYSAB 131 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N METAB 136 " --> pdb=" O LYSAB 132 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARGAB 137 " --> pdb=" O GLUAB 133 " (cutoff:3.500A) removed outlier: 3.699A 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 Processing helix chain 'AB' and resid 206 through 227 removed outlier: 3.530A pdb=" N VALAB 221 " --> pdb=" O VALAB 217 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLNAB 227 " --> pdb=" O GLUAB 223 " (cutoff:3.500A) Processing helix chain 'AC' and resid 6 through 12 removed outlier: 4.318A pdb=" N ARGAC 11 " --> pdb=" O PROAC 7 " (cutoff:3.500A) Processing helix chain 'AC' and resid 28 through 48 removed outlier: 3.527A pdb=" N ALAAC 48 " --> pdb=" O THRAC 44 " (cutoff:3.500A) Processing helix chain 'AC' and resid 72 through 78 removed outlier: 3.753A pdb=" N VALAC 76 " --> pdb=" O ARGAC 72 " (cutoff:3.500A) Processing helix chain 'AC' and resid 81 through 96 removed outlier: 4.172A pdb=" N GLUAC 85 " --> pdb=" O GLYAC 81 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYSAC 86 " --> pdb=" O GLUAC 82 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALAAC 92 " --> pdb=" O ARGAC 88 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASPAC 93 " --> pdb=" O LYSAC 89 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILEAC 94 " --> pdb=" O VALAC 90 " (cutoff:3.500A) Processing helix chain 'AC' and resid 108 through 113 removed outlier: 4.045A pdb=" N ASPAC 112 " --> pdb=" O LYSAC 108 " (cutoff:3.500A) removed outlier: 6.937A 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 removed outlier: 3.964A pdb=" N ARGAC 126 " --> pdb=" O SERAC 122 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARGAC 127 " --> pdb=" O GLNAC 123 " (cutoff:3.500A) Processing helix chain 'AC' and resid 129 through 145 removed outlier: 3.628A pdb=" N ALAAC 133 " --> pdb=" O METAC 129 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEUAC 144 " --> pdb=" O ASNAC 140 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLYAC 145 " --> pdb=" O ALAAC 141 " (cutoff:3.500A) Processing helix chain 'AD' and resid 7 through 16 removed outlier: 4.215A pdb=" N LEUAD 11 " --> pdb=" O PROAD 7 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SERAD 12 " --> pdb=" O LYSAD 8 " (cutoff:3.500A) Processing helix chain 'AD' and resid 27 through 32 removed outlier: 4.137A pdb=" N LYSAD 31 " --> pdb=" O ALAAD 27 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYSAD 32 " --> pdb=" O ILEAD 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'AD' and resid 27 through 32' Processing helix chain 'AD' and resid 49 through 66 removed outlier: 3.533A pdb=" N GLNAD 54 " --> pdb=" O ASPAD 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYSAD 58 " --> pdb=" O GLNAD 54 " (cutoff:3.500A) Processing helix chain 'AD' and resid 68 through 83 removed outlier: 3.518A pdb=" N ARGAD 81 " --> pdb=" O LYSAD 77 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LYSAD 83 " --> pdb=" O ALAAD 79 " (cutoff:3.500A) Processing helix chain 'AD' and resid 85 through 97 removed outlier: 3.961A pdb=" N ARGAD 97 " --> pdb=" O LEUAD 93 " (cutoff:3.500A) Processing helix chain 'AD' and resid 98 through 106 removed outlier: 3.828A pdb=" N GLYAD 106 " --> pdb=" O VALAD 102 " (cutoff:3.500A) Processing helix chain 'AD' and resid 110 through 121 removed outlier: 4.180A pdb=" N LYSAD 121 " --> pdb=" O LEUAD 117 " (cutoff:3.500A) Processing helix chain 'AD' and resid 146 through 151 removed outlier: 3.606A pdb=" N LYSAD 150 " --> pdb=" O ARGAD 146 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LYSAD 151 " --> pdb=" O GLUAD 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'AD' and resid 146 through 151' Processing helix chain 'AD' and resid 152 through 166 removed outlier: 3.590A pdb=" N LYSAD 156 " --> pdb=" O GLNAD 152 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLUAD 163 " --> pdb=" O LEUAD 159 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLNAD 164 " --> pdb=" O GLUAD 160 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARGAD 165 " --> pdb=" O LEUAD 161 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLUAD 166 " --> pdb=" O ALAAD 162 " (cutoff:3.500A) Processing helix chain 'AD' and resid 187 through 192 removed outlier: 3.985A pdb=" N LEUAD 191 " --> pdb=" O GLUAD 187 " (cutoff:3.500A) removed outlier: 4.866A 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: 4.560A pdb=" N ILEAD 200 " --> pdb=" O ASNAD 196 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VALAD 201 " --> pdb=" O GLUAD 197 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLUAD 202 " --> pdb=" O HISAD 198 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUAD 203 " --> pdb=" O LEUAD 199 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYRAD 204 " --> pdb=" O ILEAD 200 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SERAD 205 " --> pdb=" O VALAD 201 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYSAD 206 " --> pdb=" O GLUAD 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'AD' and resid 196 through 206' Processing helix chain 'AE' and resid 55 through 71 removed outlier: 4.045A pdb=" N ARGAE 69 " --> pdb=" O GLUAE 65 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASNAE 70 " --> pdb=" O LYSAE 66 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N METAE 71 " --> pdb=" O ALAAE 67 " (cutoff:3.500A) Processing helix chain 'AE' and resid 109 through 119 removed outlier: 4.610A pdb=" N ALAAE 113 " --> pdb=" O GLYAE 109 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VALAE 114 " --> pdb=" O ALAAE 110 " (cutoff:3.500A) Processing helix chain 'AE' and resid 132 through 147 removed outlier: 3.611A pdb=" N ARGAE 138 " --> pdb=" O ILEAE 134 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASNAE 146 " --> pdb=" O ASPAE 142 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N METAE 147 " --> pdb=" O GLYAE 143 " (cutoff:3.500A) Processing helix chain 'AE' and resid 149 through 158 Processing helix chain 'AF' and resid 11 through 19 removed outlier: 3.748A pdb=" N SERAF 15 " --> pdb=" O HISAF 11 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLUAF 16 " --> pdb=" O PROAF 12 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLNAF 17 " --> pdb=" O ASPAF 13 " (cutoff:3.500A) Proline residue: AF 19 - end of helix Processing helix chain 'AF' and resid 20 through 33 removed outlier: 4.262A pdb=" N ALAAF 27 " --> pdb=" O GLUAF 23 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALAAF 32 " --> pdb=" O ALAAF 28 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLUAF 33 " --> pdb=" O ILEAF 29 " (cutoff:3.500A) Processing helix chain 'AF' and resid 67 through 81 removed outlier: 3.661A pdb=" N ILEAF 71 " --> pdb=" O PROAF 67 " (cutoff:3.500A) Processing helix chain 'AF' and resid 100 through 106 removed outlier: 3.635A pdb=" N ALAAF 105 " --> pdb=" O PROAF 101 " (cutoff:3.500A) removed outlier: 3.558A 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 54 removed outlier: 3.630A pdb=" N ALAAG 39 " --> pdb=" O LYSAG 35 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THRAG 49 " --> pdb=" O SERAG 45 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARGAG 53 " --> pdb=" O THRAG 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SERAG 54 " --> pdb=" O LEUAG 50 " (cutoff:3.500A) Processing helix chain 'AG' and resid 57 through 70 removed outlier: 3.561A pdb=" N ALAAG 65 " --> pdb=" O ALAAG 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALAG 69 " --> pdb=" O ALAAG 65 " (cutoff:3.500A) Processing helix chain 'AG' and resid 92 through 112 removed outlier: 3.973A pdb=" N LYSAG 110 " --> pdb=" O GLUAG 106 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARGAG 111 " --> pdb=" O ALAAG 107 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLYAG 112 " --> pdb=" O ALAAG 108 " (cutoff:3.500A) Processing helix chain 'AG' and resid 115 through 130 Processing helix chain 'AG' and resid 132 through 149 removed outlier: 4.107A pdb=" N ASNAG 148 " --> pdb=" O METAG 144 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYSAG 149 " --> pdb=" O ALAAG 145 " (cutoff:3.500A) Processing helix chain 'AH' and resid 5 through 21 Processing helix chain 'AH' and resid 30 through 44 removed outlier: 3.579A pdb=" N VALAH 34 " --> pdb=" O SERAH 30 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALAAH 35 " --> pdb=" O LYSAH 31 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLYAH 44 " --> pdb=" O LEUAH 40 " (cutoff:3.500A) Processing helix chain 'AH' and resid 112 through 120 removed outlier: 3.529A pdb=" N ALAAH 119 " --> pdb=" O ALAAH 115 " (cutoff:3.500A) Processing helix chain 'AI' and resid 34 through 40 removed outlier: 4.669A pdb=" N GLYAI 40 " --> pdb=" O GLUAI 36 " (cutoff:3.500A) Processing helix chain 'AI' and resid 41 through 56 Proline residue: AI 51 - end of helix removed outlier: 3.791A pdb=" N LEUAI 54 " --> pdb=" O GLNAI 50 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VALAI 55 " --> pdb=" O PROAI 51 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASPAI 56 " --> pdb=" O LEUAI 52 " (cutoff:3.500A) Processing helix chain 'AI' and resid 71 through 92 removed outlier: 3.507A pdb=" N GLUAI 89 " --> pdb=" O ARGAI 85 " (cutoff:3.500A) Processing helix chain 'AI' and resid 93 through 102 removed outlier: 4.468A pdb=" N GLUAI 97 " --> pdb=" O SERAI 93 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 14 through 33 Processing helix chain 'AJ' and resid 80 through 90 removed outlier: 3.766A pdb=" N ALAAJ 86 " --> pdb=" O LYSAJ 82 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEUAJ 90 " --> pdb=" O ALAAJ 86 " (cutoff:3.500A) Processing helix chain 'AK' and resid 46 through 51 removed outlier: 3.998A pdb=" N GLYAK 51 " --> pdb=" O ALAAK 47 " (cutoff:3.500A) Processing helix chain 'AK' and resid 54 through 59 removed outlier: 3.931A pdb=" N SERAK 58 " --> pdb=" O GLYAK 54 " (cutoff:3.500A) removed outlier: 4.921A 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: 4.185A pdb=" N LYSAK 75 " --> pdb=" O ALAAK 71 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLUAK 76 " --> pdb=" O ASPAK 72 " (cutoff:3.500A) Processing helix chain 'AK' and resid 92 through 104 removed outlier: 4.133A pdb=" N THRAK 96 " --> pdb=" O GLYAK 92 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILEAK 97 " --> pdb=" O ARGAK 93 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARGAK 98 " --> pdb=" O GLUAK 94 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALAAK 99 " --> pdb=" O SERAK 95 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEUAK 100 " --> pdb=" O THRAK 96 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLYAK 104 " --> pdb=" O LEUAK 100 " (cutoff:3.500A) Processing helix chain 'AL' and resid 3 through 11 removed outlier: 3.507A pdb=" N ARGAL 9 " --> pdb=" O ASNAL 5 " (cutoff:3.500A) Proline residue: AL 11 - end of helix Processing helix chain 'AL' and resid 113 through 118 removed outlier: 4.237A pdb=" N TYRAL 117 " --> pdb=" O ALAAL 113 " (cutoff:3.500A) Processing helix chain 'AM' and resid 14 through 22 removed outlier: 4.138A pdb=" N THRAM 20 " --> pdb=" O VALAM 16 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SERAM 21 " --> pdb=" O ILEAM 17 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILEAM 22 " --> pdb=" O ALAAM 18 " (cutoff:3.500A) Processing helix chain 'AM' and resid 26 through 38 removed outlier: 4.021A pdb=" N SERAM 30 " --> pdb=" O GLYAM 26 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLYAM 38 " --> pdb=" O LEUAM 34 " (cutoff:3.500A) Processing helix chain 'AM' and resid 44 through 49 removed outlier: 3.754A pdb=" N LEUAM 48 " --> pdb=" O LYSAM 44 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SERAM 49 " --> pdb=" O ILEAM 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'AM' and resid 44 through 49' Processing helix chain 'AM' and resid 50 through 64 removed outlier: 4.245A pdb=" N THRAM 55 " --> pdb=" O GLYAM 51 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASPAM 58 " --> pdb=" O ASPAM 54 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLUAM 59 " --> pdb=" O THRAM 55 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYSAM 62 " --> pdb=" O ASPAM 58 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHEAM 63 " --> pdb=" O GLUAM 59 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VALAM 64 " --> pdb=" O VALAM 60 " (cutoff:3.500A) Processing helix chain 'AM' and resid 66 through 84 removed outlier: 3.690A pdb=" N LEUAM 80 " --> pdb=" O SERAM 76 " (cutoff:3.500A) Processing helix chain 'AM' and resid 85 through 94 removed outlier: 3.663A pdb=" N GLYAM 94 " --> pdb=" O ARGAM 90 " (cutoff:3.500A) Processing helix chain 'AM' and resid 106 through 111 Processing helix chain 'AN' and resid 2 through 20 removed outlier: 3.612A pdb=" N LYSAN 6 " --> pdb=" O LYSAN 2 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALAAN 7 " --> pdb=" O GLNAN 3 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASPAN 17 " --> pdb=" O VALAN 13 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYSAN 18 " --> pdb=" O ALAAN 14 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHEAN 20 " --> pdb=" O ALAAN 16 " (cutoff:3.500A) Processing helix chain 'AN' and resid 23 through 28 removed outlier: 5.518A pdb=" N LYSAN 27 " --> pdb=" O ARGAN 23 " (cutoff:3.500A) Processing helix chain 'AN' and resid 38 through 51 removed outlier: 3.643A pdb=" N TRPAN 42 " --> pdb=" O ASPAN 38 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLNAN 49 " --> pdb=" O VALAN 45 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N THRAN 50 " --> pdb=" O LEUAN 46 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEUAN 51 " --> pdb=" O LYSAN 47 " (cutoff:3.500A) Processing helix chain 'AN' and resid 80 through 91 removed outlier: 3.544A pdb=" N ARGAN 85 " --> pdb=" O ARGAN 81 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARGAN 90 " --> pdb=" O GLUAN 86 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLYAN 91 " --> pdb=" O ALAAN 87 " (cutoff:3.500A) Processing helix chain 'AO' and resid 4 through 16 Processing helix chain 'AO' and resid 24 through 43 removed outlier: 4.475A pdb=" N GLYAO 41 " --> pdb=" O ASNAO 37 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HISAO 42 " --> pdb=" O HISAO 38 " (cutoff:3.500A) Processing helix chain 'AO' and resid 49 through 74 removed outlier: 3.661A pdb=" N ARGAO 53 " --> pdb=" O ASPAO 49 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARGAO 54 " --> pdb=" O HISAO 50 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLYAO 55 " --> pdb=" O HISAO 51 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEUAO 66 " --> pdb=" O GLNAO 62 " (cutoff:3.500A) Processing helix chain 'AO' and resid 75 through 86 Processing helix chain 'AP' and resid 53 through 64 removed outlier: 4.144A pdb=" N HISAP 59 " --> pdb=" O ASPAP 55 " (cutoff:3.500A) Processing helix chain 'AP' and resid 68 through 82 removed outlier: 4.220A pdb=" N ALAAP 73 " --> pdb=" O ASPAP 69 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYSAP 80 " --> pdb=" O LYSAP 76 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALAAP 82 " --> pdb=" O VALAP 78 " (cutoff:3.500A) Processing helix chain 'AR' and resid 25 through 34 removed outlier: 4.732A pdb=" N ASNAR 31 " --> pdb=" O ALAAR 27 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYRAR 32 " --> pdb=" O THRAR 28 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILEAR 33 " --> pdb=" O LEUAR 29 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N THRAR 34 " --> pdb=" O LYSAR 30 " (cutoff:3.500A) Processing helix chain 'AR' and resid 41 through 46 Processing helix chain 'AR' and resid 48 through 66 removed outlier: 3.616A pdb=" N GLNAR 54 " --> pdb=" O LYSAR 50 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYRAR 64 " --> pdb=" O LYSAR 60 " (cutoff:3.500A) Processing helix chain 'AS' and resid 12 through 26 removed outlier: 4.088A pdb=" N VALAS 23 " --> pdb=" O VALAS 19 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLUAS 24 " --> pdb=" O GLUAS 20 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N SERAS 25 " --> pdb=" O LYSAS 21 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLYAS 26 " --> pdb=" O ALAAS 22 " (cutoff:3.500A) Processing helix chain 'AS' and resid 70 through 76 removed outlier: 4.685A pdb=" N PHEAS 74 " --> pdb=" O LYSAS 70 " (cutoff:3.500A) removed outlier: 4.505A 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 42 removed outlier: 3.947A pdb=" N METAT 27 " --> pdb=" O SERAT 23 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILEAT 32 " --> pdb=" O METAT 28 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VALAT 35 " --> pdb=" O PHEAT 31 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALAAT 41 " --> pdb=" O ALAAT 37 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLYAT 42 " --> pdb=" O ALAAT 38 " (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 removed outlier: 3.533A pdb=" N GLNAT 82 " --> pdb=" O ASNAT 78 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYSAT 85 " --> pdb=" O ALAAT 81 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEUAT 86 " --> pdb=" O GLNAT 82 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALAAT 87 " --> pdb=" O ILEAT 83 " (cutoff:3.500A) Processing helix chain 'AU' and resid 11 through 27 removed outlier: 3.780A pdb=" N GLYAU 27 " --> pdb=" O CYSAU 23 " (cutoff:3.500A) Processing helix chain 'AU' and resid 28 through 37 removed outlier: 3.515A pdb=" N ARGAU 33 " --> pdb=" O LEUAU 29 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARGAU 34 " --> pdb=" O ALAAU 30 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLUAU 36 " --> pdb=" O VALAU 32 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHEAU 37 " --> pdb=" O ARGAU 33 " (cutoff:3.500A) Processing helix chain 'AU' and resid 40 through 56 removed outlier: 3.678A pdb=" N LYSAU 46 " --> pdb=" O THRAU 42 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARGAU 55 " --> pdb=" O SERAU 51 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N HISAU 56 " --> pdb=" O ALAAU 52 " (cutoff:3.500A) Processing helix chain 'BC' and resid 10 through 15 removed outlier: 5.403A pdb=" N HISBC 15 " --> pdb=" O PROBC 11 " (cutoff:3.500A) Processing helix chain 'BC' and resid 30 through 35 removed outlier: 4.040A pdb=" N LEUBC 34 " --> pdb=" O PHEBC 30 " (cutoff:3.500A) removed outlier: 5.971A 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: 3.685A 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: 4.002A pdb=" N ALABC 211 " --> pdb=" O LYSBC 207 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARGBC 212 " --> pdb=" O ALABC 208 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARGBC 214 " --> pdb=" O ALABC 210 " (cutoff:3.500A) Processing helix chain 'BC' and resid 221 through 226 removed outlier: 4.066A pdb=" N METBC 225 " --> pdb=" O ARGBC 221 " (cutoff:3.500A) removed outlier: 5.460A 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: 3.912A pdb=" N ASPBC 264 " --> pdb=" O ASNBC 260 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYSBC 265 " --> pdb=" O LYSBC 261 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHEBC 266 " --> pdb=" O ARGBC 262 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILEBC 267 " --> pdb=" O THRBC 263 " (cutoff:3.500A) removed outlier: 5.686A 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: 4.684A pdb=" N METBC 201 " --> pdb=" O ALABC 198 " (cutoff:3.500A) Processing helix chain 'BD' and resid 56 through 61 removed outlier: 6.317A pdb=" N THRBD 61 " --> pdb=" O ALABD 57 " (cutoff:3.500A) Processing helix chain 'BD' and resid 62 through 72 removed outlier: 3.903A pdb=" N ALABD 71 " --> pdb=" O HISBD 67 " (cutoff:3.500A) Processing helix chain 'BD' and resid 98 through 103 removed outlier: 4.538A pdb=" N ALABD 102 " --> pdb=" O VALBD 98 " (cutoff:3.500A) removed outlier: 5.557A 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 removed outlier: 3.551A pdb=" N PHEBE 19 " --> pdb=" O SERBE 15 " (cutoff:3.500A) Processing helix chain 'BE' and resid 24 through 40 removed outlier: 4.011A pdb=" N GLNBE 30 " --> pdb=" O ALABE 26 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALABE 36 " --> pdb=" O VALBE 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALABE 39 " --> pdb=" O TYRBE 35 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARGBE 40 " --> pdb=" O ALABE 36 " (cutoff:3.500A) Processing helix chain 'BE' and resid 97 through 116 removed outlier: 3.676A pdb=" N VALBE 113 " --> pdb=" O LEUBE 109 " (cutoff:3.500A) Processing helix chain 'BE' and resid 130 through 142 removed outlier: 3.588A pdb=" N METBE 141 " --> pdb=" O LYSBE 137 " (cutoff:3.500A) Processing helix chain 'BE' and resid 154 through 163 removed outlier: 3.560A pdb=" N ARGBE 162 " --> pdb=" O PHEBE 158 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASNBE 163 " --> pdb=" O LEUBE 159 " (cutoff:3.500A) Processing helix chain 'BE' and resid 176 through 183 removed outlier: 3.698A pdb=" N LEUBE 180 " --> pdb=" O ASPBE 176 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILEBE 181 " --> pdb=" O PROBE 177 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHEBE 183 " --> pdb=" O SERBE 179 " (cutoff:3.500A) Processing helix chain 'BE' and resid 189 through 201 removed outlier: 3.627A pdb=" N GLUBE 197 " --> pdb=" O VALBE 193 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLUBE 198 " --> pdb=" O LYSBE 194 " (cutoff:3.500A) Processing helix chain 'BF' and resid 2 through 21 removed outlier: 3.829A pdb=" N ASPBF 6 " --> pdb=" O ALABF 2 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALBF 12 " --> pdb=" O TYRBF 8 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VALBF 13 " --> pdb=" O LYSBF 9 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N LYSBF 14 " --> pdb=" O ASPBF 10 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THRBF 18 " --> pdb=" O LYSBF 14 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLUBF 19 " --> pdb=" O LYSBF 15 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASNBF 21 " --> pdb=" O METBF 17 " (cutoff:3.500A) Processing helix chain 'BF' and resid 42 through 47 removed outlier: 4.163A pdb=" N ASPBF 46 " --> pdb=" O GLUBF 42 " (cutoff:3.500A) removed outlier: 3.810A 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: 3.639A pdb=" N ASNBF 52 " --> pdb=" O LYSBF 48 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEUBF 57 " --> pdb=" O ALABF 53 " (cutoff:3.500A) Processing helix chain 'BF' and resid 93 through 111 removed outlier: 3.714A pdb=" N TRPBF 97 " --> pdb=" O GLYBF 93 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALABF 107 " --> pdb=" O LEUBF 103 " (cutoff:3.500A) removed outlier: 4.691A 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: 3.612A pdb=" N GLYBF 166 " --> pdb=" O SERBF 162 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEUBF 170 " --> pdb=" O GLYBF 166 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHEBF 173 " --> pdb=" O LEUBF 169 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASPBF 174 " --> pdb=" O LEUBF 170 " (cutoff:3.500A) Processing helix chain 'BF' and resid 134 through 139 removed outlier: 4.042A pdb=" N ILEBF 137 " --> pdb=" O GLUBF 134 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHEBF 138 " --> pdb=" O GLNBF 135 " (cutoff:3.500A) Proline residue: BF 139 - end of helix No H-bonds generated for 'chain 'BF' and resid 134 through 139' Processing helix chain 'BG' and resid 2 through 8 removed outlier: 4.116A 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 removed outlier: 3.500A pdb=" N THRBG 67 " --> pdb=" O ALABG 63 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILEBG 77 " --> pdb=" O ASNBG 73 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THRBG 80 " --> pdb=" O VALBG 76 " (cutoff:3.500A) Processing helix chain 'BG' and resid 137 through 153 removed outlier: 3.703A pdb=" N ALABG 145 " --> pdb=" O ILEBG 141 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARGBG 149 " --> pdb=" O ALABG 145 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYRBG 151 " --> pdb=" O ASPBG 147 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARGBG 152 " --> pdb=" O LEUBG 148 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARGBG 153 " --> pdb=" O ARGBG 149 " (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 40 through 52 removed outlier: 5.226A pdb=" N ILEBH 44 " --> pdb=" O THRBH 40 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLUBH 45 " --> pdb=" O LYSBH 41 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHEBH 46 " --> pdb=" O LYSBH 42 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N PHEBH 47 " --> pdb=" O ASNBH 43 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLUBH 48 " --> pdb=" O ILEBH 44 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARGBH 50 " --> pdb=" O PHEBH 46 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALABH 52 " --> pdb=" O GLUBH 48 " (cutoff:3.500A) Processing helix chain 'BH' and resid 53 through 76 removed outlier: 3.585A pdb=" N ALABH 59 " --> pdb=" O GLUBH 55 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VALBH 61 " --> pdb=" O LYSBH 57 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALABH 67 " --> pdb=" O ALABH 63 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARGBH 68 " --> pdb=" O ALABH 64 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLUBH 70 " --> pdb=" O ASNBH 66 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYSBH 71 " --> pdb=" O ALABH 67 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILEBH 72 " --> pdb=" O ARGBH 68 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALABH 74 " --> pdb=" O GLUBH 70 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LEUBH 75 " --> pdb=" O LYSBH 71 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLUBH 76 " --> pdb=" O ILEBH 72 " (cutoff:3.500A) Processing helix chain 'BH' and resid 95 through 107 removed outlier: 3.633A pdb=" N ILEBH 99 " --> pdb=" O GLYBH 95 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALABH 100 " --> pdb=" O THRBH 96 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALABH 105 " --> pdb=" O ASPBH 101 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALABH 106 " --> pdb=" O ALABH 102 " (cutoff:3.500A) Processing helix chain 'BH' and resid 111 through 116 removed outlier: 4.424A pdb=" N VALBH 115 " --> pdb=" O ALABH 111 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ARGBH 116 " --> pdb=" O LYSBH 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'BH' and resid 111 through 116' Processing helix chain 'BI' and resid 47 through 54 removed outlier: 4.641A pdb=" N VALBI 51 " --> pdb=" O LYSBI 47 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALABI 52 " --> pdb=" O GLNBI 48 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THRBI 53 " --> pdb=" O ARGBI 49 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLYBI 54 " --> pdb=" O ASPBI 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'BI' and resid 47 through 54' Processing helix chain 'BI' and resid 55 through 65 removed outlier: 4.678A pdb=" N ARGBI 59 " --> pdb=" O GLYBI 55 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYSBI 62 " --> pdb=" O ASPBI 58 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARGBI 63 " --> pdb=" O ARGBI 59 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHEBI 64 " --> pdb=" O PHEBI 60 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASNBI 65 " --> pdb=" O ASNBI 61 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 24 through 38 removed outlier: 4.396A pdb=" N GLUBJ 31 " --> pdb=" O ARGBJ 27 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARGBJ 37 " --> pdb=" O ALABJ 33 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 88 through 96 removed outlier: 3.739A pdb=" N ALABJ 94 " --> pdb=" O GLUBJ 90 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 97 through 110 removed outlier: 4.329A pdb=" N ILEBJ 101 " --> pdb=" O PROBJ 97 " (cutoff:3.500A) removed outlier: 3.832A 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: 3.595A pdb=" N ALABJ 117 " --> pdb=" O PROBJ 113 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHEBJ 119 " --> pdb=" O GLYBJ 115 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARGBJ 120 " --> pdb=" O ARGBJ 116 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYSBJ 121 " --> pdb=" O ALABJ 117 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEUBJ 122 " --> pdb=" O METBJ 118 " (cutoff:3.500A) Processing helix chain 'BK' and resid 104 through 109 removed outlier: 4.717A pdb=" N ARGBK 108 " --> pdb=" O THRBK 104 " (cutoff:3.500A) removed outlier: 5.753A 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 removed outlier: 3.733A pdb=" N ILEBK 116 " --> pdb=" O PHEBK 112 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SERBK 117 " --> pdb=" O METBK 113 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEUBK 118 " --> pdb=" O LYSBK 114 " (cutoff:3.500A) Processing helix chain 'BL' and resid 56 through 62 removed outlier: 3.646A 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: 4.188A pdb=" N ALABL 72 " --> pdb=" O SERBL 68 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILEBL 73 " --> pdb=" O ARGBL 69 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THRBL 74 " --> pdb=" O LYSBL 70 " (cutoff:3.500A) removed outlier: 5.681A 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: 4.083A pdb=" N LEUBL 82 " --> pdb=" O ARGBL 78 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALABL 83 " --> pdb=" O LEUBL 79 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYSBL 84 " --> pdb=" O SERBL 80 " (cutoff:3.500A) removed outlier: 4.119A 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: 3.520A pdb=" N ASNBL 99 " --> pdb=" O LEUBL 95 " (cutoff:3.500A) Processing helix chain 'BL' and resid 128 through 139 removed outlier: 3.799A pdb=" N ALABL 133 " --> pdb=" O LYSBL 129 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALABL 134 " --> pdb=" O GLYBL 130 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALABL 138 " --> pdb=" O ALABL 134 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLYBL 139 " --> pdb=" O ILEBL 135 " (cutoff:3.500A) Processing helix chain 'BM' and resid 42 through 58 removed outlier: 3.544A pdb=" N METBM 53 " --> pdb=" O ALABM 49 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALABM 56 " --> pdb=" O ALABM 52 " (cutoff:3.500A) Processing helix chain 'BM' and resid 109 through 125 removed outlier: 3.755A pdb=" N GLUBM 115 " --> pdb=" O GLUBM 111 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALABM 122 " --> pdb=" O LYSBM 118 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYSBM 123 " --> pdb=" O LEUBM 119 " (cutoff:3.500A) removed outlier: 3.800A 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 removed outlier: 3.633A pdb=" N GLNBN 18 " --> pdb=" O SERBN 14 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARGBN 30 " --> pdb=" O GLYBN 26 " (cutoff:3.500A) Processing helix chain 'BN' and resid 37 through 57 removed outlier: 3.698A pdb=" N ARGBN 45 " --> pdb=" O ALABN 41 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARGBN 46 " --> pdb=" O LYSBN 42 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VALBN 47 " --> pdb=" O GLUBN 43 " (cutoff:3.500A) Proline residue: BN 50 - end of helix removed outlier: 4.707A pdb=" N THRBN 57 " --> pdb=" O THRBN 53 " (cutoff:3.500A) Processing helix chain 'BN' and resid 59 through 71 removed outlier: 3.585A pdb=" N ALABN 68 " --> pdb=" O ARGBN 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARGBN 69 " --> pdb=" O LEUBN 65 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THRBN 70 " --> pdb=" O ALABN 66 " (cutoff:3.500A) Processing helix chain 'BN' and resid 72 through 88 removed outlier: 3.567A pdb=" N VALBN 76 " --> pdb=" O ASPBN 72 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYSBN 78 " --> pdb=" O GLUBN 74 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEUBN 83 " --> pdb=" O LEUBN 79 " (cutoff:3.500A) removed outlier: 4.707A 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: 3.988A pdb=" N ARGBO 7 " --> pdb=" O LYSBO 3 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARGBO 10 " --> pdb=" O ALABO 6 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THRBO 12 " --> pdb=" O ILEBO 8 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARGBO 13 " --> pdb=" O ARGBO 9 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ALABO 14 " --> pdb=" O ARGBO 10 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLNBO 19 " --> pdb=" O ARGBO 15 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLUBO 20 " --> pdb=" O ARGBO 16 " (cutoff:3.500A) Processing helix chain 'BO' and resid 55 through 63 removed outlier: 3.841A pdb=" N GLUBO 60 " --> pdb=" O LYSBO 56 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLNBO 61 " --> pdb=" O ALABO 57 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEUBO 62 " --> pdb=" O ILEBO 58 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYSBO 63 " --> pdb=" O ALABO 59 " (cutoff:3.500A) Processing helix chain 'BO' and resid 67 through 86 removed outlier: 3.578A pdb=" N LEUBO 83 " --> pdb=" O ALABO 79 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYSBO 85 " --> pdb=" O ARGBO 81 " (cutoff:3.500A) Processing helix chain 'BO' and resid 101 through 114 removed outlier: 3.558A pdb=" N GLYBO 114 " --> pdb=" O ALABO 110 " (cutoff:3.500A) Processing helix chain 'BP' and resid 2 through 14 removed outlier: 4.144A pdb=" N GLUBP 11 " --> pdb=" O GLNBP 7 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLNBP 12 " --> pdb=" O LEUBP 8 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYSBP 14 " --> pdb=" O GLNBP 10 " (cutoff:3.500A) Processing helix chain 'BP' and resid 97 through 104 removed outlier: 4.934A pdb=" N ARGBP 101 " --> pdb=" O LEUBP 97 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N GLUBP 102 " --> pdb=" O TYRBP 98 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARGBP 103 " --> pdb=" O TYRBP 99 " (cutoff:3.500A) removed outlier: 5.667A 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 7 through 22 removed outlier: 3.557A pdb=" N GLNBQ 20 " --> pdb=" O LYSBQ 16 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYSBQ 22 " --> pdb=" O LEUBQ 18 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 26 through 31 removed outlier: 3.965A pdb=" N ARGBQ 30 " --> pdb=" O GLYBQ 26 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 32 through 37 removed outlier: 4.169A pdb=" N GLNBQ 37 " --> pdb=" O ARGBQ 33 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 39 through 73 removed outlier: 4.305A pdb=" N ARGBQ 51 " --> pdb=" O TYRBQ 47 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLNBQ 52 " --> pdb=" O ARGBQ 48 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYSBQ 54 " --> pdb=" O ARGBQ 50 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARGBQ 55 " --> pdb=" O ARGBQ 51 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARGBQ 58 " --> pdb=" O LYSBQ 54 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALABQ 63 " --> pdb=" O GLNBQ 59 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLNBQ 71 " --> pdb=" O ALABQ 67 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASNBQ 72 " --> pdb=" O ALABQ 68 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 75 through 87 removed outlier: 3.506A pdb=" N ASNBQ 81 " --> pdb=" O SERBQ 77 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 91 through 102 removed outlier: 3.693A pdb=" N ASPBQ 97 " --> pdb=" O LYSBQ 93 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VALBQ 100 " --> pdb=" O ALABQ 96 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 103 through 118 removed outlier: 3.717A pdb=" N THRBQ 107 " --> pdb=" O LYSBQ 103 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYSBQ 112 " --> pdb=" O ALABQ 108 " (cutoff:3.500A) Processing helix chain 'BS' and resid 13 through 25 removed outlier: 4.015A pdb=" N LEUBS 19 " --> pdb=" O GLNBS 15 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VALBS 20 " --> pdb=" O LYSBS 16 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEUBS 23 " --> pdb=" O LEUBS 19 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILEBS 24 " --> pdb=" O VALBS 20 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARGBS 25 " --> pdb=" O ALABS 21 " (cutoff:3.500A) Processing helix chain 'BS' and resid 28 through 40 removed outlier: 3.846A pdb=" N ASPBS 34 " --> pdb=" O SERBS 30 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYRBS 38 " --> pdb=" O ASPBS 34 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ASNBS 40 " --> pdb=" O LEUBS 36 " (cutoff:3.500A) Processing helix chain 'BS' and resid 41 through 61 removed outlier: 3.870A pdb=" N VALBS 45 " --> pdb=" O LYSBS 41 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VALBS 50 " --> pdb=" O LEUBS 46 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASNBS 61 " --> pdb=" O ASNBS 57 " (cutoff:3.500A) Processing helix chain 'BS' and resid 65 through 70 removed outlier: 3.868A pdb=" N LEUBS 69 " --> pdb=" O ASPBS 65 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LYSBS 70 " --> pdb=" O ILEBS 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'BS' and resid 65 through 70' Processing helix chain 'BT' and resid 3 through 11 removed outlier: 4.194A pdb=" N LYSBT 9 " --> pdb=" O GLUBT 5 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VALBT 10 " --> pdb=" O ARGBT 6 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEUBT 11 " --> pdb=" O LEUBT 7 " (cutoff:3.500A) Processing helix chain 'BT' and resid 17 through 27 removed outlier: 3.556A pdb=" N SERBT 21 " --> pdb=" O SERBT 17 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N METBT 24 " --> pdb=" O ALABT 20 " (cutoff:3.500A) Processing helix chain 'BT' and resid 39 through 51 removed outlier: 3.585A pdb=" N ALABT 45 " --> pdb=" O ALABT 41 " (cutoff:3.500A) Processing helix chain 'BU' and resid 66 through 71 removed outlier: 4.103A pdb=" N VALBU 70 " --> pdb=" O GLNBU 66 " (cutoff:3.500A) removed outlier: 5.377A 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: 3.715A pdb=" N ALABV 23 " --> pdb=" O ARGBV 19 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASNBV 24 " --> pdb=" O LEUBV 20 " (cutoff:3.500A) Processing helix chain 'BV' and resid 43 through 53 removed outlier: 3.517A pdb=" N ASNBV 49 " --> pdb=" O ASPBV 45 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALABV 52 " --> pdb=" O METBV 48 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYSBV 53 " --> pdb=" O ASNBV 49 " (cutoff:3.500A) Processing helix chain 'BV' and resid 54 through 59 removed outlier: 4.211A pdb=" N SERBV 58 " --> pdb=" O ALABV 54 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLUBV 59 " --> pdb=" O GLUBV 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'BV' and resid 54 through 59' Processing helix chain 'BX' and resid 52 through 63 removed outlier: 3.594A pdb=" N METBX 56 " --> pdb=" O SERBX 52 " (cutoff:3.500A) removed outlier: 4.273A 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: 6.313A pdb=" N LEUBY 6 " --> pdb=" O LYSBY 2 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ARGBY 7 " --> pdb=" O ALABY 3 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLUBY 8 " --> pdb=" O LYSBY 4 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYSBY 9 " --> pdb=" O GLUBY 5 " (cutoff:3.500A) removed outlier: 5.619A 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 removed outlier: 3.597A pdb=" N THRBY 16 " --> pdb=" O GLUBY 12 " (cutoff:3.500A) Processing helix chain 'BY' and resid 40 through 63 removed outlier: 4.373A pdb=" N LYSBY 44 " --> pdb=" O SERBY 40 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLNBY 45 " --> pdb=" O HISBY 41 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALABY 51 " --> pdb=" O ARGBY 47 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALABY 63 " --> pdb=" O GLUBY 59 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 17 through 28 Processing helix chain 'BZ' and resid 41 through 52 removed outlier: 3.767A pdb=" N METBZ 47 " --> pdb=" O ALABZ 43 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VALBZ 51 " --> pdb=" O METBZ 47 " (cutoff:3.500A) Processing helix chain 'B0' and resid 9 through 19 removed outlier: 3.514A pdb=" N SERB0 18 " --> pdb=" O GLYB0 14 " (cutoff:3.500A) removed outlier: 5.006A 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 24 removed outlier: 3.866A pdb=" N ALAB2 23 " --> pdb=" O ARGB2 19 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THRB2 24 " --> pdb=" O ALAB2 20 " (cutoff:3.500A) Processing helix chain 'B2' and resid 25 through 38 removed outlier: 3.592A pdb=" N VALB2 30 " --> pdb=" O ASNB2 26 " (cutoff:3.500A) Processing helix chain 'B3' and resid 7 through 14 removed outlier: 3.846A pdb=" N LYSB3 12 " --> pdb=" O ARGB3 8 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARGB3 13 " --> pdb=" O GLYB3 9 " (cutoff:3.500A) Processing helix chain 'B3' and resid 32 through 37 removed outlier: 4.444A pdb=" N LYSB3 36 " --> pdb=" O ILEB3 32 " (cutoff:3.500A) removed outlier: 5.582A 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: 3.588A pdb=" N LEUB3 44 " --> pdb=" O ARGB3 40 " (cutoff:3.500A) removed outlier: 3.736A 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: 4.638A pdb=" N GLYB3 56 " --> pdb=" O LYSB3 52 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LEUB3 57 " --> pdb=" O GLYB3 53 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N CYSB3 61 " --> pdb=" O LEUB3 57 " (cutoff:3.500A) Proline residue: B3 63 - end of helix Processing sheet with id= 1, first strand: chain 'AB' and resid 15 through 18 removed outlier: 5.167A pdb=" N HISAB 15 " --> pdb=" O ILEAB 41 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N HISAB 39 " --> pdb=" O GLYAB 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'AB' and resid 89 through 92 removed outlier: 3.780A pdb=" N ALAAB 185 " --> pdb=" O PHEAB 198 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'AC' and resid 54 through 59 removed outlier: 3.910A 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: 5.532A pdb=" N ARGAC 164 " --> pdb=" O GLYAC 155 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLYAC 148 " --> pdb=" O PHEAC 203 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'AD' and resid 140 through 144 removed outlier: 4.165A pdb=" N ASPAD 141 " --> pdb=" O PHEAD 182 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N TRPAD 170 " --> pdb=" O LYSAD 183 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'AE' and resid 12 through 16 removed outlier: 6.555A pdb=" N LEUAE 36 " --> pdb=" O ILEAE 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'AE' and resid 84 through 88 removed outlier: 3.588A pdb=" N ALAAE 99 " --> pdb=" O ASNAE 122 " (cutoff:3.500A) removed outlier: 6.024A 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: 3.544A pdb=" N ARGAF 38 " --> pdb=" O ASNAF 63 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N TYRAF 59 " --> pdb=" O TRPAF 42 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N HISAF 3 " --> pdb=" O THRAF 92 " (cutoff:3.500A) removed outlier: 3.716A 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: 3.614A pdb=" N GLYAF 43 " --> pdb=" O TYRAF 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LEUAF 47 " --> pdb=" O HISAF 55 " (cutoff:3.500A) removed outlier: 7.380A 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: 6.772A pdb=" N ALAAH 23 " --> pdb=" O LEUAH 63 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLUAH 58 " --> pdb=" O GLUAH 52 " (cutoff:3.500A) removed outlier: 4.024A 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: 3.776A pdb=" N CYSAH 127 " --> pdb=" O VALAH 103 " (cutoff:3.500A) removed outlier: 6.817A 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 39 through 42 removed outlier: 4.531A pdb=" N LEUAJ 71 " --> pdb=" O LEUAJ 42 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'AJ' and resid 44 through 52 Processing sheet with id= 17, first strand: chain 'AK' and resid 30 through 35 removed outlier: 3.532A pdb=" N GLUAK 83 " --> pdb=" O GLYAK 19 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VALAK 84 " --> pdb=" O THRAK 108 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'AK' and resid 83 through 87 No H-bonds generated for sheet with id= 18 Processing sheet with id= 19, first strand: chain 'AL' and resid 29 through 33 removed outlier: 5.078A pdb=" N LEUAL 81 " --> pdb=" O VALAL 98 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'AL' and resid 36 through 41 removed outlier: 3.606A pdb=" N ARGAL 36 " --> pdb=" O ARGAL 54 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYSAL 51 " --> pdb=" O ILEAL 67 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'AP' and resid 4 through 10 removed outlier: 6.768A pdb=" N TYRAP 17 " --> pdb=" O PHEAP 38 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHEAP 38 " --> pdb=" O TYRAP 17 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VALAP 19 " --> pdb=" O VALAP 36 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'AQ' and resid 7 through 11 removed outlier: 7.148A pdb=" N GLUAQ 60 " --> pdb=" O VALAQ 76 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'AQ' and resid 19 through 30 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'AS' and resid 48 through 52 Processing sheet with id= 25, first strand: chain 'BC' and resid 2 through 6 removed outlier: 3.733A pdb=" N ALABC 2 " --> pdb=" O VALBC 20 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VALBC 16 " --> pdb=" O CYSBC 6 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'BC' and resid 80 through 83 removed outlier: 3.538A pdb=" N ARGBC 80 " --> pdb=" O LEUBC 93 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEUBC 93 " --> pdb=" O GLUBC 79 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILEBC 74 " --> pdb=" O SERBC 118 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N SERBC 118 " --> pdb=" O ILEBC 74 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASPBC 114 " --> pdb=" O VALBC 78 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLYBC 127 " --> pdb=" O GLNBC 115 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLNBC 117 " --> pdb=" O GLYBC 127 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'BC' and resid 138 through 142 removed outlier: 4.219A pdb=" N SERBC 139 " --> pdb=" O ILEBC 164 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLNBC 163 " --> pdb=" O ARGBC 175 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THRBC 173 " --> pdb=" O VALBC 165 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLUBC 180 " --> pdb=" O LEUBC 176 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'BC' and resid 90 through 96 removed outlier: 5.462A pdb=" N ASNBC 90 " --> pdb=" O ALABC 106 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLUBC 100 " --> pdb=" O TYRBC 96 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'BD' and resid 11 through 16 removed outlier: 3.815A pdb=" N VALBD 20 " --> pdb=" O THRBD 16 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VALBD 26 " --> pdb=" O VALBD 9 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYSBD 7 " --> pdb=" O GLUBD 28 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEUBD 201 " --> pdb=" O GLYBD 6 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SERBD 199 " --> pdb=" O LYSBD 8 " (cutoff:3.500A) removed outlier: 13.359A pdb=" N GLYBD 198 " --> pdb=" O LYSBD 114 " (cutoff:3.500A) removed outlier: 11.741A pdb=" N LYSBD 114 " --> pdb=" O GLYBD 198 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ASPBD 200 " --> pdb=" O THRBD 112 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N THRBD 112 " --> pdb=" O ASPBD 200 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLUBD 168 " --> pdb=" O SERBD 113 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'BD' and resid 79 through 84 removed outlier: 6.087A pdb=" N ARGBD 46 " --> pdb=" O LEUBD 84 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLNBD 49 " --> pdb=" O THRBD 35 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLNBD 94 " --> pdb=" O VALBD 34 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'BD' and resid 179 through 182 Processing sheet with id= 32, first strand: chain 'BD' and resid 24 through 28 No H-bonds generated for sheet with id= 32 Processing sheet with id= 33, first strand: chain 'BD' and resid 105 through 108 removed outlier: 6.505A pdb=" N LYSBD 105 " --> pdb=" O VALBD 177 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'BE' and resid 1 through 6 removed outlier: 3.884A pdb=" N SERBE 10 " --> pdb=" O LEUBE 5 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'BE' and resid 117 through 120 removed outlier: 3.716A pdb=" N LYSBE 185 " --> pdb=" O ASPBE 145 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'BF' and resid 65 through 68 removed outlier: 3.632A pdb=" N GLYBF 86 " --> pdb=" O THRBF 68 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILEBF 85 " --> pdb=" O VALBF 40 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYSBF 33 " --> pdb=" O THRBF 157 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLYBF 39 " --> pdb=" O GLYBF 151 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLYBF 151 " --> pdb=" O GLYBF 39 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'BF' and resid 72 through 75 removed outlier: 7.134A pdb=" N LYSBF 72 " --> pdb=" O GLNBF 81 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLNBF 81 " --> pdb=" O LYSBF 72 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'BG' and resid 15 through 20 removed outlier: 6.065A pdb=" N GLNBG 22 " --> pdb=" O LEUBG 37 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLYBG 31 " --> pdb=" O GLYBG 28 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'BG' and resid 41 through 46 removed outlier: 3.627A pdb=" N THRBG 51 " --> pdb=" O LYSBG 44 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALABG 46 " --> pdb=" O THRBG 49 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THRBG 49 " --> pdb=" O ALABG 46 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'BG' and resid 94 through 99 removed outlier: 3.762A pdb=" N VALBG 102 " --> pdb=" O LYSBG 99 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASNBG 101 " --> pdb=" O LEUBG 117 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'BG' and resid 121 through 125 removed outlier: 6.111A pdb=" N THRBG 129 " --> pdb=" O LEUBG 89 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLYBG 135 " --> pdb=" O PHEBG 83 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LYSBG 86 " --> pdb=" O ALABG 165 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VALBG 90 " --> pdb=" O GLYBG 161 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'BH' and resid 2 through 5 removed outlier: 6.893A pdb=" N GLNBH 2 " --> pdb=" O ALABH 39 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'BH' and resid 78 through 82 removed outlier: 4.934A pdb=" N VALBH 78 " --> pdb=" O ILEBH 143 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASNBH 145 " --> pdb=" O VALBH 78 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'BI' and resid 13 through 16 Processing sheet with id= 45, first strand: chain 'BJ' and resid 52 through 57 removed outlier: 5.075A pdb=" N ASPBJ 19 " --> pdb=" O LEUBJ 140 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'BJ' and resid 74 through 78 removed outlier: 7.715A pdb=" N GLYBJ 83 " --> pdb=" O THRBJ 78 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'BK' and resid 18 through 21 removed outlier: 4.166A pdb=" N THRBK 6 " --> pdb=" O CYSBK 21 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASNBK 82 " --> pdb=" O METBK 7 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'BL' and resid 120 through 123 Processing sheet with id= 49, first strand: chain 'BM' and resid 37 through 40 No H-bonds generated for sheet with id= 49 Processing sheet with id= 50, first strand: chain 'BM' and resid 62 through 65 removed outlier: 3.851A pdb=" N TYRBM 103 " --> pdb=" O LEUBM 33 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEUBM 33 " --> pdb=" O LEUBM 102 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYSBM 100 " --> pdb=" O ALABM 35 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'BM' and resid 30 through 36 removed outlier: 7.681A pdb=" N SERBM 30 " --> pdb=" O LYSBM 133 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYSBM 127 " --> pdb=" O VALBM 36 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'BN' and resid 33 through 36 removed outlier: 4.752A pdb=" N METBN 110 " --> pdb=" O CYSBN 100 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'BO' and resid 49 through 53 removed outlier: 3.711A pdb=" N VALBO 49 " --> pdb=" O VALBO 39 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILEBO 35 " --> pdb=" O THRBO 53 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'BP' and resid 42 through 45 removed outlier: 6.586A 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= 55, first strand: chain 'BP' and resid 49 through 52 removed outlier: 3.725A pdb=" N ALABP 49 " --> pdb=" O THRBP 60 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N SERBP 57 " --> pdb=" O THRBP 76 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'BR' and resid 11 through 15 removed outlier: 3.607A pdb=" N METBR 40 " --> pdb=" O VALBR 4 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEUBR 39 " --> pdb=" O GLYBR 50 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'BR' and resid 18 through 23 removed outlier: 4.157A pdb=" N GLNBR 18 " --> pdb=" O ILEBR 98 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASPBR 95 " --> pdb=" O VALBR 64 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYSBR 60 " --> pdb=" O THRBR 99 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLUBR 31 " --> pdb=" O VALBR 63 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'BR' and resid 57 through 60 Processing sheet with id= 59, first strand: chain 'BR' and resid 65 through 68 removed outlier: 3.787A pdb=" N GLYBR 67 " --> pdb=" O PHEBR 93 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'BR' and resid 71 through 78 removed outlier: 4.192A pdb=" N TYRBR 83 " --> pdb=" O ARGBR 78 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'BS' and resid 2 through 8 removed outlier: 4.815A pdb=" N THRBS 100 " --> pdb=" O GLYBS 79 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'BT' and resid 29 through 33 removed outlier: 4.523A pdb=" N LYSBT 66 " --> pdb=" O ARGBT 77 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ASPBT 79 " --> pdb=" O LYSBT 64 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LYSBT 64 " --> pdb=" O ASPBT 79 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYSBT 81 " --> pdb=" O VALBT 62 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VALBT 62 " --> pdb=" O LYSBT 81 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALABT 83 " --> pdb=" O THRBT 60 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THRBT 60 " --> pdb=" O ALABT 83 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VALBT 85 " --> pdb=" O VALBT 58 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VALBT 58 " --> pdb=" O VALBT 85 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'BU' and resid 40 through 45 removed outlier: 5.575A pdb=" N ASNBU 40 " --> pdb=" O ALABU 63 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'BU' and resid 82 through 86 removed outlier: 6.985A pdb=" N ARGBU 82 " --> pdb=" O LYSBU 97 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARGBU 94 " --> pdb=" O ILEBU 103 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILEBU 103 " --> pdb=" O ARGBU 94 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLUBU 101 " --> pdb=" O PHEBU 96 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'BV' and resid 69 through 73 removed outlier: 5.590A pdb=" N PHEBV 2 " --> pdb=" O VALBV 60 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALABV 39 " --> pdb=" O ARGBV 9 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILEBV 89 " --> pdb=" O PROBV 27 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HISBV 88 " --> pdb=" O GLNBV 78 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASPBV 76 " --> pdb=" O ASPBV 90 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'BW' and resid 45 through 48 removed outlier: 6.422A pdb=" N ILEBW 82 " --> pdb=" O GLYBW 48 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'BW' and resid 50 through 54 removed outlier: 6.951A pdb=" N ASNBW 50 " --> pdb=" O LYSBW 62 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THRBW 58 " --> pdb=" O GLYBW 54 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'BX' and resid 12 through 19 removed outlier: 3.631A pdb=" N SERBX 19 " --> pdb=" O ASNBX 23 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ASNBX 23 " --> pdb=" O SERBX 19 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'BX' and resid 34 through 41 removed outlier: 3.839A pdb=" N ARGBX 45 " --> pdb=" O VALBX 40 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'BZ' and resid 34 through 39 removed outlier: 4.583A pdb=" N HISBZ 34 " --> pdb=" O GLNBZ 9 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYSBZ 6 " --> pdb=" O GLUBZ 58 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N METBZ 54 " --> pdb=" O THRBZ 10 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'B0' and resid 29 through 32 removed outlier: 4.672A pdb=" N GLUB0 36 " --> pdb=" O ASPB0 31 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'B1' and resid 19 through 24 removed outlier: 6.489A pdb=" N HISB1 19 " --> pdb=" O SERB1 13 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILEB1 48 " --> pdb=" O SERB1 14 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLUB1 51 " --> pdb=" O LEUB1 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEUB1 34 " --> pdb=" O GLUB1 51 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'B3' and resid 22 through 25 removed outlier: 5.727A pdb=" N PHEB3 22 " --> pdb=" O VALB3 50 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'B4' and resid 1 through 5 removed outlier: 6.786A pdb=" N HISB4 33 " --> pdb=" O CYSB4 27 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N CYSB4 27 " --> pdb=" O HISB4 33 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILEB4 23 " --> pdb=" O GLNB4 37 " (cutoff:3.500A) 1681 hydrogen bonds defined for protein. 4971 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4062 hydrogen bonds 6332 hydrogen bond angles 0 basepair planarities 1618 basepair parallelities 2534 stacking parallelities Total time for adding SS restraints: 446.56 Time building geometry restraints manager: 63.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 11725 1.28 - 1.42: 65869 1.42 - 1.55: 71050 1.55 - 1.68: 9449 1.68 - 1.82: 269 Bond restraints: 158362 Sorted by residual: bond pdb=" C5 5MUD3 54 " pdb=" C6 5MUD3 54 " ideal model delta sigma weight residual 1.155 1.441 -0.286 2.00e-02 2.50e+03 2.05e+02 bond pdb=" C5 5MUD2 54 " pdb=" C6 5MUD2 54 " ideal model delta sigma weight residual 1.155 1.437 -0.282 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C5 5MUBA 747 " pdb=" C6 5MUBA 747 " ideal model delta sigma weight residual 1.155 1.436 -0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C5 5MUBA1939 " pdb=" C6 5MUBA1939 " ideal model delta sigma weight residual 1.155 1.432 -0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C4 5MUBA 747 " pdb=" C5 5MUBA 747 " ideal model delta sigma weight residual 1.802 1.601 0.201 2.00e-02 2.50e+03 1.01e+02 ... (remaining 158357 not shown) Histogram of bond angle deviations from ideal: 89.59 - 101.47: 2703 101.47 - 113.36: 119201 113.36 - 125.24: 98838 125.24 - 137.13: 16393 137.13 - 149.02: 6 Bond angle restraints: 237141 Sorted by residual: angle pdb=" C1' OMGD2 17A" pdb=" N9 OMGD2 17A" pdb=" C8 OMGD2 17A" ideal model delta sigma weight residual 142.82 101.35 41.47 3.00e+00 1.11e-01 1.91e+02 angle pdb=" N ALAAL 101 " pdb=" CA ALAAL 101 " pdb=" C ALAAL 101 " ideal model delta sigma weight residual 109.54 128.13 -18.59 1.37e+00 5.33e-01 1.84e+02 angle pdb=" C1' OMGD2 17A" pdb=" N9 OMGD2 17A" pdb=" C4 OMGD2 17A" ideal model delta sigma weight residual 108.29 148.20 -39.91 3.00e+00 1.11e-01 1.77e+02 angle pdb=" C GLUAP 48 " pdb=" CA GLUAP 48 " pdb=" CB GLUAP 48 " ideal model delta sigma weight residual 110.19 89.59 20.60 1.62e+00 3.81e-01 1.62e+02 angle pdb=" C1' OMGBA2251 " pdb=" N9 OMGBA2251 " pdb=" C8 OMGBA2251 " ideal model delta sigma weight residual 142.82 105.38 37.44 3.00e+00 1.11e-01 1.56e+02 ... (remaining 237136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 81106 35.96 - 71.93: 2956 71.93 - 107.89: 189 107.89 - 143.86: 16 143.86 - 179.82: 13 Dihedral angle restraints: 84280 sinusoidal: 68098 harmonic: 16182 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 -129.83 -50.17 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" C GLUAP 48 " pdb=" N GLUAP 48 " pdb=" CA GLUAP 48 " pdb=" CB GLUAP 48 " ideal model delta harmonic sigma weight residual -122.60 -98.10 -24.50 0 2.50e+00 1.60e-01 9.60e+01 dihedral pdb=" O4' CAA 489 " pdb=" C1' CAA 489 " pdb=" N1 CAA 489 " pdb=" C2 CAA 489 " ideal model delta sinusoidal sigma weight residual 200.00 28.99 171.01 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 84277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.093: 30202 1.093 - 2.186: 0 2.186 - 3.279: 0 3.279 - 4.372: 0 4.372 - 5.464: 4 Chirality restraints: 30206 Sorted by residual: chirality pdb=" C6 ERYBA3001 " pdb=" C32 ERYBA3001 " pdb=" C5 ERYBA3001 " pdb=" C7 ERYBA3001 " both_signs ideal model delta sigma weight residual False -2.75 2.71 -5.46 2.00e-01 2.50e+01 7.47e+02 chirality pdb=" C12 ERYBA3001 " pdb=" C11 ERYBA3001 " pdb=" C13 ERYBA3001 " pdb=" C35 ERYBA3001 " both_signs ideal model delta sigma weight residual False -2.75 2.60 -5.34 2.00e-01 2.50e+01 7.13e+02 chirality pdb=" C16 ERYBA3001 " pdb=" C15 ERYBA3001 " pdb=" C17 ERYBA3001 " pdb=" C19 ERYBA3001 " both_signs ideal model delta sigma weight residual False 2.68 -2.55 5.23 2.00e-01 2.50e+01 6.84e+02 ... (remaining 30203 not shown) Planarity restraints: 12541 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MGAA1516 " 0.085 2.00e-02 2.50e+03 6.29e-01 8.90e+03 pdb=" C4' 2MGAA1516 " 0.453 2.00e-02 2.50e+03 pdb=" O4' 2MGAA1516 " 0.670 2.00e-02 2.50e+03 pdb=" C3' 2MGAA1516 " -0.593 2.00e-02 2.50e+03 pdb=" O3' 2MGAA1516 " -0.687 2.00e-02 2.50e+03 pdb=" C2' 2MGAA1516 " -0.160 2.00e-02 2.50e+03 pdb=" O2' 2MGAA1516 " 1.017 2.00e-02 2.50e+03 pdb=" C1' 2MGAA1516 " 0.201 2.00e-02 2.50e+03 pdb=" N9 2MGAA1516 " -0.986 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MCAA1407 " -0.070 2.00e-02 2.50e+03 6.14e-01 8.49e+03 pdb=" C4' 5MCAA1407 " -0.446 2.00e-02 2.50e+03 pdb=" O4' 5MCAA1407 " -0.629 2.00e-02 2.50e+03 pdb=" C3' 5MCAA1407 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 5MCAA1407 " 0.682 2.00e-02 2.50e+03 pdb=" C2' 5MCAA1407 " 0.159 2.00e-02 2.50e+03 pdb=" O2' 5MCAA1407 " -1.013 2.00e-02 2.50e+03 pdb=" C1' 5MCAA1407 " -0.216 2.00e-02 2.50e+03 pdb=" N1 5MCAA1407 " 0.940 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MGAA1207 " -0.060 2.00e-02 2.50e+03 6.13e-01 8.46e+03 pdb=" C4' 2MGAA1207 " -0.449 2.00e-02 2.50e+03 pdb=" O4' 2MGAA1207 " -0.694 2.00e-02 2.50e+03 pdb=" C3' 2MGAA1207 " 0.605 2.00e-02 2.50e+03 pdb=" O3' 2MGAA1207 " 0.651 2.00e-02 2.50e+03 pdb=" C2' 2MGAA1207 " 0.191 2.00e-02 2.50e+03 pdb=" O2' 2MGAA1207 " -0.976 2.00e-02 2.50e+03 pdb=" C1' 2MGAA1207 " -0.204 2.00e-02 2.50e+03 pdb=" N9 2MGAA1207 " 0.935 2.00e-02 2.50e+03 ... (remaining 12538 not shown) Histogram of nonbonded interaction distances: 0.06 - 1.02: 3 1.02 - 1.99: 902 1.99 - 2.96: 65246 2.96 - 3.93: 447441 3.93 - 4.90: 825181 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1338773 Sorted by model distance: nonbonded pdb=" O HOHBA3225 " pdb=" O HOHBA3249 " model vdw 0.056 2.440 nonbonded pdb=" O HOHBA3250 " pdb=" O HOHBA3263 " model vdw 0.075 2.440 nonbonded pdb=" O HOHBA3343 " pdb=" O HOHBA3405 " model vdw 0.075 2.440 nonbonded pdb=" OP1 UAA1224 " pdb="MG MGAA1607 " model vdw 1.371 2.170 nonbonded pdb=" OP2 ABA2821 " pdb="MG MGBA3109 " model vdw 1.398 2.170 ... (remaining 1338768 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=1.00 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: 3.920 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 20.390 Check model and map are aligned: 1.630 Set scattering table: 1.010 Process input model: 719.750 Find NCS groups from input model: 3.390 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 762.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.015 0.286 158362 Z= 0.883 Angle : 1.620 41.468 237141 Z= 0.641 Chirality : 0.079 5.464 30206 Planarity : 0.024 0.629 12541 Dihedral : 14.771 179.819 73837 Min Nonbonded Distance : 0.056 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.45 % Favored : 95.42 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.09), residues: 5572 helix: -3.40 (0.08), residues: 1756 sheet: -1.95 (0.13), residues: 1157 loop : -2.06 (0.10), residues: 2659 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1521 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1492 time to evaluate : 6.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 11 residues processed: 1509 average time/residue: 2.2952 time to fit residues: 4913.2145 Evaluate side-chains 1035 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1024 time to evaluate : 6.426 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 6 average time/residue: 1.3978 time to fit residues: 20.8055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 854 optimal weight: 4.9990 chunk 767 optimal weight: 20.0000 chunk 425 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 517 optimal weight: 0.8980 chunk 409 optimal weight: 8.9990 chunk 793 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 482 optimal weight: 0.9980 chunk 590 optimal weight: 0.9980 chunk 919 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 36 ASN AB 120 GLN AB 170 HIS AB 177 ASN AD 71 GLN AD 89 ASN AD 116 GLN AD 126 ASN AD 198 HIS ** AE 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 97 GLN AF 3 HIS AH 16 ASN ** AH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 21 ASN AH 67 GLN AI 32 GLN AI 50 GLN AI 110 GLN AL 5 ASN AL 77 HIS AM 8 ASN AO 62 GLN AS 14 HIS AT 21 ASN BC 200 HIS BC 239 ASN BC 260 ASN BD 49 GLN BE 115 GLN BG 22 GLN BG 38 ASN ** BG 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 133 GLN BI 20 ASN BJ 128 ASN BK 88 ASN BN 18 GLN BN 62 ASN BP 66 ASN BQ 56 GLN BU 46 GLN BV 12 GLN BY 20 ASN BY 27 ASN B0 42 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 158362 Z= 0.161 Angle : 0.657 27.062 237141 Z= 0.357 Chirality : 0.039 2.269 30206 Planarity : 0.007 0.124 12541 Dihedral : 13.693 176.039 62665 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.09 % Favored : 96.84 % Rotamer Outliers : 3.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.10), residues: 5572 helix: -1.45 (0.11), residues: 1786 sheet: -1.27 (0.15), residues: 1100 loop : -1.45 (0.11), residues: 2686 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1132 time to evaluate : 6.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 173 outliers final: 55 residues processed: 1207 average time/residue: 2.2208 time to fit residues: 3878.3160 Evaluate side-chains 1023 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 968 time to evaluate : 6.438 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 30 residues processed: 32 average time/residue: 1.1404 time to fit residues: 72.5687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 510 optimal weight: 10.0000 chunk 285 optimal weight: 10.0000 chunk 764 optimal weight: 20.0000 chunk 625 optimal weight: 8.9990 chunk 253 optimal weight: 6.9990 chunk 920 optimal weight: 10.0000 chunk 994 optimal weight: 7.9990 chunk 819 optimal weight: 9.9990 chunk 912 optimal weight: 3.9990 chunk 313 optimal weight: 8.9990 chunk 738 optimal weight: 0.3980 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 109 GLN AB 170 HIS AB 177 ASN AB 190 ASN AC 123 GLN AD 71 GLN AD 89 ASN AF 37 HIS AF 46 GLN AF 52 ASN ** AH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 21 ASN AK 119 ASN AL 77 HIS AN 3 GLN AN 62 ASN AT 84 ASN BC 239 ASN BE 136 GLN ** BF 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 45 HIS BG 104 ASN ** BG 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 73 ASN BI 20 ASN BJ 128 ASN BO 19 GLN ** BO 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BP 56 HIS BQ 37 GLN BQ 56 GLN BT 28 ASN BU 40 ASN BU 46 GLN BW 50 ASN BY 27 ASN BZ 20 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 158362 Z= 0.323 Angle : 0.713 27.916 237141 Z= 0.382 Chirality : 0.043 2.145 30206 Planarity : 0.007 0.138 12541 Dihedral : 13.804 178.445 62665 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.20 % Favored : 95.73 % Rotamer Outliers : 5.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.11), residues: 5572 helix: -0.45 (0.12), residues: 1765 sheet: -1.07 (0.15), residues: 1064 loop : -1.31 (0.11), residues: 2743 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1329 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1067 time to evaluate : 6.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 262 outliers final: 103 residues processed: 1193 average time/residue: 2.2174 time to fit residues: 3833.3875 Evaluate side-chains 1078 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 975 time to evaluate : 6.468 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 57 residues processed: 48 average time/residue: 1.1388 time to fit residues: 106.2036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 909 optimal weight: 0.8980 chunk 692 optimal weight: 7.9990 chunk 477 optimal weight: 8.9990 chunk 101 optimal weight: 30.0000 chunk 439 optimal weight: 7.9990 chunk 618 optimal weight: 10.0000 chunk 923 optimal weight: 9.9990 chunk 978 optimal weight: 1.9990 chunk 482 optimal weight: 10.0000 chunk 875 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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** AB 170 HIS AC 176 HIS ** AD 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 89 ASN ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 37 HIS ** AH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 21 ASN AJ 56 HIS AK 119 ASN AL 5 ASN AL 77 HIS AN 62 ASN ** BF 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 73 ASN BI 20 ASN BI 33 ASN BJ 128 ASN BQ 20 GLN BT 28 ASN BU 40 ASN BY 38 GLN B3 28 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 158362 Z= 0.286 Angle : 0.671 27.829 237141 Z= 0.362 Chirality : 0.041 2.126 30206 Planarity : 0.007 0.133 12541 Dihedral : 13.670 179.712 62665 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.89 % Favored : 96.03 % Rotamer Outliers : 5.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.11), residues: 5572 helix: 0.03 (0.13), residues: 1765 sheet: -0.91 (0.15), residues: 1098 loop : -1.21 (0.11), residues: 2709 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1286 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1033 time to evaluate : 6.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 253 outliers final: 134 residues processed: 1169 average time/residue: 2.2392 time to fit residues: 3811.9942 Evaluate side-chains 1111 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 977 time to evaluate : 6.635 Switching outliers to nearest non-outliers outliers start: 134 outliers final: 77 residues processed: 60 average time/residue: 1.3273 time to fit residues: 145.2704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 814 optimal weight: 4.9990 chunk 555 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 728 optimal weight: 5.9990 chunk 403 optimal weight: 10.0000 chunk 834 optimal weight: 0.4980 chunk 676 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 499 optimal weight: 10.0000 chunk 878 optimal weight: 9.9990 chunk 246 optimal weight: 5.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- 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** AB 170 HIS AC 32 ASN AD 89 ASN AD 116 GLN AD 198 HIS ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 37 HIS AH 21 ASN AJ 56 HIS AK 119 ASN AL 5 ASN AL 77 HIS AQ 51 ASN AS 14 HIS ** AS 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 61 GLN BC 115 GLN BE 115 GLN ** BF 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 28 ASN BH 73 ASN BI 20 ASN BJ 128 ASN ** BO 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BT 28 ASN ** BU 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BU 46 GLN BY 38 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 158362 Z= 0.316 Angle : 0.694 27.927 237141 Z= 0.372 Chirality : 0.042 2.106 30206 Planarity : 0.007 0.137 12541 Dihedral : 13.703 179.186 62665 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.33 % Favored : 95.60 % Rotamer Outliers : 5.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.11), residues: 5572 helix: 0.20 (0.13), residues: 1776 sheet: -0.79 (0.15), residues: 1079 loop : -1.18 (0.11), residues: 2717 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 992 time to evaluate : 6.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 246 outliers final: 147 residues processed: 1123 average time/residue: 2.2055 time to fit residues: 3594.0810 Evaluate side-chains 1101 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 954 time to evaluate : 6.619 Switching outliers to nearest non-outliers outliers start: 147 outliers final: 86 residues processed: 63 average time/residue: 1.4389 time to fit residues: 161.0089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 329 optimal weight: 10.0000 chunk 880 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 574 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 979 optimal weight: 8.9990 chunk 812 optimal weight: 6.9990 chunk 453 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 323 optimal weight: 7.9990 chunk 514 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** AB 170 HIS AD 89 ASN AD 116 GLN ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 37 HIS AH 21 ASN AI 110 GLN AJ 56 HIS AK 119 ASN AL 5 ASN AL 77 HIS AO 28 GLN AQ 9 GLN AQ 51 ASN AS 14 HIS BC 115 GLN BC 117 GLN BF 127 ASN BH 73 ASN ** BH 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BI 20 ASN BJ 128 ASN BN 62 ASN BT 28 ASN ** BU 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 158362 Z= 0.351 Angle : 0.712 28.092 237141 Z= 0.380 Chirality : 0.044 2.120 30206 Planarity : 0.007 0.138 12541 Dihedral : 13.765 179.175 62665 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.33 % Rotamer Outliers : 5.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.11), residues: 5572 helix: 0.23 (0.13), residues: 1776 sheet: -0.84 (0.15), residues: 1099 loop : -1.20 (0.11), residues: 2697 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1224 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 974 time to evaluate : 6.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 250 outliers final: 146 residues processed: 1110 average time/residue: 2.2053 time to fit residues: 3554.8704 Evaluate side-chains 1095 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 949 time to evaluate : 6.497 Switching outliers to nearest non-outliers outliers start: 146 outliers final: 86 residues processed: 61 average time/residue: 1.3184 time to fit residues: 147.4325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 944 optimal weight: 0.0040 chunk 110 optimal weight: 20.0000 chunk 557 optimal weight: 10.0000 chunk 715 optimal weight: 5.9990 chunk 554 optimal weight: 30.0000 chunk 824 optimal weight: 1.9990 chunk 546 optimal weight: 8.9990 chunk 975 optimal weight: 1.9990 chunk 610 optimal weight: 10.0000 chunk 594 optimal weight: 50.0000 chunk 450 optimal weight: 7.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- 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** AB 170 HIS AD 89 ASN AD 116 GLN ** AE 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 86 GLN AG 97 ASN AH 21 ASN AK 119 ASN AL 5 ASN AL 77 HIS AQ 45 HIS AQ 51 ASN AS 14 HIS AT 61 GLN BC 115 GLN BE 136 GLN BH 28 ASN BH 73 ASN ** BH 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BI 20 ASN BJ 128 ASN BN 62 ASN BO 19 GLN BQ 56 GLN BT 28 ASN ** BU 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 24 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 158362 Z= 0.223 Angle : 0.653 27.627 237141 Z= 0.354 Chirality : 0.040 2.119 30206 Planarity : 0.006 0.130 12541 Dihedral : 13.614 177.609 62665 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.89 % Favored : 96.03 % Rotamer Outliers : 4.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.11), residues: 5572 helix: 0.44 (0.13), residues: 1794 sheet: -0.69 (0.15), residues: 1072 loop : -1.09 (0.12), residues: 2706 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1181 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 987 time to evaluate : 6.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 194 outliers final: 121 residues processed: 1104 average time/residue: 2.1821 time to fit residues: 3522.1316 Evaluate side-chains 1076 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 955 time to evaluate : 6.471 Switching outliers to nearest non-outliers outliers start: 121 outliers final: 83 residues processed: 39 average time/residue: 1.1969 time to fit residues: 90.0216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 603 optimal weight: 10.0000 chunk 389 optimal weight: 10.0000 chunk 582 optimal weight: 10.0000 chunk 293 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 620 optimal weight: 10.0000 chunk 664 optimal weight: 10.0000 chunk 482 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 766 optimal weight: 8.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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** AB 170 HIS ** AB 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 89 ASN AD 116 GLN AD 198 HIS ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 37 HIS AG 86 GLN AH 21 ASN AJ 56 HIS AK 119 ASN AL 5 ASN AL 77 HIS AM 8 ASN AQ 45 HIS AQ 51 ASN ** AS 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 61 GLN BC 115 GLN BH 28 ASN BH 73 ASN BI 20 ASN BM 22 GLN BN 62 ASN BO 19 GLN ** BO 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BT 28 ASN ** BU 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 34 HIS ** BY 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.072 158362 Z= 0.445 Angle : 0.771 28.435 237141 Z= 0.405 Chirality : 0.047 2.119 30206 Planarity : 0.007 0.142 12541 Dihedral : 13.897 177.222 62665 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.08 % Favored : 94.85 % Rotamer Outliers : 4.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.11), residues: 5572 helix: 0.27 (0.13), residues: 1779 sheet: -0.83 (0.15), residues: 1075 loop : -1.18 (0.11), residues: 2718 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 942 time to evaluate : 6.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 230 outliers final: 166 residues processed: 1077 average time/residue: 2.2231 time to fit residues: 3493.6703 Evaluate side-chains 1103 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 937 time to evaluate : 6.488 Switching outliers to nearest non-outliers outliers start: 166 outliers final: 102 residues processed: 66 average time/residue: 1.3991 time to fit residues: 165.1395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 887 optimal weight: 3.9990 chunk 934 optimal weight: 7.9990 chunk 852 optimal weight: 4.9990 chunk 908 optimal weight: 0.9990 chunk 547 optimal weight: 5.9990 chunk 395 optimal weight: 10.0000 chunk 713 optimal weight: 10.0000 chunk 278 optimal weight: 9.9990 chunk 821 optimal weight: 2.9990 chunk 859 optimal weight: 3.9990 chunk 905 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** AB 170 HIS ** AB 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 100 GLN AD 89 ASN AD 116 GLN AD 198 HIS ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 37 HIS AG 97 ASN AH 21 ASN AK 119 ASN AL 5 ASN AL 77 HIS ** AM 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 51 ASN AT 61 GLN BC 115 GLN BG 48 ASN BH 73 ASN BI 20 ASN BJ 128 ASN BN 62 ASN BO 19 GLN BT 28 ASN ** BU 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 158362 Z= 0.216 Angle : 0.654 27.579 237141 Z= 0.354 Chirality : 0.040 2.119 30206 Planarity : 0.007 0.130 12541 Dihedral : 13.609 177.657 62665 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.86 % Favored : 96.07 % Rotamer Outliers : 3.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.11), residues: 5572 helix: 0.53 (0.13), residues: 1796 sheet: -0.69 (0.15), residues: 1051 loop : -1.09 (0.12), residues: 2725 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 974 time to evaluate : 6.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 157 outliers final: 115 residues processed: 1091 average time/residue: 2.1594 time to fit residues: 3447.1578 Evaluate side-chains 1065 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 950 time to evaluate : 6.560 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 94 residues processed: 25 average time/residue: 1.3619 time to fit residues: 67.0164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 596 optimal weight: 50.0000 chunk 961 optimal weight: 0.8980 chunk 586 optimal weight: 10.0000 chunk 455 optimal weight: 10.0000 chunk 668 optimal weight: 10.0000 chunk 1008 optimal weight: 30.0000 chunk 927 optimal weight: 4.9990 chunk 802 optimal weight: 0.0010 chunk 83 optimal weight: 20.0000 chunk 620 optimal weight: 10.0000 chunk 492 optimal weight: 20.0000 overall best weight: 5.1796 ------------------------------------------------------------------------------- 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** AB 170 HIS ** AB 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 89 ASN AD 116 GLN AD 198 HIS ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AF 37 HIS AH 21 ASN AK 119 ASN AL 5 ASN AL 77 HIS AQ 51 ASN AT 61 GLN BC 115 GLN ** BF 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 28 ASN BH 73 ASN BI 20 ASN BN 62 ASN BO 19 GLN BQ 56 GLN BT 28 ASN BT 70 HIS ** BU 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.097 158362 Z= 0.300 Angle : 0.690 27.938 237141 Z= 0.370 Chirality : 0.042 2.121 30206 Planarity : 0.007 0.136 12541 Dihedral : 13.656 177.567 62665 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.68 % Favored : 95.24 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.11), residues: 5572 helix: 0.55 (0.13), residues: 1783 sheet: -0.72 (0.15), residues: 1075 loop : -1.09 (0.12), residues: 2714 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11144 Ramachandran restraints generated. 5572 Oldfield, 0 Emsley, 5572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 940 time to evaluate : 6.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 118 residues processed: 1046 average time/residue: 2.2404 time to fit residues: 3429.2609 Evaluate side-chains 1049 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 931 time to evaluate : 6.645 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 93 residues processed: 27 average time/residue: 1.6697 time to fit residues: 81.1709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1012 random chunks: chunk 637 optimal weight: 10.0000 chunk 855 optimal weight: 2.9990 chunk 245 optimal weight: 20.0000 chunk 740 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 223 optimal weight: 2.9990 chunk 804 optimal weight: 0.0370 chunk 336 optimal weight: 10.0000 chunk 825 optimal weight: 2.9990 chunk 101 optimal weight: 30.0000 chunk 148 optimal weight: 10.0000 overall best weight: 2.6066 ------------------------------------------------------------------------------- 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** AB 170 HIS ** AB 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 89 ASN AD 116 GLN ** AE 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 97 ASN AH 21 ASN AK 119 ASN AL 5 ASN AL 77 HIS ** AM 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 51 ASN AT 61 GLN BC 115 GLN ** BF 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 73 ASN BI 20 ASN BM 3 GLN BN 62 ASN BO 19 GLN BT 28 ASN ** BU 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.117864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.079548 restraints weight = 245336.610| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 0.88 r_work: 0.2800 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.114 158362 Z= 0.178 Angle : 0.660 34.723 237141 Z= 0.357 Chirality : 0.040 2.131 30206 Planarity : 0.006 0.127 12541 Dihedral : 13.616 177.463 62665 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.95 % Favored : 95.98 % Rotamer Outliers : 2.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.11), residues: 5572 helix: 0.64 (0.13), residues: 1783 sheet: -0.66 (0.15), residues: 1060 loop : -1.02 (0.12), residues: 2729 =============================================================================== Job complete usr+sys time: 49740.56 seconds wall clock time: 862 minutes 33.62 seconds (51753.62 seconds total)