Starting phenix.real_space_refine on Sat Mar 23 08:35:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jte_8175/03_2024/5jte_8175_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jte_8175/03_2024/5jte_8175.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jte_8175/03_2024/5jte_8175_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jte_8175/03_2024/5jte_8175_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jte_8175/03_2024/5jte_8175_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jte_8175/03_2024/5jte_8175.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jte_8175/03_2024/5jte_8175.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jte_8175/03_2024/5jte_8175_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5jte_8175/03_2024/5jte_8175_neut_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 5 Type Number sf(0) Gaussians P 4784 5.49 5 S 149 5.16 5 C 73425 2.51 5 N 27311 2.21 5 O 41091 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AB PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC ARG 131": "NH1" <-> "NH2" Residue "AE PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI ARG 124": "NH1" <-> "NH2" Residue "AL ARG 56": "NH1" <-> "NH2" Residue "AP ARG 28": "NH1" <-> "NH2" Residue "AP PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AR TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC ARG 52": "NH1" <-> "NH2" Residue "BC ARG 63": "NH1" <-> "NH2" Residue "BC ARG 80": "NH1" <-> "NH2" Residue "BC ARG 133": "NH1" <-> "NH2" Residue "BC TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC ARG 167": "NH1" <-> "NH2" Residue "BC ARG 177": "NH1" <-> "NH2" Residue "BC ARG 182": "NH1" <-> "NH2" Residue "BC ARG 189": "NH1" <-> "NH2" Residue "BC ARG 203": "NH1" <-> "NH2" Residue "BC ARG 212": "NH1" <-> "NH2" Residue "BD ARG 13": "NH1" <-> "NH2" Residue "BD ARG 33": "NH1" <-> "NH2" Residue "BD TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD ARG 59": "NH1" <-> "NH2" 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 61": "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 ARG 163": "NH1" <-> "NH2" Residue "BG ARG 170": "NH1" <-> "NH2" Residue "BH ARG 27": "NH1" <-> "NH2" Residue "BI TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BI PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BL ARG 78": "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 TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP ARG 21": "NH1" <-> "NH2" Residue "BP ARG 39": "NH1" <-> "NH2" Residue "BP PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BR PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BR ARG 21": "NH1" <-> "NH2" 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 84": "NH1" <-> "NH2" Residue "BS ARG 88": "NH1" <-> "NH2" Residue "BS ARG 95": "NH1" <-> "NH2" Residue "BS ARG 110": "NH1" <-> "NH2" Residue "BT ARG 73": "NH1" <-> "NH2" Residue "BU ARG 6": "NH1" <-> "NH2" Residue "BU ARG 7": "NH1" <-> "NH2" Residue "BU ARG 82": "NH1" <-> "NH2" Residue "BU ARG 86": "NH1" <-> "NH2" Residue "BU ARG 94": "NH1" <-> "NH2" Residue "BV TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BW PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "BX TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "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 3": "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" Residue "B5 ARG -3": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 146760 Number of models: 1 Model: "" Number of chains: 59 Chain: "AA" Number of atoms: 33015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33015 Classifications: {'RNA': 1539} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 87, 'rna3p_pur': 756, 'rna3p_pyr': 578} Link IDs: {'rna2p': 205, 'rna3p': 1333} Chain breaks: 1 Chain: "AB" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} 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: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "AF" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} 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: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} 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: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} 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: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "AO" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 710 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 87} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 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: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "AT" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "AU" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "AV" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 218 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "AW" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1593 Classifications: {'RNA': 74} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p': 6, 'rna3p_pur': 30, 'rna3p_pyr': 27} Link IDs: {'rna2p': 10, 'rna3p': 63} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 3 Chain: "AX" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1656 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p': 7, 'rna3p_pur': 29, 'rna3p_pyr': 31} Link IDs: {'rna2p': 9, 'rna3p': 67} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 2 Chain: "AY" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1525 Classifications: {'RNA': 71} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p': 5, 'rna3p_pur': 32, 'rna3p_pyr': 25} Link IDs: {'rna2p': 9, 'rna3p': 61} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 3 Chain: "BA" Number of atoms: 62195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62195 Classifications: {'RNA': 2897} Modifications used: {'rna2p_pur': 278, 'rna2p_pyr': 148, 'rna3p_pur': 1394, 'rna3p_pyr': 1077} Link IDs: {'rna2p': 426, 'rna3p': 2470} Chain breaks: 1 Chain: "BB" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} 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: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} 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: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 359 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "BI" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} 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: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "BL" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "BM" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "BN" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "BO" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} 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: {'PTRANS': 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: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} 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: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 569 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} 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: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "B2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "B3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "B4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "B5" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "AW" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Chain: "BA" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ERY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 57.32, per 1000 atoms: 0.39 Number of scatterers: 146760 At special positions: 0 Unit cell: (265.92, 280.324, 218.276, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 149 16.00 P 4784 15.00 O 41091 8.00 N 27311 7.00 C 73425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 62.06 Conformation dependent library (CDL) restraints added in 7.9 seconds 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10328 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 170 helices and 64 sheets defined 37.7% alpha, 16.8% beta 1626 base pairs and 2803 stacking pairs defined. Time for finding SS restraints: 75.83 Creating SS restraints... Processing helix chain 'AB' and resid 24 through 32 removed outlier: 3.630A pdb=" N LYSAB 28 " --> pdb=" O ASNAB 24 " (cutoff:3.500A) Proline residue: AB 29 - end of helix removed outlier: 4.909A pdb=" N PHEAB 32 " --> pdb=" O LYSAB 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'AB' and resid 24 through 32' Processing helix chain 'AB' and resid 43 through 64 Proline residue: AB 48 - end of helix removed outlier: 4.437A pdb=" N GLUAB 56 " --> pdb=" O GLUAB 52 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEUAB 57 " --> pdb=" O ALAAB 53 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYSAB 59 " --> pdb=" O ALAAB 55 " (cutoff:3.500A) Processing helix chain 'AB' and resid 76 through 87 removed outlier: 4.201A pdb=" N LYSAB 81 " --> pdb=" O SERAB 77 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASPAB 82 " --> pdb=" O GLUAB 78 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ALAAB 83 " --> pdb=" O ALAAB 79 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ALAAB 84 " --> pdb=" O VALAB 80 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEUAB 85 " --> pdb=" O LYSAB 81 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SERAB 86 " --> pdb=" O ASPAB 82 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N CYSAB 87 " --> pdb=" O ALAAB 83 " (cutoff:3.500A) Processing helix chain 'AB' and resid 105 through 123 removed outlier: 4.563A pdb=" N GLNAB 109 " --> pdb=" O LYSAB 105 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SERAB 110 " --> pdb=" O THRAB 106 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THRAB 119 " --> pdb=" O LYSAB 115 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLNAB 120 " --> pdb=" O ASPAB 116 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLNAB 122 " --> pdb=" O GLUAB 118 " (cutoff:3.500A) Processing helix chain 'AB' and resid 130 through 148 removed outlier: 3.617A pdb=" N ALAAB 134 " --> pdb=" O THRAB 130 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARGAB 137 " --> pdb=" O GLUAB 133 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLUAB 140 " --> pdb=" O METAB 136 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEUAB 141 " --> pdb=" O ARGAB 137 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLUAB 142 " --> pdb=" O THRAB 138 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYSAB 143 " --> pdb=" O ARGAB 139 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SERAB 147 " --> pdb=" O LYSAB 143 " (cutoff:3.500A) Processing helix chain 'AB' and resid 150 through 155 removed outlier: 3.514A pdb=" N METAB 154 " --> pdb=" O GLYAB 150 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLYAB 155 " --> pdb=" O ILEAB 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'AB' and resid 150 through 155' Processing helix chain 'AB' and resid 169 through 180 removed outlier: 3.530A pdb=" N GLUAB 175 " --> pdb=" O ILEAB 171 " (cutoff:3.500A) Processing helix chain 'AB' and resid 206 through 223 removed outlier: 3.515A pdb=" N ARGAB 222 " --> pdb=" O ALAAB 218 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLUAB 223 " --> pdb=" O ALAAB 219 " (cutoff:3.500A) Processing helix chain 'AC' and resid 6 through 13 removed outlier: 3.666A pdb=" N ILEAC 10 " --> pdb=" O HISAC 6 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARGAC 11 " --> pdb=" O PROAC 7 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEUAC 12 " --> pdb=" O ASNAC 8 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLYAC 13 " --> pdb=" O GLYAC 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 6 through 13' Processing helix chain 'AC' and resid 28 through 48 Processing helix chain 'AC' and resid 72 through 78 removed outlier: 3.752A pdb=" N VALAC 76 " --> pdb=" O ARGAC 72 " (cutoff:3.500A) Processing helix chain 'AC' and resid 81 through 96 removed outlier: 4.405A pdb=" N LYSAC 86 " --> pdb=" O GLUAC 82 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEUAC 87 " --> pdb=" O ASPAC 83 " (cutoff:3.500A) Processing helix chain 'AC' and resid 108 through 113 removed outlier: 4.356A pdb=" N ASPAC 112 " --> pdb=" O LYSAC 108 " (cutoff:3.500A) removed outlier: 5.531A 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: 3.709A pdb=" N GLUAC 125 " --> pdb=" O THRAC 121 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARGAC 126 " --> pdb=" O SERAC 122 " (cutoff:3.500A) Processing helix chain 'AC' and resid 129 through 145 removed outlier: 4.173A pdb=" N ALAAC 141 " --> pdb=" O ALAAC 137 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEUAC 144 " --> pdb=" O ASNAC 140 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLYAC 145 " --> pdb=" O ALAAC 141 " (cutoff:3.500A) Processing helix chain 'AD' and resid 7 through 16 removed outlier: 4.912A pdb=" N LEUAD 11 " --> pdb=" O PROAD 7 " (cutoff:3.500A) Processing helix chain 'AD' and resid 49 through 66 removed outlier: 3.940A pdb=" N LYSAD 58 " --> pdb=" O GLNAD 54 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYRAD 65 " --> pdb=" O VALAD 61 " (cutoff:3.500A) Processing helix chain 'AD' and resid 68 through 83 removed outlier: 5.448A pdb=" N LYSAD 83 " --> pdb=" O ALAAD 79 " (cutoff:3.500A) Processing helix chain 'AD' and resid 85 through 97 removed outlier: 3.765A pdb=" N LEUAD 91 " --> pdb=" O GLYAD 87 " (cutoff:3.500A) Processing helix chain 'AD' and resid 98 through 106 Processing helix chain 'AD' and resid 110 through 121 removed outlier: 3.595A pdb=" N LYSAD 121 " --> pdb=" O LEUAD 117 " (cutoff:3.500A) Processing helix chain 'AD' and resid 152 through 166 removed outlier: 5.299A pdb=" N LYSAD 156 " --> pdb=" O GLNAD 152 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLNAD 164 " --> pdb=" O GLUAD 160 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLUAD 166 " --> pdb=" O ALAAD 162 " (cutoff:3.500A) Processing helix chain 'AD' and resid 187 through 192 removed outlier: 3.982A pdb=" N LEUAD 191 " --> pdb=" O GLUAD 187 " (cutoff:3.500A) removed outlier: 5.114A 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: 4.346A pdb=" N ILEAD 200 " --> pdb=" O ASNAD 196 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VALAD 201 " --> pdb=" O GLUAD 197 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYRAD 204 " --> pdb=" O ILEAD 200 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SERAD 205 " --> pdb=" O VALAD 201 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYSAD 206 " --> pdb=" O GLUAD 202 " (cutoff:3.500A) Processing helix chain 'AE' and resid 55 through 71 removed outlier: 3.891A pdb=" N ARGAE 69 " --> pdb=" O GLUAE 65 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASNAE 70 " --> pdb=" O LYSAE 66 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N METAE 71 " --> pdb=" O ALAAE 67 " (cutoff:3.500A) Processing helix chain 'AE' and resid 109 through 119 removed outlier: 6.211A pdb=" N ALAAE 113 " --> pdb=" O GLYAE 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLYAE 119 " --> pdb=" O LEUAE 115 " (cutoff:3.500A) Processing helix chain 'AE' and resid 132 through 154 removed outlier: 4.930A pdb=" N ARGAE 138 " --> pdb=" O ILEAE 134 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILEAE 141 " --> pdb=" O VALAE 137 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLYAE 143 " --> pdb=" O ALAAE 139 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLUAE 145 " --> pdb=" O ILEAE 141 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ASNAE 146 " --> pdb=" O ASPAE 142 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N METAE 147 " --> pdb=" O GLYAE 143 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ASNAE 148 " --> pdb=" O LEUAE 144 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N SERAE 149 " --> pdb=" O GLUAE 145 " (cutoff:3.500A) Proline residue: AE 150 - end of helix removed outlier: 3.828A pdb=" N ALAAE 154 " --> pdb=" O PROAE 150 " (cutoff:3.500A) Processing helix chain 'AF' and resid 16 through 33 removed outlier: 4.700A pdb=" N GLYAF 20 " --> pdb=" O GLUAF 16 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLUAF 23 " --> pdb=" O PROAF 19 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARGAF 24 " --> pdb=" O GLYAF 20 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALAAF 28 " --> pdb=" O ARGAF 24 " (cutoff:3.500A) Processing helix chain 'AF' and resid 67 through 82 removed outlier: 3.871A pdb=" N GLUAF 73 " --> pdb=" O GLUAF 69 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASPAF 82 " --> pdb=" O PHEAF 78 " (cutoff:3.500A) Processing helix chain 'AG' and resid 20 through 31 removed outlier: 3.698A pdb=" N ALAAG 24 " --> pdb=" O SERAG 20 " (cutoff:3.500A) Processing helix chain 'AG' and resid 35 through 54 removed outlier: 3.557A pdb=" N ILEAG 42 " --> pdb=" O THRAG 38 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SERAG 45 " --> pdb=" O SERAG 41 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEUAG 50 " --> pdb=" O ALAAG 46 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLNAG 52 " --> pdb=" O GLUAG 48 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARGAG 53 " --> pdb=" O THRAG 49 " (cutoff:3.500A) Processing helix chain 'AG' and resid 57 through 70 removed outlier: 4.753A pdb=" N PHEAG 62 " --> pdb=" O GLUAG 58 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLUAG 63 " --> pdb=" O LEUAG 59 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALAAG 65 " --> pdb=" O ALAAG 61 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASNAG 68 " --> pdb=" O VALAG 64 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VALAG 69 " --> pdb=" O ALAAG 65 " (cutoff:3.500A) Processing helix chain 'AG' and resid 92 through 112 removed outlier: 3.868A pdb=" N ASNAG 97 " --> pdb=" O PROAG 93 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALAAG 98 " --> pdb=" O VALAG 94 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALAAG 100 " --> pdb=" O ARGAG 96 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLYAG 112 " --> pdb=" O ALAAG 108 " (cutoff:3.500A) Processing helix chain 'AG' and resid 115 through 130 removed outlier: 4.351A pdb=" N GLUAG 129 " --> pdb=" O SERAG 125 " (cutoff:3.500A) Processing helix chain 'AG' and resid 132 through 149 removed outlier: 3.619A pdb=" N LYSAG 136 " --> pdb=" O GLYAG 132 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASNAG 148 " --> pdb=" O METAG 144 " (cutoff:3.500A) Processing helix chain 'AH' and resid 5 through 21 removed outlier: 3.509A pdb=" N ASNAH 21 " --> pdb=" O GLYAH 17 " (cutoff:3.500A) Processing helix chain 'AH' and resid 30 through 44 removed outlier: 4.029A pdb=" N GLUAH 43 " --> pdb=" O VALAH 39 " (cutoff:3.500A) Processing helix chain 'AH' and resid 112 through 120 Processing helix chain 'AI' and resid 34 through 39 removed outlier: 3.691A pdb=" N TYRAI 38 " --> pdb=" O SERAI 34 " (cutoff:3.500A) Processing helix chain 'AI' and resid 46 through 53 removed outlier: 3.538A pdb=" N GLNAI 50 " --> pdb=" O METAI 46 " (cutoff:3.500A) Proline residue: AI 51 - end of helix No H-bonds generated for 'chain 'AI' and resid 46 through 53' Processing helix chain 'AI' and resid 71 through 88 removed outlier: 4.817A pdb=" N METAI 88 " --> pdb=" O THRAI 84 " (cutoff:3.500A) Processing helix chain 'AI' and resid 92 through 102 removed outlier: 4.072A pdb=" N SERAI 96 " --> pdb=" O GLUAI 92 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLUAI 97 " --> pdb=" O SERAI 93 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYSAI 100 " --> pdb=" O SERAI 96 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALAAI 101 " --> pdb=" O GLUAI 97 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 14 through 33 removed outlier: 3.657A pdb=" N ASPAJ 19 " --> pdb=" O HISAJ 15 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLNAJ 20 " --> pdb=" O ARGAJ 16 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLUAJ 24 " --> pdb=" O GLNAJ 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILEAJ 25 " --> pdb=" O ALAAJ 21 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 80 through 89 removed outlier: 3.560A pdb=" N ALAAJ 86 " --> pdb=" O LYSAJ 82 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N METAJ 88 " --> pdb=" O VALAJ 84 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ARGAJ 89 " --> pdb=" O ASPAJ 85 " (cutoff:3.500A) Processing helix chain 'AK' and resid 46 through 51 removed outlier: 3.960A pdb=" N GLYAK 51 " --> pdb=" O ALAAK 47 " (cutoff:3.500A) Processing helix chain 'AK' and resid 54 through 59 removed outlier: 4.628A pdb=" N SERAK 58 " --> pdb=" O GLYAK 54 " (cutoff:3.500A) removed outlier: 4.698A 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 73 removed outlier: 5.075A pdb=" N ALAAK 73 " --> pdb=" O ARGAK 69 " (cutoff:3.500A) Processing helix chain 'AK' and resid 93 through 104 removed outlier: 3.990A pdb=" N ALAAK 99 " --> pdb=" O SERAK 95 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEUAK 100 " --> pdb=" O THRAK 96 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASNAK 101 " --> pdb=" O ILEAK 97 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALAAK 102 " --> pdb=" O ARGAK 98 " (cutoff:3.500A) Processing helix chain 'AL' and resid 3 through 10 removed outlier: 3.863A pdb=" N LEUAL 7 " --> pdb=" O THRAL 3 " (cutoff:3.500A) Processing helix chain 'AL' and resid 113 through 118 removed outlier: 4.336A pdb=" N TYRAL 117 " --> pdb=" O ALAAL 113 " (cutoff:3.500A) Processing helix chain 'AM' and resid 14 through 22 removed outlier: 4.246A pdb=" N THRAM 20 " --> pdb=" O VALAM 16 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILEAM 22 " --> pdb=" O ALAAM 18 " (cutoff:3.500A) Processing helix chain 'AM' and resid 26 through 38 Processing helix chain 'AM' and resid 49 through 64 removed outlier: 4.275A pdb=" N ASPAM 54 " --> pdb=" O GLUAM 50 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THRAM 55 " --> pdb=" O GLYAM 51 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEUAM 56 " --> pdb=" O GLNAM 52 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLUAM 59 " --> pdb=" O THRAM 55 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHEAM 63 " --> pdb=" O GLUAM 59 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VALAM 64 " --> pdb=" O VALAM 60 " (cutoff:3.500A) Processing helix chain 'AM' and resid 66 through 84 removed outlier: 3.595A pdb=" N ARGAM 70 " --> pdb=" O GLUAM 66 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SERAM 76 " --> pdb=" O GLUAM 72 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASPAM 82 " --> pdb=" O LYSAM 78 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLYAM 84 " --> pdb=" O LEUAM 80 " (cutoff:3.500A) Processing helix chain 'AM' and resid 85 through 94 removed outlier: 3.655A pdb=" N ARGAM 93 " --> pdb=" O LEUAM 89 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLYAM 94 " --> pdb=" O ARGAM 90 " (cutoff:3.500A) Processing helix chain 'AN' and resid 3 through 25 removed outlier: 3.558A pdb=" N ARGAN 13 " --> pdb=" O ARGAN 9 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASPAN 18 " --> pdb=" O VALAN 14 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYSAN 19 " --> pdb=" O ALAAN 15 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHEAN 21 " --> pdb=" O ALAAN 17 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ALAAN 22 " --> pdb=" O ASPAN 18 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYSAN 23 " --> pdb=" O LYSAN 19 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARGAN 24 " --> pdb=" O TYRAN 20 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALAAN 25 " --> pdb=" O PHEAN 21 " (cutoff:3.500A) Processing helix chain 'AN' and resid 26 through 34 removed outlier: 3.880A pdb=" N ILEAN 30 " --> pdb=" O GLUAN 26 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILEAN 31 " --> pdb=" O LEUAN 27 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SERAN 32 " --> pdb=" O LYSAN 28 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASPAN 33 " --> pdb=" O ALAAN 29 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N VALAN 34 " --> pdb=" O ILEAN 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'AN' and resid 26 through 34' Processing helix chain 'AN' and resid 43 through 49 removed outlier: 5.273A pdb=" N LYSAN 47 " --> pdb=" O ASNAN 43 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEUAN 48 " --> pdb=" O ALAAN 44 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLNAN 49 " --> pdb=" O VALAN 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'AN' and resid 43 through 49' Processing helix chain 'AN' and resid 80 through 91 removed outlier: 3.542A pdb=" N ARGAN 90 " --> pdb=" O GLUAN 86 " (cutoff:3.500A) Processing helix chain 'AO' and resid 4 through 16 Processing helix chain 'AO' and resid 24 through 44 removed outlier: 4.207A pdb=" N GLYAO 41 " --> pdb=" O ASNAO 37 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HISAO 42 " --> pdb=" O HISAO 38 " (cutoff:3.500A) Processing helix chain 'AO' and resid 49 through 74 removed outlier: 3.983A pdb=" N GLYAO 55 " --> pdb=" O HISAO 51 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASPAO 74 " --> pdb=" O LEUAO 70 " (cutoff:3.500A) Processing helix chain 'AO' and resid 75 through 86 Processing helix chain 'AP' and resid 53 through 64 removed outlier: 3.680A pdb=" N ILEAP 57 " --> pdb=" O ASPAP 53 " (cutoff:3.500A) Processing helix chain 'AP' and resid 68 through 79 Processing helix chain 'AR' and resid 25 through 34 removed outlier: 4.024A pdb=" N ASNAR 31 " --> pdb=" O ALAAR 27 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYRAR 32 " --> pdb=" O THRAR 28 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILEAR 33 " --> pdb=" O LEUAR 29 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N THRAR 34 " --> pdb=" O LYSAR 30 " (cutoff:3.500A) Processing helix chain 'AR' and resid 41 through 46 removed outlier: 3.675A pdb=" N THRAR 45 " --> pdb=" O PROAR 41 " (cutoff:3.500A) Processing helix chain 'AR' and resid 48 through 66 Processing helix chain 'AS' and resid 12 through 25 removed outlier: 3.669A pdb=" N LYSAS 18 " --> pdb=" O HISAS 14 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLUAS 24 " --> pdb=" O GLUAS 20 " (cutoff:3.500A) Processing helix chain 'AS' and resid 70 through 76 removed outlier: 4.710A pdb=" N PHEAS 74 " --> pdb=" O LYSAS 70 " (cutoff:3.500A) removed outlier: 4.435A 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 'AS' and resid 64 through 69 removed outlier: 4.048A pdb=" N VALAS 67 " --> pdb=" O ASPAS 64 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLYAS 68 " --> pdb=" O GLUAS 65 " (cutoff:3.500A) Processing helix chain 'AT' and resid 6 through 42 removed outlier: 4.010A pdb=" N ARGAT 10 " --> pdb=" O SERAT 6 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILEAT 12 " --> pdb=" O LYSAT 8 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLUAT 15 " --> pdb=" O ALAAT 11 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SERAT 23 " --> pdb=" O LYSAT 19 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N METAT 28 " --> pdb=" O ARGAT 24 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VALAT 35 " --> pdb=" O PHEAT 31 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALAAT 37 " --> pdb=" O LYSAT 33 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALAAT 38 " --> pdb=" O LYSAT 34 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLYAT 42 " --> pdb=" O ALAAT 38 " (cutoff:3.500A) Processing helix chain 'AT' and resid 43 through 65 Proline residue: AT 56 - end of helix Processing helix chain 'AT' and resid 68 through 87 removed outlier: 4.598A pdb=" N ALAAT 72 " --> pdb=" O HISAT 68 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALAAT 73 " --> pdb=" O LYSAT 69 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASNAT 78 " --> pdb=" O ARGAT 74 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASNAT 84 " --> pdb=" O THRAT 80 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYSAT 85 " --> pdb=" O ALAAT 81 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEUAT 86 " --> pdb=" O GLNAT 82 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALAAT 87 " --> pdb=" O ILEAT 83 " (cutoff:3.500A) Processing helix chain 'AU' and resid 18 through 24 removed outlier: 3.512A pdb=" N SERAU 22 " --> pdb=" O ARGAU 18 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLUAU 24 " --> pdb=" O LYSAU 20 " (cutoff:3.500A) Processing helix chain 'AU' and resid 27 through 34 removed outlier: 5.628A pdb=" N GLUAU 31 " --> pdb=" O GLYAU 27 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARGAU 34 " --> pdb=" O ALAAU 30 " (cutoff:3.500A) Processing helix chain 'AU' and resid 39 through 53 removed outlier: 6.614A pdb=" N THRAU 43 " --> pdb=" O GLUAU 39 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VALAU 53 " --> pdb=" O LYSAU 49 " (cutoff:3.500A) Processing helix chain 'BC' and resid 10 through 17 removed outlier: 3.847A pdb=" N ARGBC 14 " --> pdb=" O SERBC 10 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N HISBC 15 " --> pdb=" O PROBC 11 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VALBC 16 " --> pdb=" O GLYBC 12 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VALBC 17 " --> pdb=" O ARGBC 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 10 through 17' Processing helix chain 'BC' and resid 30 through 35 removed outlier: 3.940A pdb=" N LEUBC 34 " --> pdb=" O PHEBC 30 " (cutoff:3.500A) removed outlier: 5.540A 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: 3.766A 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 209 through 215 removed outlier: 4.313A pdb=" N TRPBC 213 " --> pdb=" O GLYBC 209 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARGBC 214 " --> pdb=" O ALABC 210 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLYBC 215 " --> pdb=" O ALABC 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 209 through 215' Processing helix chain 'BC' and resid 221 through 226 removed outlier: 3.734A pdb=" N METBC 225 " --> pdb=" O ARGBC 221 " (cutoff:3.500A) removed outlier: 4.557A 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: 6.022A pdb=" N ASPBC 264 " --> pdb=" O ASNBC 260 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LYSBC 265 " --> pdb=" O LYSBC 261 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N PHEBC 266 " --> pdb=" O ARGBC 262 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILEBC 267 " --> pdb=" O THRBC 263 " (cutoff:3.500A) removed outlier: 5.150A 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: 3.609A pdb=" N HISBC 200 " --> pdb=" O ASNBC 197 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N METBC 201 " --> pdb=" O ALABC 198 " (cutoff:3.500A) Processing helix chain 'BD' and resid 61 through 72 removed outlier: 3.775A pdb=" N HISBD 67 " --> pdb=" O PROBD 63 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALABD 71 " --> pdb=" O HISBD 67 " (cutoff:3.500A) Processing helix chain 'BD' and resid 98 through 105 removed outlier: 4.337A pdb=" N ALABD 102 " --> pdb=" O VALBD 98 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASPBD 103 " --> pdb=" O GLUBD 99 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VALBD 104 " --> pdb=" O LEUBD 100 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYSBD 105 " --> pdb=" O PHEBD 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'BD' and resid 98 through 105' 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: 3.708A pdb=" N PHEBE 19 " --> pdb=" O SERBE 15 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLYBE 20 " --> pdb=" O GLUBE 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 15 through 20' Processing helix chain 'BE' and resid 24 through 41 removed outlier: 3.969A pdb=" N GLNBE 30 " --> pdb=" O ALABE 26 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLYBE 38 " --> pdb=" O ALABE 34 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLNBE 41 " --> pdb=" O ALABE 37 " (cutoff:3.500A) Processing helix chain 'BE' and resid 48 through 53 removed outlier: 5.874A pdb=" N THRBE 53 " --> pdb=" O ARGBE 49 " (cutoff:3.500A) Processing helix chain 'BE' and resid 97 through 116 removed outlier: 3.661A pdb=" N ALABE 104 " --> pdb=" O METBE 100 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYSBE 106 " --> pdb=" O ARGBE 102 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLUBE 111 " --> pdb=" O SERBE 107 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEUBE 112 " --> pdb=" O ILEBE 108 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VALBE 113 " --> pdb=" O LEUBE 109 " (cutoff:3.500A) Processing helix chain 'BE' and resid 130 through 142 removed outlier: 3.924A pdb=" N LEUBE 134 " --> pdb=" O LYSBE 130 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYSBE 139 " --> pdb=" O ALABE 135 " (cutoff:3.500A) Processing helix chain 'BE' and resid 154 through 163 removed outlier: 3.657A pdb=" N LEUBE 159 " --> pdb=" O GLUBE 155 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALABE 160 " --> pdb=" O ASNBE 156 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALABE 161 " --> pdb=" O LEUBE 157 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASNBE 163 " --> pdb=" O LEUBE 159 " (cutoff:3.500A) Processing helix chain 'BE' and resid 176 through 182 removed outlier: 3.644A pdb=" N LEUBE 180 " --> pdb=" O ASPBE 176 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILEBE 181 " --> pdb=" O PROBE 177 " (cutoff:3.500A) Processing helix chain 'BE' and resid 189 through 201 removed outlier: 4.086A pdb=" N LYSBE 194 " --> pdb=" O ALABE 190 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLNBE 195 " --> pdb=" O ASPBE 191 " (cutoff:3.500A) Processing helix chain 'BF' and resid 2 through 21 removed outlier: 3.645A pdb=" N LYSBF 9 " --> pdb=" O HISBF 5 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASPBF 10 " --> pdb=" O ASPBF 6 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLUBF 11 " --> pdb=" O TYRBF 7 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VALBF 12 " --> pdb=" O TYRBF 8 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VALBF 13 " --> pdb=" O LYSBF 9 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYSBF 14 " --> pdb=" O ASPBF 10 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLUBF 19 " --> pdb=" O LYSBF 15 " (cutoff:3.500A) Processing helix chain 'BF' and resid 42 through 47 removed outlier: 4.166A pdb=" N LYSBF 47 " --> pdb=" O ALABF 43 " (cutoff:3.500A) Processing helix chain 'BF' and resid 48 through 61 Processing helix chain 'BF' and resid 93 through 111 removed outlier: 3.695A pdb=" N TRPBF 97 " --> pdb=" O GLYBF 93 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILEBF 104 " --> pdb=" O PHEBF 100 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THRBF 105 " --> pdb=" O GLUBF 101 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILEBF 106 " --> pdb=" O ARGBF 102 " (cutoff:3.500A) removed outlier: 4.748A 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: 3.592A pdb=" N GLYBF 166 " --> pdb=" O SERBF 162 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALABF 168 " --> pdb=" O GLUBF 164 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEUBF 170 " --> pdb=" O GLYBF 166 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALABF 171 " --> pdb=" O ARGBF 167 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALABF 172 " --> pdb=" O ALABF 168 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHEBF 173 " --> pdb=" O LEUBF 169 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASPBF 174 " --> pdb=" O LEUBF 170 " (cutoff:3.500A) Processing helix chain 'BF' and resid 134 through 139 removed outlier: 3.828A pdb=" N ILEBF 137 " --> pdb=" O GLUBF 134 " (cutoff:3.500A) Proline residue: BF 139 - end of helix Processing helix chain 'BG' and resid 2 through 8 removed outlier: 3.654A pdb=" N LYSBG 6 " --> pdb=" O SERBG 2 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALABG 7 " --> pdb=" O ARGBG 3 " (cutoff:3.500A) Proline residue: BG 8 - end of helix No H-bonds generated for 'chain 'BG' and resid 2 through 8' Processing helix chain 'BG' and resid 60 through 81 removed outlier: 3.551A pdb=" N GLNBG 64 " --> pdb=" O ASPBG 60 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLYBG 66 " --> pdb=" O TRPBG 62 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASNBG 73 " --> pdb=" O ARGBG 69 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VALBG 79 " --> pdb=" O METBG 75 " (cutoff:3.500A) Processing helix chain 'BG' and resid 137 through 153 removed outlier: 3.677A pdb=" N ARGBG 152 " --> pdb=" O LEUBG 148 " (cutoff:3.500A) Processing helix chain 'BH' and resid 22 through 29 removed outlier: 3.572A pdb=" N ALABH 26 " --> pdb=" O LYSBH 22 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASNBH 28 " --> pdb=" O GLYBH 24 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHEBH 29 " --> pdb=" O TYRBH 25 " (cutoff:3.500A) Processing helix chain 'BH' and resid 40 through 47 removed outlier: 5.956A pdb=" N ILEBH 44 " --> pdb=" O THRBH 40 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLUBH 45 " --> pdb=" O LYSBH 41 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHEBH 46 " --> pdb=" O LYSBH 42 " (cutoff:3.500A) Processing helix chain 'BI' and resid 34 through 50 removed outlier: 4.682A pdb=" N PHEBI 38 " --> pdb=" O ASNBI 34 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N CYSBI 39 " --> pdb=" O ILEBI 35 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHEBI 42 " --> pdb=" O PHEBI 38 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASNBI 43 " --> pdb=" O CYSBI 39 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALABI 44 " --> pdb=" O LYSBI 40 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYSBI 45 " --> pdb=" O ALABI 41 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N SERBI 48 " --> pdb=" O ALABI 44 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILEBI 49 " --> pdb=" O LYSBI 45 " (cutoff:3.500A) Processing helix chain 'BI' and resid 75 through 84 removed outlier: 3.748A pdb=" N LEUBI 79 " --> pdb=" O PROBI 75 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEUBI 80 " --> pdb=" O ALABI 76 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LYSBI 81 " --> pdb=" O ALABI 77 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYSBI 82 " --> pdb=" O VALBI 78 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALABI 83 " --> pdb=" O LEUBI 79 " (cutoff:3.500A) Processing helix chain 'BI' and resid 102 through 114 removed outlier: 4.213A pdb=" N LEUBI 106 " --> pdb=" O SERBI 102 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLUBI 108 " --> pdb=" O ALABI 104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILEBI 109 " --> pdb=" O GLNBI 105 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THRBI 112 " --> pdb=" O GLUBI 108 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALABI 114 " --> pdb=" O ALABI 110 " (cutoff:3.500A) Processing helix chain 'BI' and resid 121 through 135 removed outlier: 3.993A pdb=" N METBI 125 " --> pdb=" O ASPBI 121 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARGBI 127 " --> pdb=" O GLUBI 123 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SERBI 128 " --> pdb=" O ALABI 124 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEBI 129 " --> pdb=" O METBI 125 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLUBI 130 " --> pdb=" O THRBI 126 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THRBI 132 " --> pdb=" O SERBI 128 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALABI 133 " --> pdb=" O ILEBI 129 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SERBI 135 " --> pdb=" O GLYBI 131 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 24 through 38 removed outlier: 4.025A pdb=" N GLUBJ 31 " --> pdb=" O ARGBJ 27 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARGBJ 34 " --> pdb=" O THRBJ 30 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 88 through 96 removed outlier: 3.942A pdb=" N ILEBJ 93 " --> pdb=" O PHEBJ 89 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALABJ 94 " --> pdb=" O GLUBJ 90 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 97 through 110 removed outlier: 4.224A pdb=" N ILEBJ 101 " --> pdb=" O PROBJ 97 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALABJ 104 " --> pdb=" O VALBJ 100 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLYBJ 107 " --> pdb=" O ILEBJ 103 " (cutoff:3.500A) removed outlier: 4.213A 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 123 removed outlier: 3.736A pdb=" N LYSBJ 121 " --> pdb=" O ALABJ 117 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEUBJ 122 " --> pdb=" O METBJ 118 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYSBJ 123 " --> pdb=" O PHEBJ 119 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 67 through 72 removed outlier: 4.264A pdb=" N LYSBJ 72 " --> pdb=" O ASNBJ 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'BJ' and resid 67 through 72' Processing helix chain 'BK' and resid 109 through 119 removed outlier: 5.480A pdb=" N METBK 113 " --> pdb=" O SERBK 109 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LYSBK 114 " --> pdb=" O GLUBK 110 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILEBK 115 " --> pdb=" O LYSBK 111 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEUBK 118 " --> pdb=" O LYSBK 114 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ALABK 119 " --> pdb=" O ILEBK 115 " (cutoff:3.500A) Processing helix chain 'BL' and resid 37 through 42 removed outlier: 3.654A pdb=" N ARGBL 41 " --> pdb=" O GLYBL 37 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N SERBL 42 " --> pdb=" O GLNBL 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'BL' and resid 37 through 42' Processing helix chain 'BL' and resid 56 through 62 Proline residue: BL 62 - end of helix Processing helix chain 'BL' and resid 70 through 75 removed outlier: 3.610A pdb=" N THRBL 74 " --> pdb=" O LYSBL 70 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ALABL 75 " --> pdb=" O ALABL 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'BL' and resid 70 through 75' Processing helix chain 'BL' and resid 81 through 86 removed outlier: 6.049A pdb=" N VALBL 85 " --> pdb=" O ASPBL 81 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLUBL 86 " --> pdb=" O LEUBL 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'BL' and resid 81 through 86' Processing helix chain 'BL' and resid 93 through 99 removed outlier: 5.470A pdb=" N ALABL 97 " --> pdb=" O ASNBL 93 " (cutoff:3.500A) Processing helix chain 'BL' and resid 128 through 139 removed outlier: 3.848A pdb=" N ALABL 133 " --> pdb=" O LYSBL 129 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALABL 134 " --> pdb=" O GLYBL 130 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALABL 138 " --> pdb=" O ALABL 134 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLYBL 139 " --> pdb=" O ILEBL 135 " (cutoff:3.500A) Processing helix chain 'BM' and resid 42 through 58 removed outlier: 3.566A pdb=" N ARGBM 51 " --> pdb=" O GLUBM 47 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALABM 52 " --> pdb=" O ALABM 48 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N METBM 53 " --> pdb=" O ALABM 49 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALABM 56 " --> pdb=" O ALABM 52 " (cutoff:3.500A) Processing helix chain 'BM' and resid 109 through 125 removed outlier: 3.734A pdb=" N GLUBM 115 " --> pdb=" O GLUBM 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEUBM 119 " --> pdb=" O GLUBM 115 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALABM 120 " --> pdb=" O ALABM 116 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALABM 122 " --> pdb=" O LYSBM 118 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYSBM 123 " --> pdb=" O LEUBM 119 " (cutoff:3.500A) removed outlier: 3.545A 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: 3.647A pdb=" N ALABN 19 " --> pdb=" O SERBN 15 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHEBN 21 " --> pdb=" O ARGBN 17 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARGBN 22 " --> pdb=" O GLNBN 18 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLYBN 26 " --> pdb=" O ARGBN 22 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VALBN 29 " --> pdb=" O ALABN 25 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HISBN 31 " --> pdb=" O SERBN 27 " (cutoff:3.500A) Processing helix chain 'BN' and resid 38 through 58 removed outlier: 3.705A pdb=" N GLUBN 43 " --> pdb=" O PROBN 39 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARGBN 46 " --> pdb=" O LYSBN 42 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VALBN 47 " --> pdb=" O GLUBN 43 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLUBN 49 " --> pdb=" O ARGBN 45 " (cutoff:3.500A) Proline residue: BN 50 - end of helix removed outlier: 4.654A pdb=" N THRBN 57 " --> pdb=" O THRBN 53 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASPBN 58 " --> pdb=" O LEUBN 54 " (cutoff:3.500A) Processing helix chain 'BN' and resid 59 through 71 removed outlier: 3.823A pdb=" N ARGBN 64 " --> pdb=" O VALBN 60 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARGBN 69 " --> pdb=" O LEUBN 65 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THRBN 70 " --> pdb=" O ALABN 66 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARGBN 71 " --> pdb=" O PHEBN 67 " (cutoff:3.500A) Processing helix chain 'BN' and resid 72 through 82 removed outlier: 3.795A pdb=" N LYSBN 78 " --> pdb=" O GLUBN 74 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUBN 79 " --> pdb=" O ILEBN 75 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHEBN 80 " --> pdb=" O VALBN 76 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASNBN 81 " --> pdb=" O ALABN 77 " (cutoff:3.500A) Processing helix chain 'BN' and resid 83 through 88 removed outlier: 3.887A pdb=" N PHEBN 87 " --> pdb=" O LEUBN 83 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALABN 88 " --> pdb=" O GLYBN 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'BN' and resid 83 through 88' Processing helix chain 'BO' and resid 2 through 22 removed outlier: 3.705A pdb=" N ALABO 6 " --> pdb=" O ASPBO 2 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARGBO 7 " --> pdb=" O LYSBO 3 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILEBO 8 " --> pdb=" O LYSBO 4 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARGBO 9 " --> pdb=" O SERBO 5 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALABO 11 " --> pdb=" O ARGBO 7 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARGBO 13 " --> pdb=" O ARGBO 9 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ALABO 14 " --> pdb=" O ARGBO 10 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYSBO 17 " --> pdb=" O ARGBO 13 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEUBO 18 " --> pdb=" O ALABO 14 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLNBO 19 " --> pdb=" O ARGBO 15 " (cutoff:3.500A) Processing helix chain 'BO' and resid 55 through 63 removed outlier: 4.047A pdb=" N ALABO 59 " --> pdb=" O GLUBO 55 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLUBO 60 " --> pdb=" O LYSBO 56 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLNBO 61 " --> pdb=" O ALABO 57 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LYSBO 63 " --> pdb=" O ALABO 59 " (cutoff:3.500A) Processing helix chain 'BO' and resid 67 through 86 removed outlier: 3.877A pdb=" N ALABO 79 " --> pdb=" O GLYBO 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYSBO 85 " --> pdb=" O ARGBO 81 " (cutoff:3.500A) Processing helix chain 'BO' and resid 101 through 114 removed outlier: 3.633A pdb=" N ALABO 110 " --> pdb=" O LEUBO 106 " (cutoff:3.500A) Processing helix chain 'BP' and resid 2 through 14 removed outlier: 3.513A pdb=" N LEUBP 8 " --> pdb=" O ILEBP 4 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLUBP 11 " --> pdb=" O GLNBP 7 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLNBP 12 " --> pdb=" O LEUBP 8 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LYSBP 14 " --> pdb=" O GLNBP 10 " (cutoff:3.500A) Processing helix chain 'BP' and resid 97 through 104 removed outlier: 4.274A pdb=" N ARGBP 101 " --> pdb=" O LEUBP 97 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLUBP 102 " --> pdb=" O TYRBP 98 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARGBP 103 " --> pdb=" O TYRBP 99 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N THRBP 104 " --> pdb=" O LEUBP 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP' and resid 97 through 104' Processing helix chain 'BQ' and resid 6 through 22 removed outlier: 4.363A pdb=" N ALABQ 12 " --> pdb=" O VALBQ 8 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILEBQ 17 " --> pdb=" O ARGBQ 13 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 26 through 31 removed outlier: 4.319A pdb=" N ARGBQ 30 " --> pdb=" O GLYBQ 26 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 39 through 61 removed outlier: 4.108A pdb=" N ARGBQ 51 " --> pdb=" O TYRBQ 47 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYSBQ 54 " --> pdb=" O ARGBQ 50 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARGBQ 55 " --> pdb=" O ARGBQ 51 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHEBQ 57 " --> pdb=" O ARGBQ 53 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARGBQ 58 " --> pdb=" O LYSBQ 54 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 63 through 73 removed outlier: 4.042A pdb=" N GLNBQ 71 " --> pdb=" O ALABQ 67 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASNBQ 72 " --> pdb=" O ALABQ 68 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 75 through 87 removed outlier: 3.725A pdb=" N ASNBQ 81 " --> pdb=" O SERBQ 77 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEUBQ 83 " --> pdb=" O PHEBQ 79 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 91 through 102 removed outlier: 3.588A pdb=" N LEUBQ 95 " --> pdb=" O ASPBQ 91 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VALBQ 100 " --> pdb=" O ALABQ 96 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 103 through 118 removed outlier: 3.585A pdb=" N THRBQ 107 " --> pdb=" O LYSBQ 103 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALABQ 108 " --> pdb=" O VALBQ 104 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYSBQ 112 " --> pdb=" O ALABQ 108 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALABQ 113 " --> pdb=" O LEUBQ 109 " (cutoff:3.500A) Processing helix chain 'BS' and resid 15 through 25 removed outlier: 4.371A pdb=" N LEUBS 19 " --> pdb=" O GLNBS 15 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VALBS 20 " --> pdb=" O LYSBS 16 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEUBS 23 " --> pdb=" O LEUBS 19 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILEBS 24 " --> pdb=" O VALBS 20 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARGBS 25 " --> pdb=" O ALABS 21 " (cutoff:3.500A) Processing helix chain 'BS' and resid 28 through 39 removed outlier: 5.201A pdb=" N ALABS 32 " --> pdb=" O LYSBS 28 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASPBS 34 " --> pdb=" O SERBS 30 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILEBS 35 " --> pdb=" O GLNBS 31 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYRBS 38 " --> pdb=" O ASPBS 34 " (cutoff:3.500A) Processing helix chain 'BS' and resid 41 through 61 removed outlier: 3.505A pdb=" N VALBS 45 " --> pdb=" O LYSBS 41 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEUBS 46 " --> pdb=" O LYSBS 42 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYSBS 49 " --> pdb=" O VALBS 45 " (cutoff:3.500A) Processing helix chain 'BT' and resid 3 through 12 removed outlier: 3.761A pdb=" N LEUBT 7 " --> pdb=" O ARGBT 3 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYSBT 9 " --> pdb=" O GLUBT 5 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VALBT 10 " --> pdb=" O ARGBT 6 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEUBT 11 " --> pdb=" O LEUBT 7 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ARGBT 12 " --> pdb=" O LEUBT 8 " (cutoff:3.500A) Processing helix chain 'BT' and resid 17 through 26 removed outlier: 3.835A pdb=" N THRBT 22 " --> pdb=" O GLUBT 18 " (cutoff:3.500A) Processing helix chain 'BT' and resid 39 through 50 removed outlier: 3.696A pdb=" N VALBT 47 " --> pdb=" O ILEBT 43 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYSBT 49 " --> pdb=" O ALABT 45 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEUBT 50 " --> pdb=" O ALABT 46 " (cutoff:3.500A) Processing helix chain 'BU' and resid 66 through 71 removed outlier: 3.876A pdb=" N VALBU 70 " --> pdb=" O GLNBU 66 " (cutoff:3.500A) removed outlier: 4.896A 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: 4.368A pdb=" N ARGBV 19 " --> pdb=" O GLYBV 15 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALABV 22 " --> pdb=" O ARGBV 18 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALABV 23 " --> pdb=" O ARGBV 19 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASNBV 24 " --> pdb=" O LEUBV 20 " (cutoff:3.500A) Processing helix chain 'BV' and resid 43 through 53 removed outlier: 3.743A pdb=" N VALBV 47 " --> pdb=" O ASPBV 43 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASNBV 49 " --> pdb=" O ASPBV 45 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALABV 52 " --> pdb=" O METBV 48 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYSBV 53 " --> pdb=" O ASNBV 49 " (cutoff:3.500A) Processing helix chain 'BV' and resid 54 through 59 removed outlier: 3.797A pdb=" N SERBV 58 " --> pdb=" O ALABV 54 " (cutoff:3.500A) Processing helix chain 'BX' and resid 52 through 63 removed outlier: 4.002A pdb=" N ARGBX 57 " --> pdb=" O ALABX 53 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VALBX 58 " --> pdb=" O LYSBX 54 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILEBX 59 " --> pdb=" O GLYBX 55 " (cutoff:3.500A) Processing helix chain 'BX' and resid 64 through 75 removed outlier: 3.872A pdb=" N ALABX 69 " --> pdb=" O ASPBX 65 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARGBX 74 " --> pdb=" O GLUBX 70 " (cutoff:3.500A) Processing helix chain 'BY' and resid 1 through 7 removed outlier: 5.615A pdb=" N GLUBY 5 " --> pdb=" O METBY 1 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEUBY 6 " --> pdb=" O LYSBY 2 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARGBY 7 " --> pdb=" O ALABY 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'BY' and resid 1 through 7' Processing helix chain 'BY' and resid 9 through 22 removed outlier: 3.850A pdb=" N GLUBY 13 " --> pdb=" O LYSBY 9 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEUBY 14 " --> pdb=" O SERBY 10 " (cutoff:3.500A) Processing helix chain 'BY' and resid 24 through 35 removed outlier: 3.974A pdb=" N ARGBY 29 " --> pdb=" O GLNBY 25 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLYBY 35 " --> pdb=" O GLNBY 31 " (cutoff:3.500A) Processing helix chain 'BY' and resid 39 through 61 removed outlier: 4.733A pdb=" N LEUBY 43 " --> pdb=" O GLNBY 39 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYSBY 44 " --> pdb=" O SERBY 40 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VALBY 46 " --> pdb=" O LEUBY 42 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARGBY 47 " --> pdb=" O LEUBY 43 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 17 through 28 Processing helix chain 'BZ' and resid 41 through 52 removed outlier: 3.683A pdb=" N METBZ 47 " --> pdb=" O ALABZ 43 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VALBZ 51 " --> pdb=" O METBZ 47 " (cutoff:3.500A) Processing helix chain 'B0' and resid 9 through 21 removed outlier: 3.580A pdb=" N ARGB0 16 " --> pdb=" O LYSB0 12 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N HISB0 19 " --> pdb=" O METB0 15 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASPB0 20 " --> pdb=" O ARGB0 16 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALAB0 21 " --> pdb=" O ARGB0 17 " (cutoff:3.500A) Processing helix chain 'B1' and resid 26 through 31 Proline residue: B1 31 - end of helix Processing helix chain 'B2' and resid 8 through 16 removed outlier: 3.523A pdb=" N ARGB2 14 " --> pdb=" O LEUB2 10 " (cutoff:3.500A) Processing helix chain 'B2' and resid 17 through 25 removed outlier: 3.625A pdb=" N ARGB2 21 " --> pdb=" O GLYB2 17 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N METB2 22 " --> pdb=" O PHEB2 18 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THRB2 24 " --> pdb=" O ALAB2 20 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LYSB2 25 " --> pdb=" O ARGB2 21 " (cutoff:3.500A) Processing helix chain 'B2' and resid 26 through 38 removed outlier: 3.642A pdb=" N VALB2 30 " --> pdb=" O ASNB2 26 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEUB2 31 " --> pdb=" O GLYB2 27 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARGB2 34 " --> pdb=" O VALB2 30 " (cutoff:3.500A) Processing helix chain 'B3' and resid 7 through 14 removed outlier: 3.525A pdb=" N LYSB3 12 " --> pdb=" O ARGB3 8 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARGB3 13 " --> pdb=" O GLYB3 9 " (cutoff:3.500A) Processing helix chain 'B3' and resid 32 through 37 removed outlier: 4.823A pdb=" N LYSB3 36 " --> pdb=" O ILEB3 32 " (cutoff:3.500A) removed outlier: 5.217A 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: 3.992A pdb=" N HISB3 43 " --> pdb=" O LYSB3 39 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEUB3 44 " --> pdb=" O ARGB3 40 " (cutoff:3.500A) removed outlier: 3.604A 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: 4.365A pdb=" N GLYB3 56 " --> pdb=" O LYSB3 52 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEUB3 57 " --> pdb=" O GLYB3 53 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILEB3 59 " --> pdb=" O LEUB3 55 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALAB3 60 " --> pdb=" O GLYB3 56 " (cutoff:3.500A) removed outlier: 3.535A 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 89 through 92 removed outlier: 6.734A pdb=" N PHEAB 90 " --> pdb=" O ILEAB 67 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEUAB 68 " --> pdb=" O ALAAB 160 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHEAB 162 " --> pdb=" O LEUAB 68 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILEAB 164 " --> pdb=" O VALAB 70 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VALAB 163 " --> pdb=" O PHEAB 184 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'AC' and resid 53 through 57 removed outlier: 3.521A pdb=" N ARGAC 54 " --> pdb=" O HISAC 69 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILEAC 64 " --> pdb=" O PROAC 98 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VALAC 66 " --> pdb=" O GLNAC 100 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASNAC 102 " --> pdb=" O VALAC 66 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'AC' and resid 167 through 171 removed outlier: 3.569A pdb=" N THRAC 191 " --> pdb=" O GLYAC 194 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASPAC 181 " --> pdb=" O LYSAC 204 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'AD' and resid 141 through 144 removed outlier: 4.148A pdb=" N ASPAD 141 " --> pdb=" O PHEAD 182 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'AE' and resid 17 through 25 removed outlier: 3.690A pdb=" N ALAAE 17 " --> pdb=" O LEUAE 36 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEUAE 36 " --> pdb=" O ALAAE 17 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILEAE 30 " --> pdb=" O LYSAE 23 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALAAE 35 " --> pdb=" O GLYAE 51 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLYAE 51 " --> pdb=" O ALAAE 35 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'AE' and resid 83 through 88 removed outlier: 7.579A pdb=" N HISAE 83 " --> pdb=" O PROAE 98 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'AF' and resid 39 through 42 removed outlier: 4.037A pdb=" N GLUAF 40 " --> pdb=" O LEUAF 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRPAF 42 " --> pdb=" O TYRAF 59 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYRAF 59 " --> pdb=" O TRPAF 42 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VALAF 60 " --> pdb=" O PHEAF 8 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHEAF 8 " --> pdb=" O VALAF 60 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N METAF 62 " --> pdb=" O ILEAF 6 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILEAF 6 " --> pdb=" O METAF 62 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N HISAF 3 " --> pdb=" O THRAF 92 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THRAF 92 " --> pdb=" O HISAF 3 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VALAF 7 " --> pdb=" O METAF 88 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ARGAF 86 " --> pdb=" O METAF 9 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'AF' and resid 43 through 46 Processing sheet with id= 9, first strand: chain 'AG' and resid 73 through 79 removed outlier: 6.367A pdb=" N TYRAG 85 " --> pdb=" O ARGAG 78 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'AH' and resid 23 through 29 removed outlier: 6.000A pdb=" N ALAAH 23 " --> pdb=" O LEUAH 63 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASPAH 48 " --> pdb=" O THRAH 62 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'AH' and resid 74 through 77 removed outlier: 3.778A pdb=" N CYSAH 127 " --> pdb=" O VALAH 103 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ILEAH 101 " --> pdb=" O VALAH 129 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'AI' and resid 5 through 11 removed outlier: 4.382A pdb=" N GLYAI 10 " --> pdb=" O ALAAI 17 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'AJ' and resid 44 through 52 removed outlier: 6.595A pdb=" N ILEAJ 8 " --> pdb=" O VALAJ 74 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILEAJ 6 " --> pdb=" O ILEAJ 76 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLNAJ 99 " --> pdb=" O ARGAJ 9 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'AK' and resid 42 through 45 removed outlier: 3.524A pdb=" N ILEAK 23 " --> pdb=" O METAK 85 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASNAK 109 " --> pdb=" O LEUAK 82 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLYAK 88 " --> pdb=" O VALAK 113 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'AL' and resid 29 through 32 removed outlier: 4.830A pdb=" N LEUAL 81 " --> pdb=" O VALAL 98 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N HISAL 96 " --> pdb=" O ARGAL 83 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'AL' and resid 36 through 39 removed outlier: 3.653A pdb=" N ARGAL 36 " --> pdb=" O ARGAL 54 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LYSAL 51 " --> pdb=" O ILEAL 67 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILEAL 67 " --> pdb=" O LYSAL 51 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHEAL 61 " --> pdb=" O LEUAL 57 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'AP' and resid 4 through 11 removed outlier: 5.432A pdb=" N PHEAP 16 " --> pdb=" O HISAP 9 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'AQ' and resid 7 through 11 removed outlier: 5.608A pdb=" N GLUAQ 60 " --> pdb=" O VALAQ 76 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'AQ' and resid 19 through 30 removed outlier: 5.178A pdb=" N LYSAQ 19 " --> pdb=" O ASPAQ 48 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASPAQ 48 " --> pdb=" O LYSAQ 19 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'AS' and resid 48 through 52 removed outlier: 4.262A pdb=" N ILEAS 49 " --> pdb=" O VALAS 60 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'BC' and resid 80 through 83 removed outlier: 4.058A pdb=" N ARGBC 80 " --> pdb=" O LEUBC 93 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEUBC 93 " --> pdb=" O GLUBC 79 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILEBC 74 " --> pdb=" O SERBC 118 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SERBC 118 " --> pdb=" O ILEBC 74 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ASPBC 114 " --> pdb=" O VALBC 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'BC' and resid 137 through 140 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'BC' and resid 171 through 176 removed outlier: 4.297A pdb=" N GLUBC 180 " --> pdb=" O LEUBC 176 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'BD' and resid 3 through 8 removed outlier: 4.471A pdb=" N SERBD 199 " --> pdb=" O LYSBD 8 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASPBD 200 " --> pdb=" O THRBD 112 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N THRBD 112 " --> pdb=" O ASPBD 200 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VALBD 109 " --> pdb=" O VALBD 172 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VALBD 172 " --> pdb=" O VALBD 109 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLUBD 168 " --> pdb=" O SERBD 113 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'BD' and resid 11 through 16 removed outlier: 3.911A pdb=" N ILEBD 22 " --> pdb=" O ILEBD 14 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VALBD 20 " --> pdb=" O THRBD 16 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VALBD 189 " --> pdb=" O THRBD 25 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILEBD 27 " --> pdb=" O LEUBD 187 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASPBD 181 " --> pdb=" O LEUBD 186 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARGBD 179 " --> pdb=" O LEUBD 188 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'BD' and resid 79 through 83 removed outlier: 6.929A pdb=" N GLNBD 49 " --> pdb=" O THRBD 35 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLNBD 94 " --> pdb=" O VALBD 34 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'BE' and resid 1 through 5 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'BE' and resid 42 through 46 No H-bonds generated for sheet with id= 28 Processing sheet with id= 29, first strand: chain 'BE' and resid 117 through 120 removed outlier: 5.811A pdb=" N ARGBE 117 " --> pdb=" O ASPBE 184 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILEBE 149 " --> pdb=" O VALBE 187 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASPBE 168 " --> pdb=" O VALBE 146 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'BF' and resid 65 through 70 removed outlier: 6.456A pdb=" N LEUBF 66 " --> pdb=" O CYSBF 87 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYSBF 87 " --> pdb=" O LEUBF 66 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THRBF 68 " --> pdb=" O ILEBF 85 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYRBF 83 " --> pdb=" O ALABF 70 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYSBF 87 " --> pdb=" O METBF 38 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VALBF 89 " --> pdb=" O LEUBF 36 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYSBF 33 " --> pdb=" O THRBF 157 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THRBF 35 " --> pdb=" O THRBF 155 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THRBF 155 " --> pdb=" O THRBF 35 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASNBF 37 " --> pdb=" O ASPBF 153 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASPBF 153 " --> pdb=" O ASNBF 37 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYRBF 128 " --> pdb=" O ILEBF 156 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'BF' and resid 72 through 75 removed outlier: 5.044A pdb=" N SERBF 73 " --> pdb=" O ARGBF 80 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARGBF 80 " --> pdb=" O SERBF 73 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALABF 75 " --> pdb=" O LYSBF 78 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'BG' and resid 16 through 19 removed outlier: 4.237A pdb=" N ASPBG 16 " --> pdb=" O LYSBG 27 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYSBG 18 " --> pdb=" O THRBG 25 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THRBG 25 " --> pdb=" O LYSBG 18 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'BG' and resid 41 through 45 removed outlier: 3.588A pdb=" N LYSBG 44 " --> pdb=" O THRBG 51 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THRBG 51 " --> pdb=" O LYSBG 44 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'BG' and resid 83 through 89 removed outlier: 3.556A pdb=" N PHEBG 83 " --> pdb=" O GLYBG 135 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLYBG 135 " --> pdb=" O PHEBG 83 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYSBG 85 " --> pdb=" O LEUBG 133 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEUBG 133 " --> pdb=" O LYSBG 85 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N THRBG 129 " --> pdb=" O LEUBG 89 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'BG' and resid 94 through 98 removed outlier: 3.815A pdb=" N ALABG 97 " --> pdb=" O ASNBG 104 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILEBG 103 " --> pdb=" O HISBG 115 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HISBG 115 " --> pdb=" O ILEBG 103 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'BH' and resid 3 through 6 removed outlier: 5.731A pdb=" N LYSBH 35 " --> pdb=" O LEUBH 6 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'BJ' and resid 52 through 57 removed outlier: 3.517A pdb=" N TYRBJ 53 " --> pdb=" O ASPBJ 14 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEUBJ 57 " --> pdb=" O VALBJ 18 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLNBJ 138 " --> pdb=" O TRPBJ 15 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASPBJ 19 " --> pdb=" O LEUBJ 140 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'BJ' and resid 74 through 78 removed outlier: 3.578A pdb=" N ALABJ 87 " --> pdb=" O TYRBJ 74 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HISBJ 76 " --> pdb=" O LYSBJ 85 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYSBJ 85 " --> pdb=" O HISBJ 76 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLYBJ 83 " --> pdb=" O THRBJ 78 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'BK' and resid 6 through 10 removed outlier: 4.000A pdb=" N THRBK 6 " --> pdb=" O CYSBK 21 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VALBK 10 " --> pdb=" O ARGBK 17 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ARGBK 17 " --> pdb=" O VALBK 10 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'BK' and resid 38 through 42 removed outlier: 4.485A pdb=" N LYSBK 59 " --> pdb=" O LEUBK 87 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'BL' and resid 88 through 91 removed outlier: 3.527A pdb=" N LYSBL 141 " --> pdb=" O VALBL 120 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'BM' and resid 63 through 66 removed outlier: 7.280A pdb=" N LEUBM 102 " --> pdb=" O ARGBM 66 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYRBM 103 " --> pdb=" O LEUBM 33 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N SERBM 30 " --> pdb=" O LYSBM 133 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VALBM 131 " --> pdb=" O GLYBM 32 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYSBM 34 " --> pdb=" O THRBM 129 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYSBM 127 " --> pdb=" O VALBM 36 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'BN' and resid 33 through 37 removed outlier: 3.611A pdb=" N THRBN 36 " --> pdb=" O ALABN 111 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N METBN 110 " --> pdb=" O CYSBN 100 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLUBN 114 " --> pdb=" O ARGBN 96 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N TYRBN 94 " --> pdb=" O VALBN 116 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'BO' and resid 49 through 53 removed outlier: 3.767A pdb=" N VALBO 49 " --> pdb=" O VALBO 39 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALABO 51 " --> pdb=" O ALABO 37 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALABO 37 " --> pdb=" O ALABO 51 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THRBO 53 " --> pdb=" O ILEBO 35 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILEBO 35 " --> pdb=" O THRBO 53 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLNBO 38 " --> pdb=" O VALBO 27 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VALBO 27 " --> pdb=" O GLNBO 38 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARGBO 25 " --> pdb=" O ILEBO 40 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'BP' and resid 40 through 45 removed outlier: 6.789A pdb=" N THRBP 25 " --> pdb=" O LYSBP 87 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SERBP 85 " --> pdb=" O GLUBP 27 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SERBP 83 " --> pdb=" O LYSBP 29 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'BP' and resid 57 through 64 removed outlier: 7.941A pdb=" N SERBP 57 " --> pdb=" O THRBP 76 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'BR' and resid 3 through 6 removed outlier: 3.929A pdb=" N VALBR 14 " --> pdb=" O ALABR 3 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHEBR 5 " --> pdb=" O HISBR 12 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'BR' and resid 19 through 23 removed outlier: 3.523A pdb=" N VALBR 96 " --> pdb=" O VALBR 20 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEUBR 22 " --> pdb=" O THRBR 94 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASPBR 95 " --> pdb=" O VALBR 64 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYSBR 60 " --> pdb=" O THRBR 99 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'BR' and resid 39 through 42 removed outlier: 8.528A pdb=" N LEUBR 39 " --> pdb=" O ILEBR 49 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILEBR 41 " --> pdb=" O VALBR 47 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'BR' and resid 57 through 60 removed outlier: 4.141A pdb=" N SERBR 102 " --> pdb=" O VALBR 58 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLYBR 100 " --> pdb=" O LYSBR 60 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'BR' and resid 71 through 78 removed outlier: 4.191A pdb=" N LYSBR 85 " --> pdb=" O LYSBR 76 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYRBR 83 " --> pdb=" O ARGBR 78 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'BS' and resid 2 through 8 removed outlier: 4.266A pdb=" N VALBS 107 " --> pdb=" O THRBS 3 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'BT' and resid 28 through 33 removed outlier: 6.059A pdb=" N ASNBT 28 " --> pdb=" O LEUBT 87 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUBT 32 " --> pdb=" O ALABT 83 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARGBT 73 " --> pdb=" O HISBT 70 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARGBT 77 " --> pdb=" O LYSBT 66 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LYSBT 66 " --> pdb=" O ARGBT 77 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASPBT 79 " --> pdb=" O LYSBT 64 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LYSBT 64 " --> pdb=" O ASPBT 79 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYSBT 81 " --> pdb=" O VALBT 62 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VALBT 62 " --> pdb=" O LYSBT 81 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALABT 83 " --> pdb=" O THRBT 60 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THRBT 60 " --> pdb=" O ALABT 83 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VALBT 85 " --> pdb=" O VALBT 58 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VALBT 58 " --> pdb=" O VALBT 85 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'BU' and resid 40 through 43 removed outlier: 4.789A pdb=" N ASNBU 40 " --> pdb=" O ALABU 63 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'BU' and resid 82 through 87 removed outlier: 6.057A pdb=" N ARGBU 82 " --> pdb=" O LYSBU 97 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHEBU 95 " --> pdb=" O GLYBU 84 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'BV' and resid 69 through 73 removed outlier: 5.073A pdb=" N PHEBV 2 " --> pdb=" O VALBV 60 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLUBV 7 " --> pdb=" O GLUBV 41 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ALABV 39 " --> pdb=" O ARGBV 9 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILEBV 30 " --> pdb=" O LEUBV 38 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILEBV 89 " --> pdb=" O PROBV 27 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILEBV 29 " --> pdb=" O ILEBV 89 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASPBV 76 " --> pdb=" O ASPBV 90 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'BW' and resid 51 through 54 removed outlier: 6.853A pdb=" N GLYBW 52 " --> pdb=" O LEUBW 59 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEUBW 59 " --> pdb=" O GLYBW 52 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLYBW 54 " --> pdb=" O HISBW 57 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'BW' and resid 65 through 71 Processing sheet with id= 59, first strand: chain 'BX' and resid 12 through 17 removed outlier: 4.003A pdb=" N VALBX 13 " --> pdb=" O PHEBX 29 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THRBX 25 " --> pdb=" O ASNBX 17 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'BZ' and resid 35 through 40 removed outlier: 5.799A pdb=" N ASPBZ 40 " --> pdb=" O LYSBZ 3 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LYSBZ 3 " --> pdb=" O ASPBZ 40 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYSBZ 6 " --> pdb=" O GLUBZ 58 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLUBZ 58 " --> pdb=" O LYSBZ 6 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N METBZ 54 " --> pdb=" O THRBZ 10 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'B0' and resid 28 through 31 removed outlier: 6.151A pdb=" N SERB0 29 " --> pdb=" O LYSB0 37 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYSB0 37 " --> pdb=" O SERB0 29 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASPB0 31 " --> pdb=" O GLYB0 35 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'B1' and resid 7 through 12 No H-bonds generated for sheet with id= 62 Processing sheet with id= 63, first strand: chain 'B1' and resid 33 through 39 removed outlier: 5.796A pdb=" N LEUB1 34 " --> pdb=" O GLUB1 51 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLUB1 51 " --> pdb=" O LEUB1 34 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEUB1 36 " --> pdb=" O TYRB1 49 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYRB1 49 " --> pdb=" O LEUB1 36 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'B4' and resid 14 through 19 removed outlier: 3.729A pdb=" N ILEB4 26 " --> pdb=" O LYSB4 15 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLNB4 35 " --> pdb=" O VALB4 25 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N CYSB4 27 " --> pdb=" O HISB4 33 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HISB4 33 " --> pdb=" O CYSB4 27 " (cutoff:3.500A) 1357 hydrogen bonds defined for protein. 4014 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4070 hydrogen bonds 6332 hydrogen bond angles 0 basepair planarities 1626 basepair parallelities 2803 stacking parallelities Total time for adding SS restraints: 224.02 Time building geometry restraints manager: 67.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 22681 1.33 - 1.45: 65504 1.45 - 1.57: 61652 1.57 - 1.69: 9566 1.69 - 1.81: 263 Bond restraints: 159666 Sorted by residual: bond pdb=" C4 5MUAX 54 " pdb=" C5 5MUAX 54 " ideal model delta sigma weight residual 1.802 1.450 0.352 2.00e-02 2.50e+03 3.10e+02 bond pdb=" C4 5MUAW 54 " pdb=" C5 5MUAW 54 " ideal model delta sigma weight residual 1.802 1.451 0.351 2.00e-02 2.50e+03 3.08e+02 bond pdb=" C4 5MUAY 54 " pdb=" C5 5MUAY 54 " ideal model delta sigma weight residual 1.802 1.451 0.351 2.00e-02 2.50e+03 3.08e+02 bond pdb=" N1 5MUAY 54 " pdb=" C6 5MUAY 54 " ideal model delta sigma weight residual 1.635 1.381 0.254 2.00e-02 2.50e+03 1.62e+02 bond pdb=" N1 5MUAX 54 " pdb=" C6 5MUAX 54 " ideal model delta sigma weight residual 1.635 1.382 0.253 2.00e-02 2.50e+03 1.60e+02 ... (remaining 159661 not shown) Histogram of bond angle deviations from ideal: 100.11 - 107.15: 25514 107.15 - 114.19: 105138 114.19 - 121.23: 69272 121.23 - 128.27: 30953 128.27 - 135.32: 8409 Bond angle restraints: 239286 Sorted by residual: angle pdb=" C1' 2MAAX 37 " pdb=" N9 2MAAX 37 " pdb=" C8 2MAAX 37 " ideal model delta sigma weight residual 106.32 128.67 -22.35 3.00e+00 1.11e-01 5.55e+01 angle pdb=" C THRAL 41 " pdb=" N PROAL 42 " pdb=" CA PROAL 42 " ideal model delta sigma weight residual 119.78 126.47 -6.69 1.03e+00 9.43e-01 4.22e+01 angle pdb=" C ILEBC 135 " pdb=" N PROBC 136 " pdb=" CA PROBC 136 " ideal model delta sigma weight residual 119.78 126.14 -6.36 1.03e+00 9.43e-01 3.82e+01 angle pdb=" C THRBI 73 " pdb=" N PROBI 74 " pdb=" CA PROBI 74 " ideal model delta sigma weight residual 119.66 124.09 -4.43 7.30e-01 1.88e+00 3.67e+01 angle pdb=" C VALAL 21 " pdb=" N PROAL 22 " pdb=" CA PROAL 22 " ideal model delta sigma weight residual 119.28 125.85 -6.57 1.10e+00 8.26e-01 3.57e+01 ... (remaining 239281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 90529 35.97 - 71.94: 10436 71.94 - 107.91: 1316 107.91 - 143.89: 11 143.89 - 179.86: 30 Dihedral angle restraints: 102322 sinusoidal: 86311 harmonic: 16011 Sorted by residual: dihedral pdb=" C4' UBA2506 " pdb=" C3' UBA2506 " pdb=" C2' UBA2506 " pdb=" C1' UBA2506 " ideal model delta sinusoidal sigma weight residual -35.00 34.60 -69.60 1 8.00e+00 1.56e-02 9.77e+01 dihedral pdb=" C5' UBA2506 " pdb=" C4' UBA2506 " pdb=" C3' UBA2506 " pdb=" O3' UBA2506 " ideal model delta sinusoidal sigma weight residual 147.00 80.09 66.91 1 8.00e+00 1.56e-02 9.12e+01 dihedral pdb=" O4' UBA 846 " pdb=" C1' UBA 846 " pdb=" N1 UBA 846 " pdb=" C2 UBA 846 " ideal model delta sinusoidal sigma weight residual 200.00 44.92 155.08 1 1.50e+01 4.44e-03 8.14e+01 ... (remaining 102319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.120: 30603 1.120 - 2.240: 0 2.240 - 3.360: 0 3.360 - 4.480: 0 4.480 - 5.600: 4 Chirality restraints: 30607 Sorted by residual: chirality pdb=" C12 ERYBA9000 " pdb=" C11 ERYBA9000 " pdb=" C13 ERYBA9000 " pdb=" C35 ERYBA9000 " both_signs ideal model delta sigma weight residual False -2.75 2.85 -5.60 2.00e-01 2.50e+01 7.84e+02 chirality pdb=" C6 ERYBA9000 " pdb=" C32 ERYBA9000 " pdb=" C5 ERYBA9000 " pdb=" C7 ERYBA9000 " both_signs ideal model delta sigma weight residual False -2.75 2.75 -5.51 2.00e-01 2.50e+01 7.59e+02 chirality pdb=" C16 ERYBA9000 " pdb=" C15 ERYBA9000 " pdb=" C17 ERYBA9000 " pdb=" C19 ERYBA9000 " both_signs ideal model delta sigma weight residual False 2.68 -2.71 5.38 2.00e-01 2.50e+01 7.25e+02 ... (remaining 30604 not shown) Planarity restraints: 12515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MGAY 46 " -0.854 2.00e-02 2.50e+03 5.75e-01 7.45e+03 pdb=" C4' 7MGAY 46 " 0.221 2.00e-02 2.50e+03 pdb=" O4' 7MGAY 46 " 0.685 2.00e-02 2.50e+03 pdb=" C3' 7MGAY 46 " -0.221 2.00e-02 2.50e+03 pdb=" O3' 7MGAY 46 " 0.891 2.00e-02 2.50e+03 pdb=" C2' 7MGAY 46 " -0.605 2.00e-02 2.50e+03 pdb=" O2' 7MGAY 46 " -0.571 2.00e-02 2.50e+03 pdb=" C1' 7MGAY 46 " 0.443 2.00e-02 2.50e+03 pdb=" N9 7MGAY 46 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MUAW 54 " -0.039 2.00e-02 2.50e+03 5.72e-01 7.35e+03 pdb=" C4' 5MUAW 54 " -0.432 2.00e-02 2.50e+03 pdb=" O4' 5MUAW 54 " -0.613 2.00e-02 2.50e+03 pdb=" C3' 5MUAW 54 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 5MUAW 54 " 0.580 2.00e-02 2.50e+03 pdb=" C2' 5MUAW 54 " 0.203 2.00e-02 2.50e+03 pdb=" O2' 5MUAW 54 " -0.922 2.00e-02 2.50e+03 pdb=" C1' 5MUAW 54 " -0.231 2.00e-02 2.50e+03 pdb=" N1 5MUAW 54 " 0.865 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MUAX 54 " 0.033 2.00e-02 2.50e+03 5.68e-01 7.25e+03 pdb=" C4' 5MUAX 54 " 0.432 2.00e-02 2.50e+03 pdb=" O4' 5MUAX 54 " 0.618 2.00e-02 2.50e+03 pdb=" C3' 5MUAX 54 " -0.588 2.00e-02 2.50e+03 pdb=" O3' 5MUAX 54 " -0.567 2.00e-02 2.50e+03 pdb=" C2' 5MUAX 54 " -0.209 2.00e-02 2.50e+03 pdb=" O2' 5MUAX 54 " 0.909 2.00e-02 2.50e+03 pdb=" C1' 5MUAX 54 " 0.231 2.00e-02 2.50e+03 pdb=" N1 5MUAX 54 " -0.859 2.00e-02 2.50e+03 ... (remaining 12512 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 2 2.13 - 2.82: 39943 2.82 - 3.51: 188098 3.51 - 4.21: 475299 4.21 - 4.90: 619080 Nonbonded interactions: 1322422 Sorted by model distance: nonbonded pdb=" O3' AAW 76 " pdb=" C LYSAW 101 " model vdw 1.432 3.270 nonbonded pdb=" O3' AAX 76 " pdb=" C ASPB5 0 " model vdw 1.434 3.270 nonbonded pdb=" OD1 ASNAD 100 " pdb=" NH1 ARGAD 111 " model vdw 2.134 2.520 nonbonded pdb=" O ALAAF 27 " pdb=" OG1 THRAF 30 " model vdw 2.151 2.440 nonbonded pdb=" O2 CBA 335 " pdb=" OG SERBU 68 " model vdw 2.156 2.440 ... (remaining 1322417 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 16.430 Check model and map are aligned: 1.620 Set scattering table: 1.040 Process input model: 526.760 Find NCS groups from input model: 2.810 Set up NCS constraints: 0.330 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 554.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5455 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 0.352 159666 Z= 0.901 Angle : 1.747 22.349 239286 Z= 0.669 Chirality : 0.066 5.600 30607 Planarity : 0.013 0.575 12515 Dihedral : 22.202 179.857 91994 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 2.68 % Allowed : 7.35 % Favored : 89.97 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % Twisted General : 0.00 % 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: -1.94 (0.11), residues: 5522 helix: -3.26 (0.07), residues: 1551 sheet: -3.18 (0.14), residues: 864 loop : 0.65 (0.12), residues: 3107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRPBC 213 HIS 0.005 0.001 HISBS 7 PHE 0.017 0.001 PHEBC 30 TYR 0.018 0.001 TYRAD 75 ARG 0.009 0.000 ARGAK 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1478 time to evaluate : 6.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 132 LYS cc_start: 0.5333 (tttt) cc_final: 0.4960 (mmtt) REVERT: AB 154 MET cc_start: 0.3052 (ttm) cc_final: 0.2291 (ttm) REVERT: AC 19 ASN cc_start: 0.3574 (m-40) cc_final: 0.3015 (t0) REVERT: AD 76 TYR cc_start: 0.5529 (t80) cc_final: 0.5211 (t80) REVERT: AF 42 TRP cc_start: 0.4197 (m-10) cc_final: 0.3682 (t-100) REVERT: AG 123 GLU cc_start: 0.3993 (tp30) cc_final: 0.3756 (tp30) REVERT: AG 141 VAL cc_start: 0.6224 (t) cc_final: 0.4692 (t) REVERT: AH 25 VAL cc_start: 0.7126 (t) cc_final: 0.6754 (m) REVERT: AI 98 LEU cc_start: 0.5626 (tp) cc_final: 0.5072 (tt) REVERT: AK 24 HIS cc_start: 0.4350 (t70) cc_final: 0.4147 (t-170) REVERT: AL 35 THR cc_start: 0.6560 (m) cc_final: 0.6311 (p) REVERT: AM 107 ARG cc_start: 0.6918 (tpp-160) cc_final: 0.6414 (mmp80) REVERT: AO 32 LEU cc_start: 0.7748 (mt) cc_final: 0.7503 (mp) REVERT: AT 26 SER cc_start: 0.7413 (t) cc_final: 0.6855 (p) REVERT: AT 69 LYS cc_start: 0.5839 (pttm) cc_final: 0.5422 (tptt) REVERT: AU 33 ARG cc_start: 0.4963 (ttt180) cc_final: 0.4576 (ptt180) REVERT: BC 181 MET cc_start: 0.5941 (mmm) cc_final: 0.5696 (mtt) REVERT: BD 25 THR cc_start: 0.7116 (m) cc_final: 0.6861 (m) REVERT: BD 52 THR cc_start: 0.7126 (t) cc_final: 0.6912 (p) REVERT: BD 114 LYS cc_start: 0.6380 (mttm) cc_final: 0.6131 (mtmt) REVERT: BE 77 ILE cc_start: 0.8083 (tt) cc_final: 0.7876 (tt) REVERT: BF 92 ARG cc_start: 0.3106 (ptp90) cc_final: 0.2868 (ptp90) REVERT: BF 103 LEU cc_start: 0.4969 (tp) cc_final: 0.4698 (tp) REVERT: BG 140 VAL cc_start: 0.5763 (t) cc_final: 0.5539 (p) REVERT: BJ 41 LYS cc_start: 0.7420 (mttt) cc_final: 0.6706 (mmtt) REVERT: BL 19 LEU cc_start: 0.7539 (mp) cc_final: 0.7316 (mp) REVERT: BL 90 VAL cc_start: 0.7228 (t) cc_final: 0.6957 (p) REVERT: BM 1 MET cc_start: 0.4344 (mtp) cc_final: 0.3573 (mtp) REVERT: BM 42 THR cc_start: 0.7349 (p) cc_final: 0.7065 (p) REVERT: BM 78 LEU cc_start: 0.5286 (tt) cc_final: 0.5006 (mt) REVERT: BM 80 VAL cc_start: 0.5798 (t) cc_final: 0.5557 (t) REVERT: BM 82 MET cc_start: 0.7529 (mmp) cc_final: 0.6751 (mmm) REVERT: BM 90 GLU cc_start: 0.6404 (mm-30) cc_final: 0.6097 (mm-30) REVERT: BM 112 LEU cc_start: 0.6506 (mp) cc_final: 0.6216 (tp) REVERT: BP 92 VAL cc_start: 0.7722 (m) cc_final: 0.7505 (m) REVERT: BQ 17 ILE cc_start: 0.7836 (mm) cc_final: 0.7604 (mm) REVERT: BQ 47 TYR cc_start: 0.8347 (t80) cc_final: 0.8008 (t80) REVERT: BR 75 VAL cc_start: 0.8292 (t) cc_final: 0.8073 (t) REVERT: BS 38 TYR cc_start: 0.5602 (m-80) cc_final: 0.5340 (m-10) REVERT: BT 64 LYS cc_start: 0.5684 (mptt) cc_final: 0.5428 (mttp) REVERT: BT 91 GLN cc_start: 0.5293 (pm20) cc_final: 0.3912 (pp30) REVERT: BU 83 VAL cc_start: 0.5526 (t) cc_final: 0.5254 (t) REVERT: BV 47 VAL cc_start: 0.7068 (t) cc_final: 0.6752 (t) REVERT: BW 67 VAL cc_start: 0.7238 (t) cc_final: 0.7023 (t) REVERT: BX 35 SER cc_start: 0.6632 (t) cc_final: 0.6412 (m) REVERT: BY 26 PHE cc_start: 0.5423 (t80) cc_final: 0.4731 (t80) REVERT: B1 46 HIS cc_start: 0.6286 (m90) cc_final: 0.6007 (m-70) REVERT: B3 26 HIS cc_start: 0.7260 (m-70) cc_final: 0.6728 (m-70) outliers start: 0 outliers final: 0 residues processed: 1478 average time/residue: 1.5140 time to fit residues: 3650.8244 Evaluate side-chains 897 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 897 time to evaluate : 6.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1015 random chunks: chunk 857 optimal weight: 7.9990 chunk 769 optimal weight: 2.9990 chunk 426 optimal weight: 0.8980 chunk 262 optimal weight: 8.9990 chunk 518 optimal weight: 2.9990 chunk 411 optimal weight: 5.9990 chunk 795 optimal weight: 8.9990 chunk 307 optimal weight: 3.9990 chunk 483 optimal weight: 0.9980 chunk 592 optimal weight: 9.9990 chunk 921 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 15 HIS ** AB 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 102 ASN AC 176 HIS ** AD 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AD 74 ASN ** AD 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AD 136 GLN AF 37 HIS AF 55 HIS AG 148 ASN AJ 64 GLN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 46 ASN AN 62 ASN AP 63 GLN AQ 31 HIS ** AS 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AT 21 ASN AT 52 ASN AT 78 ASN BC 53 HIS BC 90 ASN BC 134 ASN BC 163 GLN ** BC 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 164 GLN BE 41 GLN ** BE 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 163 ASN BF 63 GLN BF 127 ASN ** BG 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 115 HIS BG 116 GLN ** BI 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BJ 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BK 9 ASN BK 29 HIS BM 45 GLN ** BN 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 34 HIS BP 12 GLN BP 66 ASN BQ 37 GLN ** BQ 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 56 GLN BQ 72 ASN BR 6 GLN BS 7 HIS BS 60 HIS ** BT 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BU 74 ASN BV 44 HIS ** BV 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 17 ASN BX 36 HIS BY 27 ASN BZ 20 HIS BZ 34 HIS B0 41 HIS B4 13 ASN ** B4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5626 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 159666 Z= 0.191 Angle : 0.650 27.044 239286 Z= 0.326 Chirality : 0.039 2.020 30607 Planarity : 0.006 0.143 12515 Dihedral : 23.087 179.931 80910 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.96 % Allowed : 6.54 % Favored : 92.50 % Rotamer: Outliers : 2.50 % Allowed : 9.42 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % Twisted General : 0.00 % 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: -1.68 (0.11), residues: 5522 helix: -1.45 (0.11), residues: 1653 sheet: -2.94 (0.14), residues: 894 loop : -0.10 (0.12), residues: 2975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPAQ 73 HIS 0.012 0.001 HISBM 13 PHE 0.028 0.002 PHEBM 117 TYR 0.022 0.002 TYRAR 64 ARG 0.018 0.001 ARGAJ 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1046 time to evaluate : 6.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 132 LYS cc_start: 0.5003 (tttt) cc_final: 0.4653 (mmtt) REVERT: AB 154 MET cc_start: 0.2932 (ttm) cc_final: 0.2347 (ttm) REVERT: AC 52 VAL cc_start: 0.5692 (p) cc_final: 0.5474 (m) REVERT: AD 76 TYR cc_start: 0.5896 (t80) cc_final: 0.5378 (t80) REVERT: AD 117 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7289 (mp) REVERT: AD 198 HIS cc_start: 0.5043 (t70) cc_final: 0.4724 (t-170) REVERT: AE 137 VAL cc_start: 0.7216 (t) cc_final: 0.6921 (m) REVERT: AF 8 PHE cc_start: 0.5235 (p90) cc_final: 0.4962 (p90) REVERT: AF 42 TRP cc_start: 0.4172 (m-10) cc_final: 0.3857 (t-100) REVERT: AG 28 ASN cc_start: 0.7134 (m-40) cc_final: 0.6914 (t0) REVERT: AG 123 GLU cc_start: 0.4268 (tp30) cc_final: 0.3928 (tp30) REVERT: AH 25 VAL cc_start: 0.6635 (t) cc_final: 0.6366 (m) REVERT: AJ 53 ILE cc_start: 0.7162 (tp) cc_final: 0.6860 (tp) REVERT: AL 94 ARG cc_start: 0.5816 (mtt180) cc_final: 0.4934 (mpp80) REVERT: AM 95 LEU cc_start: 0.6533 (mt) cc_final: 0.6208 (mm) REVERT: AQ 17 MET cc_start: 0.3586 (ppp) cc_final: 0.2323 (ptt) REVERT: AT 26 SER cc_start: 0.7181 (t) cc_final: 0.6563 (p) REVERT: AT 69 LYS cc_start: 0.5739 (pttm) cc_final: 0.5231 (tptt) REVERT: AU 33 ARG cc_start: 0.5317 (ttt180) cc_final: 0.4910 (ptt-90) REVERT: BC 177 ARG cc_start: 0.6621 (tpm170) cc_final: 0.5975 (tpt170) REVERT: BC 258 ARG cc_start: 0.6328 (ttt-90) cc_final: 0.6083 (ttt-90) REVERT: BD 22 ILE cc_start: 0.7452 (pt) cc_final: 0.6781 (mt) REVERT: BD 52 THR cc_start: 0.6952 (t) cc_final: 0.6605 (p) REVERT: BD 77 ARG cc_start: 0.6794 (ptm-80) cc_final: 0.6451 (ptm-80) REVERT: BE 51 GLU cc_start: 0.5429 (tp30) cc_final: 0.5159 (tp30) REVERT: BE 67 ARG cc_start: 0.7005 (mmm-85) cc_final: 0.6446 (mmt90) REVERT: BE 143 LEU cc_start: 0.4386 (mt) cc_final: 0.3937 (mp) REVERT: BF 81 GLN cc_start: 0.6268 (mm-40) cc_final: 0.6050 (mm110) REVERT: BG 75 MET cc_start: 0.4233 (OUTLIER) cc_final: 0.3895 (mmp) REVERT: BJ 41 LYS cc_start: 0.7269 (mttt) cc_final: 0.6684 (tptm) REVERT: BJ 67 ASN cc_start: 0.5723 (t0) cc_final: 0.5148 (t0) REVERT: BJ 109 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6341 (mm) REVERT: BK 106 GLU cc_start: 0.6045 (mp0) cc_final: 0.5235 (mm-30) REVERT: BL 103 ILE cc_start: 0.6036 (mp) cc_final: 0.5577 (mt) REVERT: BM 1 MET cc_start: 0.4730 (mtp) cc_final: 0.3803 (mtp) REVERT: BM 78 LEU cc_start: 0.5523 (tt) cc_final: 0.5062 (mt) REVERT: BM 82 MET cc_start: 0.7637 (mmp) cc_final: 0.7148 (mmp) REVERT: BM 90 GLU cc_start: 0.6438 (mm-30) cc_final: 0.6220 (mm-30) REVERT: BO 100 HIS cc_start: 0.6314 (t70) cc_final: 0.6106 (t70) REVERT: BP 13 MET cc_start: 0.7010 (mtp) cc_final: 0.6789 (mtp) REVERT: BQ 20 GLN cc_start: 0.7193 (mp10) cc_final: 0.6396 (mm-40) REVERT: BS 52 GLU cc_start: 0.5554 (tp30) cc_final: 0.5349 (tp30) REVERT: BT 15 HIS cc_start: 0.7245 (t-90) cc_final: 0.6469 (t-90) REVERT: BT 64 LYS cc_start: 0.5931 (mptt) cc_final: 0.5321 (mttt) REVERT: BT 91 GLN cc_start: 0.5287 (pm20) cc_final: 0.4524 (pp30) REVERT: BX 35 SER cc_start: 0.6718 (t) cc_final: 0.6454 (m) REVERT: B0 10 ARG cc_start: 0.7001 (ptp90) cc_final: 0.6513 (ptm160) REVERT: B3 26 HIS cc_start: 0.7273 (m-70) cc_final: 0.6995 (m-70) outliers start: 115 outliers final: 62 residues processed: 1099 average time/residue: 1.3995 time to fit residues: 2607.3825 Evaluate side-chains 937 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 872 time to evaluate : 6.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 183 VAL Chi-restraints excluded: chain AC residue 173 VAL Chi-restraints excluded: chain AD residue 117 LEU Chi-restraints excluded: chain AD residue 136 GLN Chi-restraints excluded: chain AD residue 203 LEU Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AG residue 50 LEU Chi-restraints excluded: chain AG residue 94 VAL Chi-restraints excluded: chain AH residue 99 LEU Chi-restraints excluded: chain AI residue 87 LEU Chi-restraints excluded: chain AL residue 37 VAL Chi-restraints excluded: chain AL residue 52 VAL Chi-restraints excluded: chain AL residue 79 VAL Chi-restraints excluded: chain AL residue 81 LEU Chi-restraints excluded: chain AL residue 82 ILE Chi-restraints excluded: chain AL residue 97 THR Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AM residue 114 LYS Chi-restraints excluded: chain AN residue 16 LEU Chi-restraints excluded: chain AN residue 79 LEU Chi-restraints excluded: chain AO residue 12 VAL Chi-restraints excluded: chain AP residue 75 ILE Chi-restraints excluded: chain AQ residue 29 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AR residue 42 SER Chi-restraints excluded: chain AT residue 84 ASN Chi-restraints excluded: chain BC residue 64 ILE Chi-restraints excluded: chain BC residue 192 LEU Chi-restraints excluded: chain BD residue 62 LYS Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 207 VAL Chi-restraints excluded: chain BE residue 12 LEU Chi-restraints excluded: chain BE residue 73 ILE Chi-restraints excluded: chain BE residue 97 ASN Chi-restraints excluded: chain BE residue 133 LEU Chi-restraints excluded: chain BE residue 169 VAL Chi-restraints excluded: chain BF residue 118 SER Chi-restraints excluded: chain BG residue 10 VAL Chi-restraints excluded: chain BG residue 75 MET Chi-restraints excluded: chain BG residue 133 LEU Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BJ residue 109 LEU Chi-restraints excluded: chain BK residue 62 VAL Chi-restraints excluded: chain BK residue 65 THR Chi-restraints excluded: chain BL residue 77 ILE Chi-restraints excluded: chain BM residue 136 MET Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 59 SER Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BP residue 76 THR Chi-restraints excluded: chain BQ residue 110 VAL Chi-restraints excluded: chain BR residue 72 VAL Chi-restraints excluded: chain BS residue 71 VAL Chi-restraints excluded: chain BT residue 22 THR Chi-restraints excluded: chain BT residue 63 VAL Chi-restraints excluded: chain BU residue 68 SER Chi-restraints excluded: chain BW residue 35 SER Chi-restraints excluded: chain BX residue 58 VAL Chi-restraints excluded: chain BZ residue 32 ILE Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B1 residue 48 ILE Chi-restraints excluded: chain B2 residue 24 THR Chi-restraints excluded: chain B3 residue 6 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1015 random chunks: chunk 512 optimal weight: 20.0000 chunk 286 optimal weight: 20.0000 chunk 767 optimal weight: 9.9990 chunk 627 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 923 optimal weight: 0.4980 chunk 997 optimal weight: 20.0000 chunk 822 optimal weight: 5.9990 chunk 915 optimal weight: 3.9990 chunk 314 optimal weight: 10.0000 chunk 740 optimal weight: 0.9980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 177 ASN ** AD 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AD 74 ASN ** AD 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 136 GLN AF 63 ASN AI 81 HIS AJ 64 GLN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 96 HIS AM 14 HIS AN 60 GLN ** AS 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AT 3 ASN AT 48 GLN AT 52 ASN AT 75 HIS ** AT 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 134 ASN ** BD 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 126 ASN BD 150 GLN BD 173 GLN ** BE 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 63 GLN BF 127 ASN ** BG 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 12 GLN BJ 40 HIS BK 9 ASN ** BM 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 34 HIS ** BQ 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BR 12 HIS BS 15 GLN BT 28 ASN ** BU 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BW 76 ASN ** BX 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 36 HIS BY 58 ASN B0 6 ASN B1 19 HIS B1 46 HIS B4 13 ASN B4 35 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5849 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 159666 Z= 0.238 Angle : 0.703 27.142 239286 Z= 0.359 Chirality : 0.042 2.197 30607 Planarity : 0.007 0.144 12515 Dihedral : 23.181 179.120 80910 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.08 % Favored : 92.01 % Rotamer: Outliers : 3.63 % Allowed : 12.60 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % Twisted General : 0.00 % 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: -1.75 (0.11), residues: 5522 helix: -0.89 (0.12), residues: 1673 sheet: -2.54 (0.15), residues: 871 loop : -0.76 (0.11), residues: 2978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRPBR 92 HIS 0.023 0.002 HISBM 13 PHE 0.031 0.003 PHEBM 9 TYR 0.029 0.003 TYRBP 98 ARG 0.019 0.001 ARGAF 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1045 time to evaluate : 6.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 66 LYS cc_start: 0.3511 (OUTLIER) cc_final: 0.3193 (pttm) REVERT: AB 132 LYS cc_start: 0.5375 (tttt) cc_final: 0.4794 (mmtt) REVERT: AC 52 VAL cc_start: 0.5392 (p) cc_final: 0.5191 (m) REVERT: AC 129 MET cc_start: 0.5278 (mtt) cc_final: 0.4836 (mtp) REVERT: AD 76 TYR cc_start: 0.6083 (t80) cc_final: 0.5690 (t80) REVERT: AE 11 LEU cc_start: 0.5129 (OUTLIER) cc_final: 0.4855 (pp) REVERT: AE 50 TYR cc_start: 0.6079 (t80) cc_final: 0.5248 (t80) REVERT: AE 115 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7027 (mm) REVERT: AF 8 PHE cc_start: 0.6207 (p90) cc_final: 0.5977 (p90) REVERT: AF 63 ASN cc_start: 0.6337 (t0) cc_final: 0.5917 (t0) REVERT: AG 26 PHE cc_start: 0.6681 (t80) cc_final: 0.6409 (t80) REVERT: AH 46 ILE cc_start: 0.7945 (mm) cc_final: 0.7528 (pt) REVERT: AH 80 ARG cc_start: 0.7842 (mtm110) cc_final: 0.7524 (mtm180) REVERT: AL 36 ARG cc_start: 0.6137 (ptp-170) cc_final: 0.5820 (ptt180) REVERT: AL 88 LYS cc_start: 0.4791 (ptmt) cc_final: 0.4473 (pttm) REVERT: AN 83 LYS cc_start: 0.7169 (mmmt) cc_final: 0.6793 (mmmt) REVERT: AR 21 ILE cc_start: 0.4005 (OUTLIER) cc_final: 0.3791 (mt) REVERT: AR 38 LYS cc_start: 0.5575 (mmtt) cc_final: 0.4720 (mtmt) REVERT: AS 10 PHE cc_start: 0.6406 (t80) cc_final: 0.5032 (m-80) REVERT: AT 49 LYS cc_start: 0.6491 (tppt) cc_final: 0.6054 (mmtm) REVERT: AT 61 GLN cc_start: 0.4859 (mm-40) cc_final: 0.4597 (mm-40) REVERT: AT 69 LYS cc_start: 0.5851 (pttm) cc_final: 0.5254 (tttp) REVERT: AU 32 VAL cc_start: 0.6116 (t) cc_final: 0.5876 (t) REVERT: BC 100 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5491 (tp30) REVERT: BC 177 ARG cc_start: 0.6902 (tpm170) cc_final: 0.6677 (tpm170) REVERT: BD 22 ILE cc_start: 0.7757 (pt) cc_final: 0.7007 (mt) REVERT: BD 52 THR cc_start: 0.7394 (t) cc_final: 0.6894 (p) REVERT: BD 84 LEU cc_start: 0.4634 (mt) cc_final: 0.3865 (tt) REVERT: BD 100 LEU cc_start: 0.5537 (pp) cc_final: 0.5246 (mt) REVERT: BD 165 MET cc_start: 0.7749 (ttt) cc_final: 0.7534 (ttt) REVERT: BD 167 ASN cc_start: 0.7518 (t0) cc_final: 0.7287 (t0) REVERT: BE 25 GLU cc_start: 0.6527 (mp0) cc_final: 0.5762 (mt-10) REVERT: BF 36 LEU cc_start: 0.8259 (tt) cc_final: 0.7904 (pp) REVERT: BI 136 MET cc_start: 0.2774 (mpp) cc_final: 0.2398 (mmm) REVERT: BJ 41 LYS cc_start: 0.7425 (mttt) cc_final: 0.6840 (tptm) REVERT: BJ 67 ASN cc_start: 0.6184 (t0) cc_final: 0.5239 (t0) REVERT: BJ 71 ASP cc_start: 0.7958 (m-30) cc_final: 0.7433 (m-30) REVERT: BK 18 ARG cc_start: 0.6457 (tpp-160) cc_final: 0.5866 (mmm-85) REVERT: BK 29 HIS cc_start: 0.5570 (m170) cc_final: 0.5289 (m170) REVERT: BK 95 ILE cc_start: 0.5587 (mm) cc_final: 0.5337 (mp) REVERT: BK 106 GLU cc_start: 0.5975 (mp0) cc_final: 0.5090 (mm-30) REVERT: BK 113 MET cc_start: 0.4039 (mmm) cc_final: 0.3740 (mmp) REVERT: BL 55 MET cc_start: 0.7173 (tpp) cc_final: 0.6916 (mmt) REVERT: BM 44 ARG cc_start: 0.6937 (mmt90) cc_final: 0.6584 (mmm-85) REVERT: BM 78 LEU cc_start: 0.5447 (tt) cc_final: 0.5167 (mt) REVERT: BM 136 MET cc_start: 0.2655 (ttp) cc_final: 0.1948 (ttp) REVERT: BN 20 MET cc_start: 0.6941 (tmm) cc_final: 0.6658 (tpp) REVERT: BN 49 GLU cc_start: 0.6043 (mt-10) cc_final: 0.5800 (mt-10) REVERT: BN 76 VAL cc_start: 0.7436 (p) cc_final: 0.7208 (t) REVERT: BO 115 LEU cc_start: 0.5607 (tp) cc_final: 0.5387 (tt) REVERT: BQ 20 GLN cc_start: 0.6965 (mp10) cc_final: 0.6570 (mm-40) REVERT: BS 31 GLN cc_start: 0.6973 (tm-30) cc_final: 0.6759 (tt0) REVERT: BS 62 ASP cc_start: 0.3906 (OUTLIER) cc_final: 0.3206 (m-30) REVERT: BS 84 ARG cc_start: 0.7927 (mmt-90) cc_final: 0.7508 (mmt-90) REVERT: BS 88 ARG cc_start: 0.7130 (mmm-85) cc_final: 0.6788 (mtp85) REVERT: BT 15 HIS cc_start: 0.6748 (t-90) cc_final: 0.6485 (t70) REVERT: BT 91 GLN cc_start: 0.5329 (pm20) cc_final: 0.4661 (pp30) REVERT: BV 93 ARG cc_start: 0.4800 (mtt90) cc_final: 0.4524 (mtm-85) REVERT: BY 30 MET cc_start: 0.5544 (OUTLIER) cc_final: 0.5148 (mmp) REVERT: BY 56 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7193 (tt) REVERT: BZ 16 ARG cc_start: 0.5586 (mmp80) cc_final: 0.5242 (mmm160) REVERT: B0 10 ARG cc_start: 0.6964 (ptp90) cc_final: 0.6225 (ptm160) REVERT: B4 11 CYS cc_start: 0.6441 (p) cc_final: 0.4106 (m) outliers start: 167 outliers final: 98 residues processed: 1139 average time/residue: 1.3755 time to fit residues: 2661.4593 Evaluate side-chains 984 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 878 time to evaluate : 6.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 66 LYS Chi-restraints excluded: chain AB residue 183 VAL Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AC residue 67 THR Chi-restraints excluded: chain AC residue 87 LEU Chi-restraints excluded: chain AC residue 173 VAL Chi-restraints excluded: chain AD residue 53 VAL Chi-restraints excluded: chain AD residue 113 GLU Chi-restraints excluded: chain AD residue 203 LEU Chi-restraints excluded: chain AE residue 11 LEU Chi-restraints excluded: chain AE residue 22 SER Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AE residue 105 ILE Chi-restraints excluded: chain AE residue 115 LEU Chi-restraints excluded: chain AF residue 38 ARG Chi-restraints excluded: chain AG residue 6 VAL Chi-restraints excluded: chain AG residue 50 LEU Chi-restraints excluded: chain AG residue 94 VAL Chi-restraints excluded: chain AH residue 101 ILE Chi-restraints excluded: chain AH residue 106 THR Chi-restraints excluded: chain AI residue 116 VAL Chi-restraints excluded: chain AJ residue 51 VAL Chi-restraints excluded: chain AL residue 37 VAL Chi-restraints excluded: chain AL residue 65 SER Chi-restraints excluded: chain AL residue 79 VAL Chi-restraints excluded: chain AL residue 82 ILE Chi-restraints excluded: chain AL residue 97 THR Chi-restraints excluded: chain AL residue 104 CYS Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AN residue 16 LEU Chi-restraints excluded: chain AN residue 82 ILE Chi-restraints excluded: chain AO residue 11 ILE Chi-restraints excluded: chain AO residue 12 VAL Chi-restraints excluded: chain AP residue 19 VAL Chi-restraints excluded: chain AP residue 70 ARG Chi-restraints excluded: chain AQ residue 29 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AQ residue 76 VAL Chi-restraints excluded: chain AR residue 21 ILE Chi-restraints excluded: chain AR residue 42 SER Chi-restraints excluded: chain AR residue 45 THR Chi-restraints excluded: chain AR residue 55 LEU Chi-restraints excluded: chain AT residue 58 VAL Chi-restraints excluded: chain AT residue 84 ASN Chi-restraints excluded: chain BC residue 64 ILE Chi-restraints excluded: chain BC residue 65 VAL Chi-restraints excluded: chain BC residue 100 GLU Chi-restraints excluded: chain BC residue 250 VAL Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 207 VAL Chi-restraints excluded: chain BE residue 73 ILE Chi-restraints excluded: chain BE residue 77 ILE Chi-restraints excluded: chain BE residue 84 THR Chi-restraints excluded: chain BE residue 105 LEU Chi-restraints excluded: chain BE residue 133 LEU Chi-restraints excluded: chain BE residue 146 VAL Chi-restraints excluded: chain BE residue 169 VAL Chi-restraints excluded: chain BF residue 25 VAL Chi-restraints excluded: chain BF residue 118 SER Chi-restraints excluded: chain BG residue 10 VAL Chi-restraints excluded: chain BG residue 90 VAL Chi-restraints excluded: chain BG residue 133 LEU Chi-restraints excluded: chain BH residue 3 VAL Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BJ residue 109 LEU Chi-restraints excluded: chain BK residue 57 VAL Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 62 VAL Chi-restraints excluded: chain BL residue 60 ARG Chi-restraints excluded: chain BL residue 77 ILE Chi-restraints excluded: chain BL residue 78 ARG Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BL residue 127 VAL Chi-restraints excluded: chain BL residue 135 ILE Chi-restraints excluded: chain BM residue 7 THR Chi-restraints excluded: chain BM residue 34 LYS Chi-restraints excluded: chain BM residue 42 THR Chi-restraints excluded: chain BM residue 67 VAL Chi-restraints excluded: chain BM residue 111 GLU Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 59 SER Chi-restraints excluded: chain BO residue 24 THR Chi-restraints excluded: chain BO residue 58 ILE Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BP residue 50 ILE Chi-restraints excluded: chain BP residue 55 LEU Chi-restraints excluded: chain BQ residue 110 VAL Chi-restraints excluded: chain BR residue 19 THR Chi-restraints excluded: chain BS residue 62 ASP Chi-restraints excluded: chain BS residue 71 VAL Chi-restraints excluded: chain BS residue 105 VAL Chi-restraints excluded: chain BU residue 25 VAL Chi-restraints excluded: chain BU residue 28 VAL Chi-restraints excluded: chain BU residue 68 SER Chi-restraints excluded: chain BW residue 35 SER Chi-restraints excluded: chain BX residue 58 VAL Chi-restraints excluded: chain BY residue 30 MET Chi-restraints excluded: chain BY residue 56 LEU Chi-restraints excluded: chain BZ residue 23 THR Chi-restraints excluded: chain BZ residue 32 ILE Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B2 residue 26 ASN Chi-restraints excluded: chain B3 residue 6 THR Chi-restraints excluded: chain B3 residue 7 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1015 random chunks: chunk 912 optimal weight: 10.0000 chunk 694 optimal weight: 10.0000 chunk 479 optimal weight: 10.0000 chunk 102 optimal weight: 40.0000 chunk 440 optimal weight: 10.0000 chunk 620 optimal weight: 20.0000 chunk 926 optimal weight: 2.9990 chunk 981 optimal weight: 0.8980 chunk 484 optimal weight: 10.0000 chunk 878 optimal weight: 8.9990 chunk 264 optimal weight: 0.0170 overall best weight: 4.5826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 177 ASN ** AD 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 63 ASN AG 130 ASN ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 46 ASN AN 60 GLN AO 28 GLN ** AP 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AT 20 HIS AT 55 GLN ** AT 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 58 HIS BC 163 GLN BC 260 ASN BE 30 GLN ** BE 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 139 GLN BG 143 GLN BH 2 GLN BK 9 ASN ** BK 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 107 ASN BO 34 HIS BS 60 HIS BT 28 ASN BZ 9 GLN BZ 34 HIS B0 19 HIS B0 38 HIS B2 13 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 159666 Z= 0.250 Angle : 0.704 26.955 239286 Z= 0.356 Chirality : 0.042 2.075 30607 Planarity : 0.007 0.149 12515 Dihedral : 23.240 179.866 80910 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.89 % Allowed : 6.70 % Favored : 92.41 % Rotamer: Outliers : 4.66 % Allowed : 14.78 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % 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: -1.89 (0.11), residues: 5522 helix: -0.78 (0.12), residues: 1687 sheet: -2.33 (0.15), residues: 893 loop : -1.09 (0.11), residues: 2942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRPBX 39 HIS 0.011 0.002 HISBX 34 PHE 0.034 0.003 PHEBO 97 TYR 0.033 0.003 TYRAH 128 ARG 0.023 0.001 ARGBF 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 982 time to evaluate : 6.222 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: AB 132 LYS cc_start: 0.5433 (tttt) cc_final: 0.4880 (mmtt) REVERT: AB 167 ASP cc_start: 0.3503 (p0) cc_final: 0.2552 (t70) REVERT: AC 127 ARG cc_start: 0.5688 (OUTLIER) cc_final: 0.5317 (ptt-90) REVERT: AD 105 MET cc_start: 0.2916 (mtp) cc_final: 0.2686 (mtt) REVERT: AD 135 TYR cc_start: 0.6513 (t80) cc_final: 0.6097 (t80) REVERT: AE 11 LEU cc_start: 0.5541 (OUTLIER) cc_final: 0.5084 (tp) REVERT: AE 62 LYS cc_start: 0.5474 (mmmt) cc_final: 0.5121 (mtpp) REVERT: AE 115 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6954 (mm) REVERT: AF 9 MET cc_start: 0.7252 (mmt) cc_final: 0.6376 (tpp) REVERT: AG 26 PHE cc_start: 0.6724 (t80) cc_final: 0.6508 (t80) REVERT: AG 74 GLU cc_start: 0.5579 (tp30) cc_final: 0.4885 (tp30) REVERT: AH 46 ILE cc_start: 0.8160 (mm) cc_final: 0.7768 (pt) REVERT: AH 128 TYR cc_start: 0.7304 (m-80) cc_final: 0.7103 (m-80) REVERT: AI 83 ILE cc_start: 0.7886 (mp) cc_final: 0.7584 (mm) REVERT: AJ 62 ARG cc_start: 0.6610 (mtp-110) cc_final: 0.6381 (ttm-80) REVERT: AL 21 VAL cc_start: 0.6824 (OUTLIER) cc_final: 0.6551 (m) REVERT: AM 27 LYS cc_start: 0.7058 (tttp) cc_final: 0.6146 (tmtt) REVERT: AN 21 PHE cc_start: 0.3031 (OUTLIER) cc_final: 0.1460 (m-80) REVERT: AN 83 LYS cc_start: 0.7175 (mmmt) cc_final: 0.6818 (mmmt) REVERT: AO 59 MET cc_start: 0.7362 (mmm) cc_final: 0.7016 (mmt) REVERT: AP 74 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6130 (mt) REVERT: AR 21 ILE cc_start: 0.3934 (OUTLIER) cc_final: 0.3709 (mt) REVERT: AT 83 ILE cc_start: 0.2486 (OUTLIER) cc_final: 0.2250 (pt) REVERT: AU 29 LEU cc_start: 0.1954 (OUTLIER) cc_final: 0.1738 (tt) REVERT: BC 28 LYS cc_start: 0.7092 (mttt) cc_final: 0.6468 (mmtt) REVERT: BC 100 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5366 (tp30) REVERT: BC 163 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7574 (tp40) REVERT: BC 177 ARG cc_start: 0.6825 (tpm170) cc_final: 0.6557 (tpm170) REVERT: BD 14 ILE cc_start: 0.6045 (mm) cc_final: 0.5495 (mt) REVERT: BD 22 ILE cc_start: 0.7754 (pt) cc_final: 0.6984 (mt) REVERT: BD 99 GLU cc_start: 0.5519 (mp0) cc_final: 0.5295 (pt0) REVERT: BE 5 LEU cc_start: 0.3206 (mp) cc_final: 0.2967 (mt) REVERT: BE 25 GLU cc_start: 0.6846 (mp0) cc_final: 0.5937 (mt-10) REVERT: BE 46 GLN cc_start: 0.7146 (mt0) cc_final: 0.6808 (mt0) REVERT: BG 88 GLN cc_start: 0.5957 (tt0) cc_final: 0.5707 (tt0) REVERT: BH 27 ARG cc_start: 0.6037 (mmp80) cc_final: 0.5394 (mtm-85) REVERT: BI 136 MET cc_start: 0.3279 (mpp) cc_final: 0.2032 (mpp) REVERT: BJ 41 LYS cc_start: 0.7654 (mttt) cc_final: 0.6718 (tptm) REVERT: BJ 67 ASN cc_start: 0.5733 (t0) cc_final: 0.5112 (t0) REVERT: BJ 71 ASP cc_start: 0.7932 (m-30) cc_final: 0.7493 (m-30) REVERT: BK 18 ARG cc_start: 0.6274 (tpp-160) cc_final: 0.5417 (mmm-85) REVERT: BK 106 GLU cc_start: 0.6074 (mp0) cc_final: 0.5223 (mm-30) REVERT: BL 55 MET cc_start: 0.7293 (tpp) cc_final: 0.6976 (mmt) REVERT: BL 136 GLU cc_start: 0.6425 (tt0) cc_final: 0.6197 (tt0) REVERT: BM 114 ARG cc_start: 0.5144 (tpp80) cc_final: 0.4901 (tpp80) REVERT: BN 23 ASN cc_start: 0.7054 (m-40) cc_final: 0.6392 (t0) REVERT: BN 49 GLU cc_start: 0.5931 (mt-10) cc_final: 0.5625 (mt-10) REVERT: BR 84 ARG cc_start: 0.7624 (ptt180) cc_final: 0.7381 (ptm-80) REVERT: BR 90 ARG cc_start: 0.6985 (mtm-85) cc_final: 0.6604 (mtm180) REVERT: BS 82 MET cc_start: 0.5154 (mpp) cc_final: 0.4921 (mpp) REVERT: BS 84 ARG cc_start: 0.8037 (mmt-90) cc_final: 0.7590 (mmt-90) REVERT: BZ 16 ARG cc_start: 0.5862 (mmp80) cc_final: 0.5354 (mmm160) REVERT: BZ 45 ARG cc_start: 0.6251 (tpp-160) cc_final: 0.5870 (ttm-80) REVERT: BZ 47 MET cc_start: 0.5078 (mtp) cc_final: 0.4786 (mtm) REVERT: B0 10 ARG cc_start: 0.7499 (ptp90) cc_final: 0.7271 (ptp90) REVERT: B0 25 VAL cc_start: 0.5456 (OUTLIER) cc_final: 0.5150 (t) REVERT: B4 11 CYS cc_start: 0.6024 (p) cc_final: 0.4277 (m) outliers start: 214 outliers final: 131 residues processed: 1112 average time/residue: 1.3533 time to fit residues: 2558.3382 Evaluate side-chains 1006 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 863 time to evaluate : 6.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 40 ILE Chi-restraints excluded: chain AB residue 171 ILE Chi-restraints excluded: chain AB residue 183 VAL Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AC residue 127 ARG Chi-restraints excluded: chain AC residue 134 MET Chi-restraints excluded: chain AC residue 173 VAL Chi-restraints excluded: chain AC residue 202 ILE Chi-restraints excluded: chain AD residue 19 LEU Chi-restraints excluded: chain AD residue 203 LEU Chi-restraints excluded: chain AE residue 11 LEU Chi-restraints excluded: chain AE residue 22 SER Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AE residue 105 ILE Chi-restraints excluded: chain AE residue 115 LEU Chi-restraints excluded: chain AF residue 5 GLU Chi-restraints excluded: chain AG residue 6 VAL Chi-restraints excluded: chain AG residue 30 LEU Chi-restraints excluded: chain AG residue 94 VAL Chi-restraints excluded: chain AH residue 106 THR Chi-restraints excluded: chain AI residue 30 ILE Chi-restraints excluded: chain AI residue 87 LEU Chi-restraints excluded: chain AI residue 104 VAL Chi-restraints excluded: chain AI residue 116 VAL Chi-restraints excluded: chain AK residue 32 VAL Chi-restraints excluded: chain AK residue 33 THR Chi-restraints excluded: chain AK residue 114 THR Chi-restraints excluded: chain AL residue 21 VAL Chi-restraints excluded: chain AL residue 52 VAL Chi-restraints excluded: chain AL residue 65 SER Chi-restraints excluded: chain AL residue 79 VAL Chi-restraints excluded: chain AL residue 82 ILE Chi-restraints excluded: chain AL residue 97 THR Chi-restraints excluded: chain AL residue 104 CYS Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AN residue 16 LEU Chi-restraints excluded: chain AN residue 21 PHE Chi-restraints excluded: chain AN residue 64 CYS Chi-restraints excluded: chain AN residue 82 ILE Chi-restraints excluded: chain AO residue 12 VAL Chi-restraints excluded: chain AP residue 20 VAL Chi-restraints excluded: chain AP residue 31 ARG Chi-restraints excluded: chain AP residue 74 LEU Chi-restraints excluded: chain AP residue 75 ILE Chi-restraints excluded: chain AQ residue 29 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AR residue 21 ILE Chi-restraints excluded: chain AR residue 42 SER Chi-restraints excluded: chain AR residue 45 THR Chi-restraints excluded: chain AS residue 11 ILE Chi-restraints excluded: chain AS residue 63 THR Chi-restraints excluded: chain AT residue 26 SER Chi-restraints excluded: chain AT residue 83 ILE Chi-restraints excluded: chain AT residue 84 ASN Chi-restraints excluded: chain AU residue 29 LEU Chi-restraints excluded: chain BC residue 65 VAL Chi-restraints excluded: chain BC residue 100 GLU Chi-restraints excluded: chain BC residue 120 VAL Chi-restraints excluded: chain BC residue 163 GLN Chi-restraints excluded: chain BC residue 192 LEU Chi-restraints excluded: chain BC residue 228 VAL Chi-restraints excluded: chain BC residue 250 VAL Chi-restraints excluded: chain BD residue 40 LEU Chi-restraints excluded: chain BD residue 50 VAL Chi-restraints excluded: chain BD residue 62 LYS Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 207 VAL Chi-restraints excluded: chain BE residue 53 THR Chi-restraints excluded: chain BE residue 73 ILE Chi-restraints excluded: chain BE residue 77 ILE Chi-restraints excluded: chain BE residue 97 ASN Chi-restraints excluded: chain BE residue 110 SER Chi-restraints excluded: chain BE residue 133 LEU Chi-restraints excluded: chain BE residue 146 VAL Chi-restraints excluded: chain BE residue 169 VAL Chi-restraints excluded: chain BF residue 25 VAL Chi-restraints excluded: chain BF residue 51 ASP Chi-restraints excluded: chain BF residue 111 ILE Chi-restraints excluded: chain BF residue 123 ASP Chi-restraints excluded: chain BG residue 4 VAL Chi-restraints excluded: chain BG residue 10 VAL Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 60 ASP Chi-restraints excluded: chain BG residue 90 VAL Chi-restraints excluded: chain BG residue 121 ILE Chi-restraints excluded: chain BG residue 133 LEU Chi-restraints excluded: chain BG residue 168 VAL Chi-restraints excluded: chain BH residue 3 VAL Chi-restraints excluded: chain BI residue 13 VAL Chi-restraints excluded: chain BI residue 49 ILE Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BJ residue 109 LEU Chi-restraints excluded: chain BK residue 31 ARG Chi-restraints excluded: chain BK residue 57 VAL Chi-restraints excluded: chain BK residue 62 VAL Chi-restraints excluded: chain BK residue 76 VAL Chi-restraints excluded: chain BL residue 60 ARG Chi-restraints excluded: chain BL residue 81 ASP Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BL residue 116 VAL Chi-restraints excluded: chain BL residue 127 VAL Chi-restraints excluded: chain BM residue 34 LYS Chi-restraints excluded: chain BM residue 54 THR Chi-restraints excluded: chain BM residue 67 VAL Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 59 SER Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BP residue 28 VAL Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BP residue 48 ILE Chi-restraints excluded: chain BQ residue 9 ILE Chi-restraints excluded: chain BQ residue 110 VAL Chi-restraints excluded: chain BR residue 19 THR Chi-restraints excluded: chain BS residue 3 THR Chi-restraints excluded: chain BS residue 25 ARG Chi-restraints excluded: chain BS residue 71 VAL Chi-restraints excluded: chain BS residue 74 ILE Chi-restraints excluded: chain BS residue 105 VAL Chi-restraints excluded: chain BS residue 107 VAL Chi-restraints excluded: chain BT residue 85 VAL Chi-restraints excluded: chain BT residue 86 THR Chi-restraints excluded: chain BU residue 18 ASP Chi-restraints excluded: chain BU residue 49 VAL Chi-restraints excluded: chain BU residue 68 SER Chi-restraints excluded: chain BU residue 70 VAL Chi-restraints excluded: chain BV residue 89 ILE Chi-restraints excluded: chain BW residue 40 GLN Chi-restraints excluded: chain BW residue 51 VAL Chi-restraints excluded: chain BW residue 67 VAL Chi-restraints excluded: chain BX residue 58 VAL Chi-restraints excluded: chain BY residue 20 ASN Chi-restraints excluded: chain BZ residue 32 ILE Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B0 residue 25 VAL Chi-restraints excluded: chain B0 residue 44 THR Chi-restraints excluded: chain B1 residue 47 VAL Chi-restraints excluded: chain B2 residue 24 THR Chi-restraints excluded: chain B2 residue 26 ASN Chi-restraints excluded: chain B3 residue 6 THR Chi-restraints excluded: chain B3 residue 7 VAL Chi-restraints excluded: chain B3 residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1015 random chunks: chunk 817 optimal weight: 20.0000 chunk 556 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 730 optimal weight: 9.9990 chunk 404 optimal weight: 10.0000 chunk 837 optimal weight: 9.9990 chunk 678 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 500 optimal weight: 10.0000 chunk 880 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 63 ASN ** AJ 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 96 HIS AN 60 GLN AN 71 HIS AO 28 GLN AP 18 GLN ** AS 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AS 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 41 GLN ** BE 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 12 GLN ** BK 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 45 GLN BN 16 HIS BO 34 HIS ** BP 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 56 HIS ** BQ 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BR 6 GLN BS 7 HIS BT 28 ASN ** BX 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BZ 9 GLN B0 4 GLN ** B2 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.6238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.145 159666 Z= 0.418 Angle : 0.950 29.233 239286 Z= 0.470 Chirality : 0.051 2.084 30607 Planarity : 0.008 0.153 12515 Dihedral : 23.739 179.726 80910 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.82 % Favored : 90.28 % Rotamer: Outliers : 6.22 % Allowed : 17.28 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.10), residues: 5522 helix: -1.28 (0.12), residues: 1658 sheet: -2.39 (0.15), residues: 895 loop : -1.72 (0.11), residues: 2969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRPAC 22 HIS 0.025 0.003 HISB2 16 PHE 0.037 0.004 PHEAP 16 TYR 0.037 0.004 TYRAH 128 ARG 0.021 0.001 ARGAP 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1005 time to evaluate : 8.172 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: AB 132 LYS cc_start: 0.5756 (tttt) cc_final: 0.4906 (mmmt) REVERT: AD 76 TYR cc_start: 0.5882 (t80) cc_final: 0.5493 (t80) REVERT: AD 136 GLN cc_start: 0.6345 (tp40) cc_final: 0.6049 (tp40) REVERT: AE 52 LYS cc_start: 0.7040 (ptpt) cc_final: 0.6544 (ptpp) REVERT: AE 62 LYS cc_start: 0.5659 (mmmt) cc_final: 0.5137 (mtpp) REVERT: AE 115 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7415 (mm) REVERT: AG 26 PHE cc_start: 0.6801 (t80) cc_final: 0.6294 (t80) REVERT: AH 31 LYS cc_start: 0.7037 (mmtt) cc_final: 0.6817 (ttmm) REVERT: AH 46 ILE cc_start: 0.8343 (mm) cc_final: 0.7975 (pt) REVERT: AH 85 ILE cc_start: 0.7448 (mt) cc_final: 0.7216 (mt) REVERT: AI 83 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7558 (mm) REVERT: AI 130 ARG cc_start: 0.4257 (mmm160) cc_final: 0.2527 (mtm-85) REVERT: AJ 52 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7374 (mt) REVERT: AK 82 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6233 (pp) REVERT: AL 36 ARG cc_start: 0.6587 (ptp-170) cc_final: 0.5758 (ptt180) REVERT: AN 21 PHE cc_start: 0.3496 (OUTLIER) cc_final: 0.2131 (m-80) REVERT: AN 47 LYS cc_start: 0.6247 (tppt) cc_final: 0.6016 (mmtp) REVERT: AN 97 LYS cc_start: 0.8022 (pttm) cc_final: 0.7519 (ptpt) REVERT: AO 53 ARG cc_start: 0.7192 (ttm-80) cc_final: 0.6701 (ttm170) REVERT: AO 59 MET cc_start: 0.7265 (mmm) cc_final: 0.6905 (mmt) REVERT: AO 84 ARG cc_start: 0.5190 (ttp80) cc_final: 0.4833 (mtm180) REVERT: AP 26 ASN cc_start: 0.5934 (m110) cc_final: 0.5490 (m110) REVERT: AR 38 LYS cc_start: 0.5868 (mmtt) cc_final: 0.4865 (mtmt) REVERT: AT 49 LYS cc_start: 0.7177 (tppt) cc_final: 0.6528 (mmtm) REVERT: BC 100 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5746 (tp30) REVERT: BC 177 ARG cc_start: 0.7067 (tpm170) cc_final: 0.6730 (tpm170) REVERT: BD 14 ILE cc_start: 0.6079 (mm) cc_final: 0.5827 (mt) REVERT: BE 25 GLU cc_start: 0.6613 (mp0) cc_final: 0.5712 (mt-10) REVERT: BF 17 MET cc_start: 0.4134 (mmm) cc_final: 0.3698 (mmt) REVERT: BI 136 MET cc_start: 0.3149 (mpp) cc_final: 0.1866 (mpp) REVERT: BJ 41 LYS cc_start: 0.7722 (mttt) cc_final: 0.6703 (tptm) REVERT: BJ 45 THR cc_start: 0.7044 (m) cc_final: 0.6778 (t) REVERT: BJ 55 ILE cc_start: 0.8419 (mt) cc_final: 0.8192 (tt) REVERT: BJ 67 ASN cc_start: 0.5842 (t0) cc_final: 0.5367 (t0) REVERT: BJ 71 ASP cc_start: 0.7929 (m-30) cc_final: 0.7266 (m-30) REVERT: BJ 106 LYS cc_start: 0.7315 (ttmm) cc_final: 0.6023 (tttp) REVERT: BJ 116 ARG cc_start: 0.7017 (mtm-85) cc_final: 0.6712 (mtm-85) REVERT: BJ 140 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6435 (tt) REVERT: BK 20 MET cc_start: 0.6036 (tpt) cc_final: 0.5760 (tmm) REVERT: BK 106 GLU cc_start: 0.6036 (mp0) cc_final: 0.4967 (mm-30) REVERT: BN 49 GLU cc_start: 0.6027 (mt-10) cc_final: 0.5683 (mt-10) REVERT: BN 76 VAL cc_start: 0.7572 (OUTLIER) cc_final: 0.7236 (t) REVERT: BO 13 ARG cc_start: 0.5956 (OUTLIER) cc_final: 0.5389 (ttt90) REVERT: BP 113 ARG cc_start: 0.5346 (mtm-85) cc_final: 0.5085 (mtp180) REVERT: BQ 83 LEU cc_start: 0.7403 (tt) cc_final: 0.7140 (tp) REVERT: BR 11 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.6211 (mt0) REVERT: BS 31 GLN cc_start: 0.7219 (tt0) cc_final: 0.6550 (pt0) REVERT: BS 84 ARG cc_start: 0.8123 (mmt-90) cc_final: 0.7881 (mmt-90) REVERT: BU 19 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5388 (ptmt) REVERT: BU 45 HIS cc_start: 0.6588 (OUTLIER) cc_final: 0.5990 (p90) REVERT: BV 71 LYS cc_start: 0.6613 (mmtm) cc_final: 0.5632 (ptpt) REVERT: BV 93 ARG cc_start: 0.4883 (mtt-85) cc_final: 0.4594 (mtt-85) REVERT: BW 32 LEU cc_start: 0.6918 (mt) cc_final: 0.6653 (mt) REVERT: BZ 16 ARG cc_start: 0.6180 (mmp80) cc_final: 0.5886 (mmm160) REVERT: B0 10 ARG cc_start: 0.7457 (ptp90) cc_final: 0.6653 (ptm160) REVERT: B1 20 PHE cc_start: 0.8177 (p90) cc_final: 0.7962 (p90) REVERT: B2 37 LYS cc_start: 0.7373 (tttt) cc_final: 0.7047 (ttpt) REVERT: B3 6 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7588 (p) REVERT: B4 11 CYS cc_start: 0.5318 (p) cc_final: 0.4638 (m) REVERT: B4 35 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.6709 (mt0) outliers start: 286 outliers final: 200 residues processed: 1188 average time/residue: 1.4000 time to fit residues: 2845.6580 Evaluate side-chains 1122 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 908 time to evaluate : 6.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 70 VAL Chi-restraints excluded: chain AB residue 93 ASN Chi-restraints excluded: chain AB residue 171 ILE Chi-restraints excluded: chain AB residue 183 VAL Chi-restraints excluded: chain AB residue 187 VAL Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AD residue 53 VAL Chi-restraints excluded: chain AD residue 67 VAL Chi-restraints excluded: chain AD residue 77 LYS Chi-restraints excluded: chain AD residue 78 GLU Chi-restraints excluded: chain AD residue 134 SER Chi-restraints excluded: chain AD residue 137 VAL Chi-restraints excluded: chain AD residue 203 LEU Chi-restraints excluded: chain AE residue 15 LEU Chi-restraints excluded: chain AE residue 22 SER Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AE residue 105 ILE Chi-restraints excluded: chain AE residue 115 LEU Chi-restraints excluded: chain AE residue 148 ASN Chi-restraints excluded: chain AF residue 64 VAL Chi-restraints excluded: chain AF residue 84 VAL Chi-restraints excluded: chain AG residue 6 VAL Chi-restraints excluded: chain AG residue 23 LEU Chi-restraints excluded: chain AG residue 30 LEU Chi-restraints excluded: chain AG residue 42 ILE Chi-restraints excluded: chain AG residue 50 LEU Chi-restraints excluded: chain AG residue 75 VAL Chi-restraints excluded: chain AG residue 94 VAL Chi-restraints excluded: chain AH residue 25 VAL Chi-restraints excluded: chain AH residue 71 VAL Chi-restraints excluded: chain AH residue 106 THR Chi-restraints excluded: chain AH residue 125 ILE Chi-restraints excluded: chain AI residue 83 ILE Chi-restraints excluded: chain AI residue 104 VAL Chi-restraints excluded: chain AI residue 116 VAL Chi-restraints excluded: chain AJ residue 52 LEU Chi-restraints excluded: chain AK residue 33 THR Chi-restraints excluded: chain AK residue 82 LEU Chi-restraints excluded: chain AK residue 114 THR Chi-restraints excluded: chain AL residue 21 VAL Chi-restraints excluded: chain AL residue 37 VAL Chi-restraints excluded: chain AL residue 52 VAL Chi-restraints excluded: chain AL residue 65 SER Chi-restraints excluded: chain AL residue 79 VAL Chi-restraints excluded: chain AL residue 82 ILE Chi-restraints excluded: chain AL residue 97 THR Chi-restraints excluded: chain AL residue 104 CYS Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 76 SER Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AN residue 21 PHE Chi-restraints excluded: chain AN residue 82 ILE Chi-restraints excluded: chain AO residue 12 VAL Chi-restraints excluded: chain AP residue 18 GLN Chi-restraints excluded: chain AP residue 20 VAL Chi-restraints excluded: chain AP residue 66 THR Chi-restraints excluded: chain AP residue 70 ARG Chi-restraints excluded: chain AP residue 74 LEU Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AQ residue 76 VAL Chi-restraints excluded: chain AR residue 21 ILE Chi-restraints excluded: chain AR residue 40 VAL Chi-restraints excluded: chain AR residue 42 SER Chi-restraints excluded: chain AR residue 45 THR Chi-restraints excluded: chain AR residue 55 LEU Chi-restraints excluded: chain AR residue 67 LEU Chi-restraints excluded: chain AS residue 11 ILE Chi-restraints excluded: chain AS residue 39 THR Chi-restraints excluded: chain AS residue 49 ILE Chi-restraints excluded: chain AS residue 63 THR Chi-restraints excluded: chain AT residue 26 SER Chi-restraints excluded: chain AT residue 54 MET Chi-restraints excluded: chain AT residue 84 ASN Chi-restraints excluded: chain BC residue 65 VAL Chi-restraints excluded: chain BC residue 100 GLU Chi-restraints excluded: chain BC residue 184 VAL Chi-restraints excluded: chain BC residue 192 LEU Chi-restraints excluded: chain BC residue 195 VAL Chi-restraints excluded: chain BC residue 201 MET Chi-restraints excluded: chain BC residue 228 VAL Chi-restraints excluded: chain BC residue 232 HIS Chi-restraints excluded: chain BC residue 250 VAL Chi-restraints excluded: chain BC residue 258 ARG Chi-restraints excluded: chain BC residue 269 ARG Chi-restraints excluded: chain BD residue 1 MET Chi-restraints excluded: chain BD residue 21 SER Chi-restraints excluded: chain BD residue 26 VAL Chi-restraints excluded: chain BD residue 40 LEU Chi-restraints excluded: chain BD residue 50 VAL Chi-restraints excluded: chain BD residue 52 THR Chi-restraints excluded: chain BD residue 62 LYS Chi-restraints excluded: chain BD residue 92 VAL Chi-restraints excluded: chain BD residue 109 VAL Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 207 VAL Chi-restraints excluded: chain BE residue 53 THR Chi-restraints excluded: chain BE residue 73 ILE Chi-restraints excluded: chain BE residue 110 SER Chi-restraints excluded: chain BE residue 120 VAL Chi-restraints excluded: chain BE residue 146 VAL Chi-restraints excluded: chain BE residue 169 VAL Chi-restraints excluded: chain BF residue 25 VAL Chi-restraints excluded: chain BF residue 34 ILE Chi-restraints excluded: chain BF residue 38 MET Chi-restraints excluded: chain BF residue 51 ASP Chi-restraints excluded: chain BF residue 74 VAL Chi-restraints excluded: chain BF residue 123 ASP Chi-restraints excluded: chain BF residue 153 ASP Chi-restraints excluded: chain BF residue 177 PHE Chi-restraints excluded: chain BG residue 4 VAL Chi-restraints excluded: chain BG residue 10 VAL Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 41 VAL Chi-restraints excluded: chain BG residue 60 ASP Chi-restraints excluded: chain BG residue 67 THR Chi-restraints excluded: chain BG residue 90 VAL Chi-restraints excluded: chain BG residue 133 LEU Chi-restraints excluded: chain BH residue 3 VAL Chi-restraints excluded: chain BI residue 13 VAL Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BJ residue 109 LEU Chi-restraints excluded: chain BJ residue 124 VAL Chi-restraints excluded: chain BJ residue 140 LEU Chi-restraints excluded: chain BK residue 31 ARG Chi-restraints excluded: chain BK residue 47 ILE Chi-restraints excluded: chain BK residue 57 VAL Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 62 VAL Chi-restraints excluded: chain BK residue 65 THR Chi-restraints excluded: chain BK residue 76 VAL Chi-restraints excluded: chain BK residue 98 ARG Chi-restraints excluded: chain BK residue 118 LEU Chi-restraints excluded: chain BL residue 60 ARG Chi-restraints excluded: chain BL residue 78 ARG Chi-restraints excluded: chain BL residue 81 ASP Chi-restraints excluded: chain BL residue 96 LYS Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BL residue 116 VAL Chi-restraints excluded: chain BL residue 127 VAL Chi-restraints excluded: chain BM residue 10 ARG Chi-restraints excluded: chain BM residue 34 LYS Chi-restraints excluded: chain BM residue 42 THR Chi-restraints excluded: chain BM residue 54 THR Chi-restraints excluded: chain BM residue 67 VAL Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BM residue 95 LEU Chi-restraints excluded: chain BM residue 128 THR Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 59 SER Chi-restraints excluded: chain BN residue 76 VAL Chi-restraints excluded: chain BO residue 13 ARG Chi-restraints excluded: chain BO residue 24 THR Chi-restraints excluded: chain BO residue 52 SER Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BP residue 48 ILE Chi-restraints excluded: chain BP residue 55 LEU Chi-restraints excluded: chain BP residue 60 THR Chi-restraints excluded: chain BQ residue 9 ILE Chi-restraints excluded: chain BQ residue 13 ARG Chi-restraints excluded: chain BQ residue 62 ILE Chi-restraints excluded: chain BQ residue 98 ILE Chi-restraints excluded: chain BQ residue 110 VAL Chi-restraints excluded: chain BR residue 11 GLN Chi-restraints excluded: chain BR residue 19 THR Chi-restraints excluded: chain BR residue 20 VAL Chi-restraints excluded: chain BS residue 3 THR Chi-restraints excluded: chain BS residue 23 LEU Chi-restraints excluded: chain BS residue 25 ARG Chi-restraints excluded: chain BS residue 71 VAL Chi-restraints excluded: chain BS residue 94 ASP Chi-restraints excluded: chain BS residue 105 VAL Chi-restraints excluded: chain BS residue 107 VAL Chi-restraints excluded: chain BT residue 15 HIS Chi-restraints excluded: chain BT residue 47 VAL Chi-restraints excluded: chain BT residue 52 GLU Chi-restraints excluded: chain BT residue 63 VAL Chi-restraints excluded: chain BT residue 85 VAL Chi-restraints excluded: chain BT residue 86 THR Chi-restraints excluded: chain BU residue 18 ASP Chi-restraints excluded: chain BU residue 19 LYS Chi-restraints excluded: chain BU residue 25 VAL Chi-restraints excluded: chain BU residue 42 VAL Chi-restraints excluded: chain BU residue 45 HIS Chi-restraints excluded: chain BU residue 58 ILE Chi-restraints excluded: chain BU residue 68 SER Chi-restraints excluded: chain BV residue 1 MET Chi-restraints excluded: chain BV residue 47 VAL Chi-restraints excluded: chain BV residue 89 ILE Chi-restraints excluded: chain BW residue 40 GLN Chi-restraints excluded: chain BW residue 51 VAL Chi-restraints excluded: chain BW residue 67 VAL Chi-restraints excluded: chain BX residue 4 VAL Chi-restraints excluded: chain BX residue 33 LEU Chi-restraints excluded: chain BX residue 48 THR Chi-restraints excluded: chain BX residue 58 VAL Chi-restraints excluded: chain BX residue 72 ARG Chi-restraints excluded: chain BY residue 12 GLU Chi-restraints excluded: chain BY residue 20 ASN Chi-restraints excluded: chain BZ residue 14 ILE Chi-restraints excluded: chain BZ residue 32 ILE Chi-restraints excluded: chain BZ residue 36 VAL Chi-restraints excluded: chain BZ residue 41 THR Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B1 residue 5 ILE Chi-restraints excluded: chain B1 residue 13 SER Chi-restraints excluded: chain B1 residue 28 ARG Chi-restraints excluded: chain B2 residue 24 THR Chi-restraints excluded: chain B2 residue 26 ASN Chi-restraints excluded: chain B2 residue 44 VAL Chi-restraints excluded: chain B3 residue 6 THR Chi-restraints excluded: chain B3 residue 7 VAL Chi-restraints excluded: chain B4 residue 35 GLN Chi-restraints excluded: chain B5 residue -7 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1015 random chunks: chunk 330 optimal weight: 6.9990 chunk 883 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 576 optimal weight: 9.9990 chunk 242 optimal weight: 20.0000 chunk 982 optimal weight: 0.9980 chunk 815 optimal weight: 0.0070 chunk 454 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 324 optimal weight: 20.0000 chunk 515 optimal weight: 9.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AD 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 12 GLN AF 63 ASN ** AG 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 29 ASN ** AK 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 60 GLN AP 18 GLN AT 20 HIS ** AT 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 90 GLN BE 163 ASN ** BF 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BI 43 ASN ** BM 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 34 HIS BP 12 GLN BT 28 ASN BW 12 ASN BZ 9 GLN B2 16 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 159666 Z= 0.191 Angle : 0.679 27.505 239286 Z= 0.346 Chirality : 0.040 2.063 30607 Planarity : 0.006 0.150 12515 Dihedral : 23.494 179.897 80910 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.89 % Allowed : 7.12 % Favored : 92.00 % Rotamer: Outliers : 4.83 % Allowed : 19.74 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % 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 (0.11), residues: 5522 helix: -0.77 (0.12), residues: 1657 sheet: -2.26 (0.15), residues: 902 loop : -1.58 (0.11), residues: 2963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRPAC 22 HIS 0.009 0.001 HISBX 36 PHE 0.027 0.002 PHEBY 26 TYR 0.029 0.002 TYRAH 128 ARG 0.011 0.001 ARGBH 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 970 time to evaluate : 6.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 64 LYS cc_start: 0.4899 (mttt) cc_final: 0.4699 (ttmt) REVERT: AB 132 LYS cc_start: 0.5330 (tttt) cc_final: 0.4699 (mmmt) REVERT: AD 136 GLN cc_start: 0.6257 (tp40) cc_final: 0.5947 (tp40) REVERT: AE 62 LYS cc_start: 0.5454 (mmmt) cc_final: 0.4962 (mtpp) REVERT: AE 115 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7117 (mm) REVERT: AF 74 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6370 (mm) REVERT: AG 5 ARG cc_start: 0.5624 (tmt170) cc_final: 0.5340 (tpt170) REVERT: AG 26 PHE cc_start: 0.6833 (t80) cc_final: 0.6174 (t80) REVERT: AG 74 GLU cc_start: 0.6148 (tp30) cc_final: 0.5553 (tp30) REVERT: AG 143 ARG cc_start: 0.6490 (mtt180) cc_final: 0.6012 (mmm-85) REVERT: AH 31 LYS cc_start: 0.7178 (mmtt) cc_final: 0.6846 (ttmm) REVERT: AH 41 LYS cc_start: 0.6915 (tptp) cc_final: 0.6188 (pttm) REVERT: AH 46 ILE cc_start: 0.8213 (mm) cc_final: 0.7980 (pt) REVERT: AH 85 ILE cc_start: 0.7460 (mt) cc_final: 0.7200 (mt) REVERT: AI 83 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7488 (mm) REVERT: AI 130 ARG cc_start: 0.4639 (mmm160) cc_final: 0.2817 (mtm-85) REVERT: AJ 52 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7102 (mt) REVERT: AK 22 HIS cc_start: 0.6261 (m90) cc_final: 0.5973 (m170) REVERT: AL 36 ARG cc_start: 0.6220 (ptp-170) cc_final: 0.5541 (ptt180) REVERT: AN 21 PHE cc_start: 0.3334 (OUTLIER) cc_final: 0.2126 (m-80) REVERT: AN 97 LYS cc_start: 0.7866 (pttm) cc_final: 0.7486 (ptpt) REVERT: AO 59 MET cc_start: 0.7386 (mmm) cc_final: 0.6999 (mmt) REVERT: AO 84 ARG cc_start: 0.5118 (ttp80) cc_final: 0.4458 (mtm180) REVERT: AP 8 ARG cc_start: 0.6720 (ptm160) cc_final: 0.6361 (ptm-80) REVERT: AP 18 GLN cc_start: 0.5381 (OUTLIER) cc_final: 0.5142 (mm110) REVERT: AP 26 ASN cc_start: 0.5986 (m110) cc_final: 0.5647 (m110) REVERT: AP 66 THR cc_start: 0.5540 (t) cc_final: 0.5309 (t) REVERT: AP 74 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6280 (mt) REVERT: AR 57 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.5440 (tpt-90) REVERT: AS 14 HIS cc_start: 0.5705 (p-80) cc_final: 0.5485 (p-80) REVERT: AT 26 SER cc_start: 0.7178 (OUTLIER) cc_final: 0.6324 (p) REVERT: AT 49 LYS cc_start: 0.7240 (tppt) cc_final: 0.6621 (mmtm) REVERT: AT 75 HIS cc_start: 0.6266 (OUTLIER) cc_final: 0.5566 (m-70) REVERT: BC 100 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5404 (tp30) REVERT: BC 103 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7133 (m-10) REVERT: BC 177 ARG cc_start: 0.7073 (tpm170) cc_final: 0.6682 (tpm170) REVERT: BD 169 ARG cc_start: 0.6823 (mtp85) cc_final: 0.6614 (mtp85) REVERT: BE 25 GLU cc_start: 0.6557 (mp0) cc_final: 0.5765 (mt-10) REVERT: BF 48 LYS cc_start: 0.4465 (mmtt) cc_final: 0.3790 (ptpt) REVERT: BF 117 LEU cc_start: 0.6265 (mt) cc_final: 0.5726 (mt) REVERT: BG 22 GLN cc_start: 0.4107 (mm-40) cc_final: 0.3898 (mm-40) REVERT: BG 88 GLN cc_start: 0.6079 (tt0) cc_final: 0.5691 (tt0) REVERT: BG 133 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6484 (pp) REVERT: BG 143 GLN cc_start: 0.5768 (OUTLIER) cc_final: 0.4914 (tt0) REVERT: BH 27 ARG cc_start: 0.7219 (ptp-170) cc_final: 0.6551 (ttp-110) REVERT: BH 33 GLN cc_start: 0.3685 (tt0) cc_final: 0.3352 (tt0) REVERT: BI 136 MET cc_start: 0.3079 (mpp) cc_final: 0.2186 (mpp) REVERT: BJ 41 LYS cc_start: 0.7502 (mttt) cc_final: 0.6508 (tptm) REVERT: BJ 55 ILE cc_start: 0.8605 (mt) cc_final: 0.8325 (tt) REVERT: BJ 71 ASP cc_start: 0.7871 (m-30) cc_final: 0.7446 (m-30) REVERT: BJ 74 TYR cc_start: 0.7321 (m-80) cc_final: 0.6981 (m-10) REVERT: BK 106 GLU cc_start: 0.5993 (mp0) cc_final: 0.5034 (mm-30) REVERT: BK 113 MET cc_start: 0.5753 (mpp) cc_final: 0.5309 (mmp) REVERT: BL 55 MET cc_start: 0.7274 (tpp) cc_final: 0.7061 (tpp) REVERT: BL 58 TYR cc_start: 0.6503 (p90) cc_final: 0.6009 (p90) REVERT: BM 17 ASN cc_start: 0.6338 (t0) cc_final: 0.5935 (t0) REVERT: BM 47 GLU cc_start: 0.6623 (tm-30) cc_final: 0.6373 (tm-30) REVERT: BN 76 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.7178 (t) REVERT: BO 3 LYS cc_start: 0.6338 (ttmm) cc_final: 0.5657 (mmtm) REVERT: BS 31 GLN cc_start: 0.7104 (tt0) cc_final: 0.6493 (pt0) REVERT: BS 84 ARG cc_start: 0.8068 (mmt-90) cc_final: 0.7646 (mmt-90) REVERT: BU 19 LYS cc_start: 0.6275 (OUTLIER) cc_final: 0.5379 (ptmt) REVERT: BV 50 MET cc_start: 0.5723 (tpt) cc_final: 0.5487 (tpt) REVERT: BV 71 LYS cc_start: 0.6858 (mmtm) cc_final: 0.5512 (ptpt) REVERT: BW 32 LEU cc_start: 0.6734 (mt) cc_final: 0.6492 (mt) REVERT: BX 37 ARG cc_start: 0.6900 (ttm110) cc_final: 0.6419 (mtp-110) REVERT: BX 72 ARG cc_start: 0.6109 (mtm110) cc_final: 0.5789 (mtm-85) REVERT: BZ 45 ARG cc_start: 0.6395 (tpp-160) cc_final: 0.5951 (ttm-80) REVERT: B0 10 ARG cc_start: 0.7488 (ptp90) cc_final: 0.7234 (ptp90) REVERT: B1 20 PHE cc_start: 0.8106 (p90) cc_final: 0.7729 (p90) REVERT: B4 11 CYS cc_start: 0.5614 (p) cc_final: 0.4624 (m) outliers start: 222 outliers final: 156 residues processed: 1103 average time/residue: 1.3732 time to fit residues: 2617.1219 Evaluate side-chains 1074 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 902 time to evaluate : 6.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 57 LEU Chi-restraints excluded: chain AB residue 70 VAL Chi-restraints excluded: chain AB residue 171 ILE Chi-restraints excluded: chain AB residue 183 VAL Chi-restraints excluded: chain AB residue 187 VAL Chi-restraints excluded: chain AC residue 151 VAL Chi-restraints excluded: chain AC residue 162 ILE Chi-restraints excluded: chain AC residue 173 VAL Chi-restraints excluded: chain AC residue 202 ILE Chi-restraints excluded: chain AD residue 53 VAL Chi-restraints excluded: chain AD residue 55 LEU Chi-restraints excluded: chain AD residue 67 VAL Chi-restraints excluded: chain AD residue 161 LEU Chi-restraints excluded: chain AD residue 191 LEU Chi-restraints excluded: chain AD residue 203 LEU Chi-restraints excluded: chain AE residue 22 SER Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AE residue 105 ILE Chi-restraints excluded: chain AE residue 115 LEU Chi-restraints excluded: chain AF residue 64 VAL Chi-restraints excluded: chain AF residue 74 LEU Chi-restraints excluded: chain AG residue 6 VAL Chi-restraints excluded: chain AG residue 23 LEU Chi-restraints excluded: chain AG residue 27 VAL Chi-restraints excluded: chain AG residue 30 LEU Chi-restraints excluded: chain AG residue 91 VAL Chi-restraints excluded: chain AG residue 94 VAL Chi-restraints excluded: chain AG residue 104 ILE Chi-restraints excluded: chain AG residue 106 GLU Chi-restraints excluded: chain AI residue 30 ILE Chi-restraints excluded: chain AI residue 83 ILE Chi-restraints excluded: chain AI residue 104 VAL Chi-restraints excluded: chain AJ residue 52 LEU Chi-restraints excluded: chain AJ residue 53 ILE Chi-restraints excluded: chain AK residue 35 THR Chi-restraints excluded: chain AK residue 114 THR Chi-restraints excluded: chain AL residue 21 VAL Chi-restraints excluded: chain AL residue 65 SER Chi-restraints excluded: chain AL residue 67 ILE Chi-restraints excluded: chain AL residue 79 VAL Chi-restraints excluded: chain AL residue 82 ILE Chi-restraints excluded: chain AL residue 97 THR Chi-restraints excluded: chain AL residue 104 CYS Chi-restraints excluded: chain AM residue 7 ILE Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AN residue 16 LEU Chi-restraints excluded: chain AN residue 21 PHE Chi-restraints excluded: chain AN residue 82 ILE Chi-restraints excluded: chain AO residue 12 VAL Chi-restraints excluded: chain AO residue 75 VAL Chi-restraints excluded: chain AP residue 18 GLN Chi-restraints excluded: chain AP residue 70 ARG Chi-restraints excluded: chain AP residue 74 LEU Chi-restraints excluded: chain AQ residue 22 VAL Chi-restraints excluded: chain AQ residue 29 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AQ residue 76 VAL Chi-restraints excluded: chain AR residue 45 THR Chi-restraints excluded: chain AR residue 55 LEU Chi-restraints excluded: chain AR residue 57 ARG Chi-restraints excluded: chain AR residue 70 TYR Chi-restraints excluded: chain AS residue 49 ILE Chi-restraints excluded: chain AS residue 51 VAL Chi-restraints excluded: chain AS residue 63 THR Chi-restraints excluded: chain AT residue 26 SER Chi-restraints excluded: chain AT residue 54 MET Chi-restraints excluded: chain AT residue 75 HIS Chi-restraints excluded: chain AU residue 10 GLU Chi-restraints excluded: chain BC residue 65 VAL Chi-restraints excluded: chain BC residue 100 GLU Chi-restraints excluded: chain BC residue 103 TYR Chi-restraints excluded: chain BC residue 141 VAL Chi-restraints excluded: chain BC residue 144 VAL Chi-restraints excluded: chain BC residue 192 LEU Chi-restraints excluded: chain BC residue 195 VAL Chi-restraints excluded: chain BC residue 228 VAL Chi-restraints excluded: chain BD residue 1 MET Chi-restraints excluded: chain BD residue 40 LEU Chi-restraints excluded: chain BD residue 50 VAL Chi-restraints excluded: chain BD residue 62 LYS Chi-restraints excluded: chain BD residue 109 VAL Chi-restraints excluded: chain BD residue 131 ASP Chi-restraints excluded: chain BD residue 133 THR Chi-restraints excluded: chain BD residue 142 VAL Chi-restraints excluded: chain BD residue 145 SER Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 207 VAL Chi-restraints excluded: chain BE residue 14 VAL Chi-restraints excluded: chain BE residue 97 ASN Chi-restraints excluded: chain BE residue 110 SER Chi-restraints excluded: chain BE residue 146 VAL Chi-restraints excluded: chain BE residue 149 ILE Chi-restraints excluded: chain BE residue 169 VAL Chi-restraints excluded: chain BE residue 181 ILE Chi-restraints excluded: chain BF residue 34 ILE Chi-restraints excluded: chain BF residue 68 THR Chi-restraints excluded: chain BF residue 123 ASP Chi-restraints excluded: chain BF residue 153 ASP Chi-restraints excluded: chain BF residue 177 PHE Chi-restraints excluded: chain BG residue 4 VAL Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 41 VAL Chi-restraints excluded: chain BG residue 67 THR Chi-restraints excluded: chain BG residue 90 VAL Chi-restraints excluded: chain BG residue 133 LEU Chi-restraints excluded: chain BG residue 143 GLN Chi-restraints excluded: chain BH residue 3 VAL Chi-restraints excluded: chain BI residue 49 ILE Chi-restraints excluded: chain BJ residue 57 LEU Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BJ residue 109 LEU Chi-restraints excluded: chain BJ residue 140 LEU Chi-restraints excluded: chain BK residue 1 MET Chi-restraints excluded: chain BK residue 9 ASN Chi-restraints excluded: chain BK residue 47 ILE Chi-restraints excluded: chain BK residue 57 VAL Chi-restraints excluded: chain BK residue 62 VAL Chi-restraints excluded: chain BK residue 65 THR Chi-restraints excluded: chain BK residue 76 VAL Chi-restraints excluded: chain BK residue 118 LEU Chi-restraints excluded: chain BL residue 78 ARG Chi-restraints excluded: chain BL residue 81 ASP Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BL residue 127 VAL Chi-restraints excluded: chain BM residue 67 VAL Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BM residue 95 LEU Chi-restraints excluded: chain BM residue 126 ILE Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 14 SER Chi-restraints excluded: chain BN residue 23 ASN Chi-restraints excluded: chain BN residue 59 SER Chi-restraints excluded: chain BN residue 76 VAL Chi-restraints excluded: chain BO residue 24 THR Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BP residue 28 VAL Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BQ residue 9 ILE Chi-restraints excluded: chain BQ residue 110 VAL Chi-restraints excluded: chain BS residue 3 THR Chi-restraints excluded: chain BS residue 25 ARG Chi-restraints excluded: chain BS residue 71 VAL Chi-restraints excluded: chain BS residue 105 VAL Chi-restraints excluded: chain BS residue 107 VAL Chi-restraints excluded: chain BT residue 52 GLU Chi-restraints excluded: chain BT residue 85 VAL Chi-restraints excluded: chain BT residue 86 THR Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BU residue 19 LYS Chi-restraints excluded: chain BU residue 25 VAL Chi-restraints excluded: chain BU residue 42 VAL Chi-restraints excluded: chain BU residue 68 SER Chi-restraints excluded: chain BV residue 47 VAL Chi-restraints excluded: chain BV residue 89 ILE Chi-restraints excluded: chain BW residue 40 GLN Chi-restraints excluded: chain BW residue 67 VAL Chi-restraints excluded: chain BX residue 33 LEU Chi-restraints excluded: chain BX residue 48 THR Chi-restraints excluded: chain BX residue 58 VAL Chi-restraints excluded: chain BY residue 20 ASN Chi-restraints excluded: chain BZ residue 7 ILE Chi-restraints excluded: chain BZ residue 32 ILE Chi-restraints excluded: chain BZ residue 36 VAL Chi-restraints excluded: chain B1 residue 5 ILE Chi-restraints excluded: chain B1 residue 28 ARG Chi-restraints excluded: chain B2 residue 24 THR Chi-restraints excluded: chain B2 residue 26 ASN Chi-restraints excluded: chain B2 residue 44 VAL Chi-restraints excluded: chain B3 residue 6 THR Chi-restraints excluded: chain B3 residue 7 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1015 random chunks: chunk 946 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 559 optimal weight: 20.0000 chunk 717 optimal weight: 5.9990 chunk 555 optimal weight: 10.0000 chunk 826 optimal weight: 0.5980 chunk 548 optimal weight: 20.0000 chunk 978 optimal weight: 20.0000 chunk 612 optimal weight: 40.0000 chunk 596 optimal weight: 10.0000 chunk 451 optimal weight: 10.0000 overall best weight: 6.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 89 GLN ** AD 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 116 GLN AD 120 HIS ** AG 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 148 ASN ** AK 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AM 14 HIS ** AN 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 60 GLN ** AP 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 13 GLN ** BD 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 23 ASN BO 34 HIS ** BP 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 56 GLN ** BR 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 15 GLN BW 12 ASN BX 17 ASN BZ 9 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.6798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 159666 Z= 0.340 Angle : 0.839 29.267 239286 Z= 0.416 Chirality : 0.046 2.063 30607 Planarity : 0.007 0.153 12515 Dihedral : 23.660 179.024 80910 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.13 % Favored : 90.00 % Rotamer: Outliers : 6.51 % Allowed : 19.28 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.10), residues: 5522 helix: -0.99 (0.12), residues: 1637 sheet: -2.25 (0.16), residues: 900 loop : -1.87 (0.11), residues: 2985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRPAC 22 HIS 0.011 0.002 HISAD 41 PHE 0.035 0.003 PHEAG 62 TYR 0.033 0.003 TYRBJ 75 ARG 0.012 0.001 ARGBF 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 955 time to evaluate : 6.296 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: AB 132 LYS cc_start: 0.5157 (tttt) cc_final: 0.4568 (mmmt) REVERT: AC 102 ASN cc_start: 0.3431 (m110) cc_final: 0.3120 (m-40) REVERT: AC 147 LYS cc_start: 0.5315 (OUTLIER) cc_final: 0.4809 (mmtt) REVERT: AD 136 GLN cc_start: 0.6270 (tp40) cc_final: 0.5979 (tp40) REVERT: AE 11 LEU cc_start: 0.5998 (tp) cc_final: 0.5616 (tp) REVERT: AE 115 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7315 (mm) REVERT: AG 26 PHE cc_start: 0.6806 (t80) cc_final: 0.6482 (t80) REVERT: AG 47 LEU cc_start: 0.4795 (OUTLIER) cc_final: 0.4308 (mp) REVERT: AG 74 GLU cc_start: 0.6268 (tp30) cc_final: 0.5583 (tp30) REVERT: AH 41 LYS cc_start: 0.7049 (tptp) cc_final: 0.6250 (pttm) REVERT: AH 46 ILE cc_start: 0.8258 (mm) cc_final: 0.8005 (pt) REVERT: AH 85 ILE cc_start: 0.7580 (mt) cc_final: 0.7320 (mt) REVERT: AI 83 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7508 (mm) REVERT: AJ 13 PHE cc_start: 0.6283 (OUTLIER) cc_final: 0.5232 (m-80) REVERT: AJ 52 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7215 (mt) REVERT: AK 22 HIS cc_start: 0.6261 (m90) cc_final: 0.5786 (m170) REVERT: AL 36 ARG cc_start: 0.6367 (ptp-170) cc_final: 0.5419 (ptt180) REVERT: AM 45 ILE cc_start: 0.5187 (OUTLIER) cc_final: 0.4873 (mm) REVERT: AN 21 PHE cc_start: 0.3399 (OUTLIER) cc_final: 0.2173 (m-80) REVERT: AN 97 LYS cc_start: 0.7773 (pttm) cc_final: 0.7512 (ptpt) REVERT: AO 53 ARG cc_start: 0.7243 (ttm-80) cc_final: 0.6664 (ttm170) REVERT: AO 59 MET cc_start: 0.7383 (mmm) cc_final: 0.7096 (mmt) REVERT: AP 8 ARG cc_start: 0.7176 (ptm160) cc_final: 0.6686 (ptm-80) REVERT: AP 66 THR cc_start: 0.5726 (OUTLIER) cc_final: 0.5459 (t) REVERT: AR 57 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.5295 (tpt-90) REVERT: AT 49 LYS cc_start: 0.7287 (tppt) cc_final: 0.6784 (mmtm) REVERT: AT 75 HIS cc_start: 0.6523 (OUTLIER) cc_final: 0.5594 (m-70) REVERT: BC 100 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5343 (tp30) REVERT: BC 103 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7104 (m-10) REVERT: BC 177 ARG cc_start: 0.7135 (tpm170) cc_final: 0.6680 (tpm170) REVERT: BC 189 ARG cc_start: 0.5189 (OUTLIER) cc_final: 0.4925 (mtt90) REVERT: BD 88 GLU cc_start: 0.4707 (OUTLIER) cc_final: 0.4423 (pt0) REVERT: BE 25 GLU cc_start: 0.6448 (mp0) cc_final: 0.5585 (mt-10) REVERT: BE 111 GLU cc_start: 0.6035 (tp30) cc_final: 0.5471 (tt0) REVERT: BF 48 LYS cc_start: 0.4750 (mmtt) cc_final: 0.3948 (ptpp) REVERT: BF 92 ARG cc_start: 0.5927 (ptp90) cc_final: 0.5415 (ptp90) REVERT: BF 117 LEU cc_start: 0.6329 (mt) cc_final: 0.5805 (mt) REVERT: BG 143 GLN cc_start: 0.5792 (OUTLIER) cc_final: 0.5184 (tt0) REVERT: BH 33 GLN cc_start: 0.4605 (tt0) cc_final: 0.4186 (tt0) REVERT: BI 136 MET cc_start: 0.2835 (mpp) cc_final: 0.2000 (mpp) REVERT: BJ 41 LYS cc_start: 0.7573 (mttt) cc_final: 0.6549 (tptm) REVERT: BJ 45 THR cc_start: 0.6914 (m) cc_final: 0.6604 (t) REVERT: BJ 55 ILE cc_start: 0.8595 (mt) cc_final: 0.8298 (tt) REVERT: BJ 71 ASP cc_start: 0.7852 (m-30) cc_final: 0.7503 (m-30) REVERT: BJ 106 LYS cc_start: 0.7297 (ttmm) cc_final: 0.5971 (tttp) REVERT: BJ 116 ARG cc_start: 0.6978 (mtm-85) cc_final: 0.6644 (mtm-85) REVERT: BK 93 GLN cc_start: 0.7958 (tm-30) cc_final: 0.6927 (pt0) REVERT: BK 106 GLU cc_start: 0.5975 (mp0) cc_final: 0.5060 (mm-30) REVERT: BL 96 LYS cc_start: 0.5933 (OUTLIER) cc_final: 0.5728 (mmtm) REVERT: BM 17 ASN cc_start: 0.6206 (t0) cc_final: 0.5990 (t0) REVERT: BM 117 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.5850 (m-10) REVERT: BN 49 GLU cc_start: 0.5663 (mt-10) cc_final: 0.5344 (mt-10) REVERT: BO 3 LYS cc_start: 0.6269 (ttmm) cc_final: 0.5538 (mmtm) REVERT: BR 79 ARG cc_start: 0.7180 (ptm160) cc_final: 0.6976 (ptm160) REVERT: BS 84 ARG cc_start: 0.8169 (mmt-90) cc_final: 0.7753 (mmt-90) REVERT: BU 19 LYS cc_start: 0.6379 (OUTLIER) cc_final: 0.5440 (ptmt) REVERT: BV 50 MET cc_start: 0.5635 (tpt) cc_final: 0.5429 (tpt) REVERT: BV 71 LYS cc_start: 0.6649 (mmtm) cc_final: 0.5523 (ptpt) REVERT: BW 32 LEU cc_start: 0.7139 (mt) cc_final: 0.6858 (mt) REVERT: BX 37 ARG cc_start: 0.6893 (ttm110) cc_final: 0.6224 (mtp-110) REVERT: BX 72 ARG cc_start: 0.6259 (mtm110) cc_final: 0.5913 (mtm-85) REVERT: BZ 45 ARG cc_start: 0.6456 (tpp-160) cc_final: 0.6043 (ttm-80) REVERT: B0 10 ARG cc_start: 0.7587 (ptp90) cc_final: 0.6624 (ptm160) REVERT: B0 28 LEU cc_start: 0.5917 (OUTLIER) cc_final: 0.5644 (tp) REVERT: B0 48 TYR cc_start: 0.6237 (m-10) cc_final: 0.6024 (m-10) REVERT: B1 20 PHE cc_start: 0.8134 (p90) cc_final: 0.7752 (p90) REVERT: B3 52 LYS cc_start: 0.5552 (ttpt) cc_final: 0.5110 (tppt) REVERT: B4 11 CYS cc_start: 0.5237 (p) cc_final: 0.4550 (m) outliers start: 299 outliers final: 227 residues processed: 1143 average time/residue: 1.3263 time to fit residues: 2595.1209 Evaluate side-chains 1150 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 903 time to evaluate : 6.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 37 LYS Chi-restraints excluded: chain AB residue 41 ILE Chi-restraints excluded: chain AB residue 57 LEU Chi-restraints excluded: chain AB residue 70 VAL Chi-restraints excluded: chain AB residue 89 GLN Chi-restraints excluded: chain AB residue 92 VAL Chi-restraints excluded: chain AB residue 93 ASN Chi-restraints excluded: chain AB residue 171 ILE Chi-restraints excluded: chain AB residue 183 VAL Chi-restraints excluded: chain AC residue 147 LYS Chi-restraints excluded: chain AC residue 151 VAL Chi-restraints excluded: chain AC residue 162 ILE Chi-restraints excluded: chain AC residue 173 VAL Chi-restraints excluded: chain AC residue 202 ILE Chi-restraints excluded: chain AD residue 19 LEU Chi-restraints excluded: chain AD residue 53 VAL Chi-restraints excluded: chain AD residue 67 VAL Chi-restraints excluded: chain AD residue 161 LEU Chi-restraints excluded: chain AD residue 191 LEU Chi-restraints excluded: chain AD residue 203 LEU Chi-restraints excluded: chain AE residue 15 LEU Chi-restraints excluded: chain AE residue 22 SER Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AE residue 105 ILE Chi-restraints excluded: chain AE residue 115 LEU Chi-restraints excluded: chain AE residue 120 VAL Chi-restraints excluded: chain AE residue 124 LEU Chi-restraints excluded: chain AE residue 148 ASN Chi-restraints excluded: chain AF residue 26 THR Chi-restraints excluded: chain AF residue 64 VAL Chi-restraints excluded: chain AF residue 74 LEU Chi-restraints excluded: chain AG residue 6 VAL Chi-restraints excluded: chain AG residue 23 LEU Chi-restraints excluded: chain AG residue 27 VAL Chi-restraints excluded: chain AG residue 30 LEU Chi-restraints excluded: chain AG residue 47 LEU Chi-restraints excluded: chain AG residue 75 VAL Chi-restraints excluded: chain AG residue 94 VAL Chi-restraints excluded: chain AG residue 104 ILE Chi-restraints excluded: chain AG residue 106 GLU Chi-restraints excluded: chain AH residue 110 VAL Chi-restraints excluded: chain AH residue 118 GLN Chi-restraints excluded: chain AI residue 30 ILE Chi-restraints excluded: chain AI residue 83 ILE Chi-restraints excluded: chain AI residue 104 VAL Chi-restraints excluded: chain AI residue 116 VAL Chi-restraints excluded: chain AJ residue 13 PHE Chi-restraints excluded: chain AJ residue 52 LEU Chi-restraints excluded: chain AJ residue 53 ILE Chi-restraints excluded: chain AK residue 35 THR Chi-restraints excluded: chain AK residue 114 THR Chi-restraints excluded: chain AL residue 21 VAL Chi-restraints excluded: chain AL residue 52 VAL Chi-restraints excluded: chain AL residue 65 SER Chi-restraints excluded: chain AL residue 67 ILE Chi-restraints excluded: chain AL residue 79 VAL Chi-restraints excluded: chain AL residue 82 ILE Chi-restraints excluded: chain AL residue 97 THR Chi-restraints excluded: chain AL residue 102 LEU Chi-restraints excluded: chain AL residue 104 CYS Chi-restraints excluded: chain AM residue 7 ILE Chi-restraints excluded: chain AM residue 14 HIS Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 45 ILE Chi-restraints excluded: chain AM residue 76 SER Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AN residue 16 LEU Chi-restraints excluded: chain AN residue 21 PHE Chi-restraints excluded: chain AN residue 82 ILE Chi-restraints excluded: chain AO residue 12 VAL Chi-restraints excluded: chain AO residue 75 VAL Chi-restraints excluded: chain AP residue 4 ILE Chi-restraints excluded: chain AP residue 23 ASP Chi-restraints excluded: chain AP residue 66 THR Chi-restraints excluded: chain AP residue 70 ARG Chi-restraints excluded: chain AP residue 74 LEU Chi-restraints excluded: chain AQ residue 29 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AQ residue 76 VAL Chi-restraints excluded: chain AR residue 45 THR Chi-restraints excluded: chain AR residue 55 LEU Chi-restraints excluded: chain AR residue 57 ARG Chi-restraints excluded: chain AR residue 70 TYR Chi-restraints excluded: chain AS residue 49 ILE Chi-restraints excluded: chain AS residue 51 VAL Chi-restraints excluded: chain AS residue 63 THR Chi-restraints excluded: chain AT residue 26 SER Chi-restraints excluded: chain AT residue 54 MET Chi-restraints excluded: chain AT residue 75 HIS Chi-restraints excluded: chain BC residue 65 VAL Chi-restraints excluded: chain BC residue 90 ASN Chi-restraints excluded: chain BC residue 100 GLU Chi-restraints excluded: chain BC residue 103 TYR Chi-restraints excluded: chain BC residue 133 ARG Chi-restraints excluded: chain BC residue 141 VAL Chi-restraints excluded: chain BC residue 144 VAL Chi-restraints excluded: chain BC residue 184 VAL Chi-restraints excluded: chain BC residue 189 ARG Chi-restraints excluded: chain BC residue 192 LEU Chi-restraints excluded: chain BC residue 195 VAL Chi-restraints excluded: chain BC residue 228 VAL Chi-restraints excluded: chain BC residue 252 THR Chi-restraints excluded: chain BC residue 263 THR Chi-restraints excluded: chain BC residue 269 ARG Chi-restraints excluded: chain BD residue 1 MET Chi-restraints excluded: chain BD residue 21 SER Chi-restraints excluded: chain BD residue 28 GLU Chi-restraints excluded: chain BD residue 40 LEU Chi-restraints excluded: chain BD residue 50 VAL Chi-restraints excluded: chain BD residue 52 THR Chi-restraints excluded: chain BD residue 62 LYS Chi-restraints excluded: chain BD residue 88 GLU Chi-restraints excluded: chain BD residue 109 VAL Chi-restraints excluded: chain BD residue 133 THR Chi-restraints excluded: chain BD residue 142 VAL Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 207 VAL Chi-restraints excluded: chain BE residue 14 VAL Chi-restraints excluded: chain BE residue 53 THR Chi-restraints excluded: chain BE residue 73 ILE Chi-restraints excluded: chain BE residue 77 ILE Chi-restraints excluded: chain BE residue 110 SER Chi-restraints excluded: chain BE residue 131 THR Chi-restraints excluded: chain BE residue 146 VAL Chi-restraints excluded: chain BE residue 149 ILE Chi-restraints excluded: chain BE residue 169 VAL Chi-restraints excluded: chain BE residue 181 ILE Chi-restraints excluded: chain BF residue 25 VAL Chi-restraints excluded: chain BF residue 31 VAL Chi-restraints excluded: chain BF residue 51 ASP Chi-restraints excluded: chain BF residue 123 ASP Chi-restraints excluded: chain BF residue 153 ASP Chi-restraints excluded: chain BF residue 177 PHE Chi-restraints excluded: chain BG residue 4 VAL Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 67 THR Chi-restraints excluded: chain BG residue 90 VAL Chi-restraints excluded: chain BG residue 121 ILE Chi-restraints excluded: chain BG residue 132 VAL Chi-restraints excluded: chain BG residue 141 ILE Chi-restraints excluded: chain BG residue 143 GLN Chi-restraints excluded: chain BG residue 168 VAL Chi-restraints excluded: chain BH residue 3 VAL Chi-restraints excluded: chain BI residue 13 VAL Chi-restraints excluded: chain BI residue 49 ILE Chi-restraints excluded: chain BI residue 140 VAL Chi-restraints excluded: chain BJ residue 57 LEU Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BJ residue 105 VAL Chi-restraints excluded: chain BJ residue 109 LEU Chi-restraints excluded: chain BJ residue 140 LEU Chi-restraints excluded: chain BK residue 1 MET Chi-restraints excluded: chain BK residue 7 MET Chi-restraints excluded: chain BK residue 9 ASN Chi-restraints excluded: chain BK residue 25 LEU Chi-restraints excluded: chain BK residue 47 ILE Chi-restraints excluded: chain BK residue 57 VAL Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 62 VAL Chi-restraints excluded: chain BK residue 65 THR Chi-restraints excluded: chain BK residue 76 VAL Chi-restraints excluded: chain BK residue 118 LEU Chi-restraints excluded: chain BL residue 78 ARG Chi-restraints excluded: chain BL residue 81 ASP Chi-restraints excluded: chain BL residue 96 LYS Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BL residue 116 VAL Chi-restraints excluded: chain BL residue 127 VAL Chi-restraints excluded: chain BL residue 136 GLU Chi-restraints excluded: chain BM residue 67 VAL Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BM residue 95 LEU Chi-restraints excluded: chain BM residue 117 PHE Chi-restraints excluded: chain BM residue 126 ILE Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 14 SER Chi-restraints excluded: chain BN residue 23 ASN Chi-restraints excluded: chain BN residue 59 SER Chi-restraints excluded: chain BN residue 75 ILE Chi-restraints excluded: chain BN residue 76 VAL Chi-restraints excluded: chain BN residue 117 ASP Chi-restraints excluded: chain BO residue 24 THR Chi-restraints excluded: chain BO residue 52 SER Chi-restraints excluded: chain BO residue 65 THR Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BP residue 13 MET Chi-restraints excluded: chain BP residue 28 VAL Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BP residue 48 ILE Chi-restraints excluded: chain BP residue 55 LEU Chi-restraints excluded: chain BP residue 60 THR Chi-restraints excluded: chain BP residue 93 ARG Chi-restraints excluded: chain BQ residue 6 ARG Chi-restraints excluded: chain BQ residue 9 ILE Chi-restraints excluded: chain BQ residue 13 ARG Chi-restraints excluded: chain BQ residue 110 VAL Chi-restraints excluded: chain BR residue 19 THR Chi-restraints excluded: chain BS residue 3 THR Chi-restraints excluded: chain BS residue 25 ARG Chi-restraints excluded: chain BS residue 71 VAL Chi-restraints excluded: chain BS residue 74 ILE Chi-restraints excluded: chain BS residue 105 VAL Chi-restraints excluded: chain BS residue 107 VAL Chi-restraints excluded: chain BT residue 10 VAL Chi-restraints excluded: chain BT residue 15 HIS Chi-restraints excluded: chain BT residue 16 VAL Chi-restraints excluded: chain BT residue 52 GLU Chi-restraints excluded: chain BT residue 63 VAL Chi-restraints excluded: chain BT residue 85 VAL Chi-restraints excluded: chain BT residue 86 THR Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BU residue 18 ASP Chi-restraints excluded: chain BU residue 19 LYS Chi-restraints excluded: chain BU residue 25 VAL Chi-restraints excluded: chain BU residue 42 VAL Chi-restraints excluded: chain BU residue 68 SER Chi-restraints excluded: chain BV residue 1 MET Chi-restraints excluded: chain BV residue 47 VAL Chi-restraints excluded: chain BV residue 72 VAL Chi-restraints excluded: chain BW residue 40 GLN Chi-restraints excluded: chain BW residue 51 VAL Chi-restraints excluded: chain BW residue 67 VAL Chi-restraints excluded: chain BX residue 4 VAL Chi-restraints excluded: chain BX residue 8 THR Chi-restraints excluded: chain BX residue 33 LEU Chi-restraints excluded: chain BX residue 48 THR Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 58 VAL Chi-restraints excluded: chain BY residue 20 ASN Chi-restraints excluded: chain BZ residue 7 ILE Chi-restraints excluded: chain BZ residue 23 THR Chi-restraints excluded: chain BZ residue 27 LEU Chi-restraints excluded: chain BZ residue 32 ILE Chi-restraints excluded: chain B0 residue 28 LEU Chi-restraints excluded: chain B1 residue 5 ILE Chi-restraints excluded: chain B1 residue 28 ARG Chi-restraints excluded: chain B1 residue 48 ILE Chi-restraints excluded: chain B2 residue 24 THR Chi-restraints excluded: chain B2 residue 26 ASN Chi-restraints excluded: chain B2 residue 44 VAL Chi-restraints excluded: chain B3 residue 6 THR Chi-restraints excluded: chain B3 residue 7 VAL Chi-restraints excluded: chain B3 residue 49 MET Chi-restraints excluded: chain B4 residue 17 VAL Chi-restraints excluded: chain B5 residue -7 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1015 random chunks: chunk 605 optimal weight: 8.9990 chunk 390 optimal weight: 10.0000 chunk 584 optimal weight: 10.0000 chunk 294 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 621 optimal weight: 20.0000 chunk 666 optimal weight: 10.0000 chunk 483 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 768 optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AB 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 148 ASN ** AI 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 60 GLN ** AS 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 86 ASN ** BC 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 15 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.7434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 159666 Z= 0.413 Angle : 0.932 29.788 239286 Z= 0.460 Chirality : 0.051 2.067 30607 Planarity : 0.008 0.154 12515 Dihedral : 23.963 179.095 80910 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.80 % Allowed : 10.29 % Favored : 88.92 % Rotamer: Outliers : 6.96 % Allowed : 19.91 % Favored : 73.12 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % 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: -3.05 (0.10), residues: 5522 helix: -1.43 (0.12), residues: 1642 sheet: -2.53 (0.15), residues: 925 loop : -2.20 (0.10), residues: 2955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRPAC 22 HIS 0.083 0.003 HISAM 14 PHE 0.033 0.003 PHEBY 26 TYR 0.036 0.003 TYRAH 128 ARG 0.028 0.001 ARGBO 16 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 978 time to evaluate : 6.317 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: AC 38 LYS cc_start: 0.5927 (mmtp) cc_final: 0.5654 (tptt) REVERT: AC 102 ASN cc_start: 0.3512 (m110) cc_final: 0.3162 (m-40) REVERT: AC 147 LYS cc_start: 0.5692 (OUTLIER) cc_final: 0.5099 (mmtt) REVERT: AD 75 TYR cc_start: 0.5758 (m-80) cc_final: 0.5372 (m-80) REVERT: AD 78 GLU cc_start: 0.4848 (OUTLIER) cc_final: 0.4053 (mp0) REVERT: AD 136 GLN cc_start: 0.6295 (tp40) cc_final: 0.6095 (tp40) REVERT: AE 11 LEU cc_start: 0.6131 (tp) cc_final: 0.5769 (tp) REVERT: AE 115 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7332 (mm) REVERT: AF 61 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6154 (pp) REVERT: AG 26 PHE cc_start: 0.6859 (t80) cc_final: 0.6547 (t80) REVERT: AG 47 LEU cc_start: 0.4798 (OUTLIER) cc_final: 0.4286 (mp) REVERT: AG 74 GLU cc_start: 0.6465 (tp30) cc_final: 0.6072 (tp30) REVERT: AG 76 LYS cc_start: 0.5675 (mttt) cc_final: 0.5115 (mmtp) REVERT: AH 41 LYS cc_start: 0.7026 (tptp) cc_final: 0.6151 (pttm) REVERT: AH 85 ILE cc_start: 0.7623 (mt) cc_final: 0.7404 (mt) REVERT: AI 30 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6160 (mt) REVERT: AI 83 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7420 (mm) REVERT: AJ 13 PHE cc_start: 0.6426 (OUTLIER) cc_final: 0.5395 (m-80) REVERT: AJ 52 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7394 (mt) REVERT: AJ 68 ARG cc_start: 0.7270 (tpt170) cc_final: 0.6751 (tpt170) REVERT: AL 30 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.6548 (mttt) REVERT: AL 36 ARG cc_start: 0.6476 (ptp-170) cc_final: 0.5476 (ptt180) REVERT: AL 120 LYS cc_start: 0.7006 (mmmt) cc_final: 0.6061 (mmtm) REVERT: AM 75 MET cc_start: 0.5539 (mtt) cc_final: 0.5279 (mtt) REVERT: AN 97 LYS cc_start: 0.7770 (pttm) cc_final: 0.7566 (ptpt) REVERT: AO 53 ARG cc_start: 0.7359 (ttm-80) cc_final: 0.6776 (ttm170) REVERT: AO 59 MET cc_start: 0.7373 (mmm) cc_final: 0.6657 (mmt) REVERT: AP 8 ARG cc_start: 0.6988 (ptm160) cc_final: 0.6295 (ptm-80) REVERT: AP 19 VAL cc_start: 0.6856 (p) cc_final: 0.6563 (t) REVERT: AQ 28 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6990 (t80) REVERT: AR 57 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.5336 (tpt-90) REVERT: AT 75 HIS cc_start: 0.6598 (OUTLIER) cc_final: 0.5784 (m-70) REVERT: BC 100 GLU cc_start: 0.5961 (OUTLIER) cc_final: 0.5202 (tp30) REVERT: BC 103 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7273 (m-10) REVERT: BC 177 ARG cc_start: 0.7148 (tpm170) cc_final: 0.6674 (tpm170) REVERT: BC 189 ARG cc_start: 0.5040 (OUTLIER) cc_final: 0.4799 (mtt90) REVERT: BC 265 LYS cc_start: 0.7481 (mttt) cc_final: 0.6879 (mmmt) REVERT: BD 88 GLU cc_start: 0.4818 (OUTLIER) cc_final: 0.4467 (pt0) REVERT: BE 7 ASP cc_start: 0.2993 (OUTLIER) cc_final: 0.1139 (t0) REVERT: BE 25 GLU cc_start: 0.6317 (mp0) cc_final: 0.5528 (mt-10) REVERT: BE 112 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6538 (mt) REVERT: BF 48 LYS cc_start: 0.4799 (mmtt) cc_final: 0.4065 (ptpp) REVERT: BF 64 LYS cc_start: 0.4531 (mptt) cc_final: 0.4072 (mmtm) REVERT: BF 77 PHE cc_start: 0.4771 (m-80) cc_final: 0.4507 (m-80) REVERT: BF 117 LEU cc_start: 0.6450 (mt) cc_final: 0.6015 (mt) REVERT: BF 142 ASP cc_start: 0.4239 (t0) cc_final: 0.2494 (m-30) REVERT: BG 143 GLN cc_start: 0.5814 (OUTLIER) cc_final: 0.5361 (tt0) REVERT: BH 33 GLN cc_start: 0.4687 (tt0) cc_final: 0.4208 (tt0) REVERT: BI 136 MET cc_start: 0.3004 (mpp) cc_final: 0.2098 (mpp) REVERT: BJ 41 LYS cc_start: 0.7546 (mttt) cc_final: 0.6566 (tptm) REVERT: BJ 45 THR cc_start: 0.6978 (m) cc_final: 0.6657 (t) REVERT: BJ 55 ILE cc_start: 0.8490 (mt) cc_final: 0.8204 (tt) REVERT: BJ 71 ASP cc_start: 0.7866 (m-30) cc_final: 0.7663 (m-30) REVERT: BJ 106 LYS cc_start: 0.7272 (ttmm) cc_final: 0.6006 (tttp) REVERT: BJ 116 ARG cc_start: 0.6991 (mtm-85) cc_final: 0.6694 (mtm-85) REVERT: BK 18 ARG cc_start: 0.6276 (tpp-160) cc_final: 0.5875 (tpt170) REVERT: BK 106 GLU cc_start: 0.6015 (mp0) cc_final: 0.5054 (mm-30) REVERT: BM 12 MET cc_start: 0.7375 (mtt) cc_final: 0.7164 (mtp) REVERT: BM 17 ASN cc_start: 0.6335 (t0) cc_final: 0.6065 (t0) REVERT: BN 49 GLU cc_start: 0.5963 (mt-10) cc_final: 0.5672 (mt-10) REVERT: BO 3 LYS cc_start: 0.6327 (ttmm) cc_final: 0.5634 (mmtm) REVERT: BP 97 LEU cc_start: 0.7810 (mp) cc_final: 0.7539 (mp) REVERT: BS 84 ARG cc_start: 0.8167 (mmt-90) cc_final: 0.7857 (mmt-90) REVERT: BU 19 LYS cc_start: 0.6414 (OUTLIER) cc_final: 0.5719 (ptmt) REVERT: BU 79 LYS cc_start: 0.4129 (mtpp) cc_final: 0.3870 (mmmt) REVERT: BV 50 MET cc_start: 0.5472 (tpt) cc_final: 0.4995 (tpt) REVERT: BW 32 LEU cc_start: 0.7196 (mt) cc_final: 0.6987 (mt) REVERT: BX 72 ARG cc_start: 0.6345 (mtm110) cc_final: 0.5996 (mtm-85) REVERT: BY 30 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5769 (mmp) REVERT: BZ 16 ARG cc_start: 0.6227 (mmp80) cc_final: 0.5762 (mmm160) REVERT: BZ 45 ARG cc_start: 0.6437 (tpp-160) cc_final: 0.5991 (ttm-80) REVERT: B0 4 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7263 (pt0) REVERT: B0 48 TYR cc_start: 0.6193 (m-10) cc_final: 0.5752 (m-10) REVERT: B4 11 CYS cc_start: 0.5131 (p) cc_final: 0.4493 (m) REVERT: B4 35 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6970 (mt0) outliers start: 320 outliers final: 240 residues processed: 1176 average time/residue: 1.3185 time to fit residues: 2669.1479 Evaluate side-chains 1190 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 926 time to evaluate : 5.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 37 LYS Chi-restraints excluded: chain AB residue 57 LEU Chi-restraints excluded: chain AB residue 70 VAL Chi-restraints excluded: chain AB residue 89 GLN Chi-restraints excluded: chain AB residue 93 ASN Chi-restraints excluded: chain AB residue 183 VAL Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AC residue 67 THR Chi-restraints excluded: chain AC residue 147 LYS Chi-restraints excluded: chain AC residue 151 VAL Chi-restraints excluded: chain AC residue 173 VAL Chi-restraints excluded: chain AC residue 202 ILE Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AD residue 19 LEU Chi-restraints excluded: chain AD residue 53 VAL Chi-restraints excluded: chain AD residue 67 VAL Chi-restraints excluded: chain AD residue 78 GLU Chi-restraints excluded: chain AD residue 98 LEU Chi-restraints excluded: chain AD residue 134 SER Chi-restraints excluded: chain AD residue 161 LEU Chi-restraints excluded: chain AD residue 191 LEU Chi-restraints excluded: chain AD residue 203 LEU Chi-restraints excluded: chain AE residue 15 LEU Chi-restraints excluded: chain AE residue 22 SER Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AE residue 105 ILE Chi-restraints excluded: chain AE residue 115 LEU Chi-restraints excluded: chain AE residue 124 LEU Chi-restraints excluded: chain AE residue 148 ASN Chi-restraints excluded: chain AF residue 26 THR Chi-restraints excluded: chain AF residue 61 LEU Chi-restraints excluded: chain AF residue 64 VAL Chi-restraints excluded: chain AF residue 74 LEU Chi-restraints excluded: chain AF residue 90 MET Chi-restraints excluded: chain AG residue 6 VAL Chi-restraints excluded: chain AG residue 23 LEU Chi-restraints excluded: chain AG residue 27 VAL Chi-restraints excluded: chain AG residue 30 LEU Chi-restraints excluded: chain AG residue 47 LEU Chi-restraints excluded: chain AG residue 94 VAL Chi-restraints excluded: chain AG residue 101 MET Chi-restraints excluded: chain AG residue 104 ILE Chi-restraints excluded: chain AG residue 106 GLU Chi-restraints excluded: chain AH residue 30 SER Chi-restraints excluded: chain AH residue 106 THR Chi-restraints excluded: chain AH residue 110 VAL Chi-restraints excluded: chain AH residue 118 GLN Chi-restraints excluded: chain AI residue 30 ILE Chi-restraints excluded: chain AI residue 83 ILE Chi-restraints excluded: chain AI residue 104 VAL Chi-restraints excluded: chain AI residue 116 VAL Chi-restraints excluded: chain AJ residue 13 PHE Chi-restraints excluded: chain AJ residue 52 LEU Chi-restraints excluded: chain AJ residue 53 ILE Chi-restraints excluded: chain AK residue 33 THR Chi-restraints excluded: chain AK residue 35 THR Chi-restraints excluded: chain AK residue 114 THR Chi-restraints excluded: chain AL residue 21 VAL Chi-restraints excluded: chain AL residue 30 LYS Chi-restraints excluded: chain AL residue 37 VAL Chi-restraints excluded: chain AL residue 52 VAL Chi-restraints excluded: chain AL residue 65 SER Chi-restraints excluded: chain AL residue 67 ILE Chi-restraints excluded: chain AL residue 79 VAL Chi-restraints excluded: chain AL residue 82 ILE Chi-restraints excluded: chain AL residue 97 THR Chi-restraints excluded: chain AL residue 102 LEU Chi-restraints excluded: chain AL residue 104 CYS Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 76 SER Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AN residue 16 LEU Chi-restraints excluded: chain AN residue 79 LEU Chi-restraints excluded: chain AN residue 82 ILE Chi-restraints excluded: chain AO residue 12 VAL Chi-restraints excluded: chain AO residue 75 VAL Chi-restraints excluded: chain AP residue 4 ILE Chi-restraints excluded: chain AP residue 23 ASP Chi-restraints excluded: chain AP residue 36 VAL Chi-restraints excluded: chain AP residue 70 ARG Chi-restraints excluded: chain AP residue 74 LEU Chi-restraints excluded: chain AQ residue 13 VAL Chi-restraints excluded: chain AQ residue 28 PHE Chi-restraints excluded: chain AQ residue 29 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AQ residue 76 VAL Chi-restraints excluded: chain AR residue 45 THR Chi-restraints excluded: chain AR residue 55 LEU Chi-restraints excluded: chain AR residue 57 ARG Chi-restraints excluded: chain AR residue 70 TYR Chi-restraints excluded: chain AS residue 49 ILE Chi-restraints excluded: chain AS residue 51 VAL Chi-restraints excluded: chain AS residue 63 THR Chi-restraints excluded: chain AT residue 26 SER Chi-restraints excluded: chain AT residue 54 MET Chi-restraints excluded: chain AT residue 75 HIS Chi-restraints excluded: chain BC residue 25 HIS Chi-restraints excluded: chain BC residue 65 VAL Chi-restraints excluded: chain BC residue 90 ASN Chi-restraints excluded: chain BC residue 100 GLU Chi-restraints excluded: chain BC residue 103 TYR Chi-restraints excluded: chain BC residue 116 ILE Chi-restraints excluded: chain BC residue 133 ARG Chi-restraints excluded: chain BC residue 141 VAL Chi-restraints excluded: chain BC residue 144 VAL Chi-restraints excluded: chain BC residue 184 VAL Chi-restraints excluded: chain BC residue 189 ARG Chi-restraints excluded: chain BC residue 192 LEU Chi-restraints excluded: chain BC residue 195 VAL Chi-restraints excluded: chain BC residue 201 MET Chi-restraints excluded: chain BC residue 223 THR Chi-restraints excluded: chain BC residue 232 HIS Chi-restraints excluded: chain BC residue 252 THR Chi-restraints excluded: chain BC residue 258 ARG Chi-restraints excluded: chain BC residue 263 THR Chi-restraints excluded: chain BC residue 269 ARG Chi-restraints excluded: chain BD residue 21 SER Chi-restraints excluded: chain BD residue 40 LEU Chi-restraints excluded: chain BD residue 50 VAL Chi-restraints excluded: chain BD residue 52 THR Chi-restraints excluded: chain BD residue 62 LYS Chi-restraints excluded: chain BD residue 88 GLU Chi-restraints excluded: chain BD residue 109 VAL Chi-restraints excluded: chain BD residue 133 THR Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 207 VAL Chi-restraints excluded: chain BE residue 7 ASP Chi-restraints excluded: chain BE residue 14 VAL Chi-restraints excluded: chain BE residue 24 ASN Chi-restraints excluded: chain BE residue 53 THR Chi-restraints excluded: chain BE residue 73 ILE Chi-restraints excluded: chain BE residue 77 ILE Chi-restraints excluded: chain BE residue 110 SER Chi-restraints excluded: chain BE residue 112 LEU Chi-restraints excluded: chain BE residue 131 THR Chi-restraints excluded: chain BE residue 146 VAL Chi-restraints excluded: chain BE residue 149 ILE Chi-restraints excluded: chain BE residue 169 VAL Chi-restraints excluded: chain BF residue 31 VAL Chi-restraints excluded: chain BF residue 49 LEU Chi-restraints excluded: chain BF residue 51 ASP Chi-restraints excluded: chain BF residue 61 SER Chi-restraints excluded: chain BF residue 123 ASP Chi-restraints excluded: chain BF residue 153 ASP Chi-restraints excluded: chain BF residue 177 PHE Chi-restraints excluded: chain BG residue 10 VAL Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 67 THR Chi-restraints excluded: chain BG residue 90 VAL Chi-restraints excluded: chain BG residue 121 ILE Chi-restraints excluded: chain BG residue 132 VAL Chi-restraints excluded: chain BG residue 143 GLN Chi-restraints excluded: chain BG residue 168 VAL Chi-restraints excluded: chain BH residue 3 VAL Chi-restraints excluded: chain BI residue 11 LEU Chi-restraints excluded: chain BI residue 13 VAL Chi-restraints excluded: chain BI residue 49 ILE Chi-restraints excluded: chain BI residue 140 VAL Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BJ residue 93 ILE Chi-restraints excluded: chain BJ residue 105 VAL Chi-restraints excluded: chain BJ residue 109 LEU Chi-restraints excluded: chain BJ residue 124 VAL Chi-restraints excluded: chain BJ residue 140 LEU Chi-restraints excluded: chain BK residue 1 MET Chi-restraints excluded: chain BK residue 7 MET Chi-restraints excluded: chain BK residue 9 ASN Chi-restraints excluded: chain BK residue 25 LEU Chi-restraints excluded: chain BK residue 47 ILE Chi-restraints excluded: chain BK residue 57 VAL Chi-restraints excluded: chain BK residue 62 VAL Chi-restraints excluded: chain BK residue 65 THR Chi-restraints excluded: chain BK residue 76 VAL Chi-restraints excluded: chain BK residue 118 LEU Chi-restraints excluded: chain BL residue 78 ARG Chi-restraints excluded: chain BL residue 81 ASP Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BL residue 116 VAL Chi-restraints excluded: chain BL residue 127 VAL Chi-restraints excluded: chain BL residue 129 LYS Chi-restraints excluded: chain BL residue 136 GLU Chi-restraints excluded: chain BM residue 67 VAL Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BM residue 95 LEU Chi-restraints excluded: chain BM residue 117 PHE Chi-restraints excluded: chain BM residue 126 ILE Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 14 SER Chi-restraints excluded: chain BN residue 36 THR Chi-restraints excluded: chain BN residue 59 SER Chi-restraints excluded: chain BN residue 75 ILE Chi-restraints excluded: chain BN residue 76 VAL Chi-restraints excluded: chain BN residue 117 ASP Chi-restraints excluded: chain BO residue 24 THR Chi-restraints excluded: chain BO residue 26 LEU Chi-restraints excluded: chain BO residue 52 SER Chi-restraints excluded: chain BO residue 65 THR Chi-restraints excluded: chain BP residue 4 ILE Chi-restraints excluded: chain BP residue 13 MET Chi-restraints excluded: chain BP residue 20 PHE Chi-restraints excluded: chain BP residue 28 VAL Chi-restraints excluded: chain BP residue 32 VAL Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BP residue 48 ILE Chi-restraints excluded: chain BP residue 55 LEU Chi-restraints excluded: chain BP residue 60 THR Chi-restraints excluded: chain BP residue 93 ARG Chi-restraints excluded: chain BP residue 102 GLU Chi-restraints excluded: chain BQ residue 6 ARG Chi-restraints excluded: chain BQ residue 9 ILE Chi-restraints excluded: chain BQ residue 13 ARG Chi-restraints excluded: chain BQ residue 74 ILE Chi-restraints excluded: chain BQ residue 98 ILE Chi-restraints excluded: chain BQ residue 110 VAL Chi-restraints excluded: chain BR residue 19 THR Chi-restraints excluded: chain BR residue 58 VAL Chi-restraints excluded: chain BS residue 3 THR Chi-restraints excluded: chain BS residue 25 ARG Chi-restraints excluded: chain BS residue 71 VAL Chi-restraints excluded: chain BS residue 74 ILE Chi-restraints excluded: chain BS residue 96 ILE Chi-restraints excluded: chain BS residue 105 VAL Chi-restraints excluded: chain BS residue 107 VAL Chi-restraints excluded: chain BT residue 10 VAL Chi-restraints excluded: chain BT residue 85 VAL Chi-restraints excluded: chain BT residue 86 THR Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BU residue 19 LYS Chi-restraints excluded: chain BU residue 25 VAL Chi-restraints excluded: chain BU residue 42 VAL Chi-restraints excluded: chain BU residue 61 LYS Chi-restraints excluded: chain BU residue 68 SER Chi-restraints excluded: chain BV residue 35 GLU Chi-restraints excluded: chain BV residue 47 VAL Chi-restraints excluded: chain BV residue 72 VAL Chi-restraints excluded: chain BW residue 40 GLN Chi-restraints excluded: chain BW residue 67 VAL Chi-restraints excluded: chain BX residue 4 VAL Chi-restraints excluded: chain BX residue 33 LEU Chi-restraints excluded: chain BX residue 48 THR Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 58 VAL Chi-restraints excluded: chain BY residue 20 ASN Chi-restraints excluded: chain BY residue 30 MET Chi-restraints excluded: chain BZ residue 7 ILE Chi-restraints excluded: chain BZ residue 23 THR Chi-restraints excluded: chain BZ residue 27 LEU Chi-restraints excluded: chain BZ residue 32 ILE Chi-restraints excluded: chain BZ residue 41 THR Chi-restraints excluded: chain B0 residue 4 GLN Chi-restraints excluded: chain B1 residue 5 ILE Chi-restraints excluded: chain B1 residue 13 SER Chi-restraints excluded: chain B1 residue 28 ARG Chi-restraints excluded: chain B1 residue 48 ILE Chi-restraints excluded: chain B2 residue 24 THR Chi-restraints excluded: chain B2 residue 26 ASN Chi-restraints excluded: chain B2 residue 44 VAL Chi-restraints excluded: chain B3 residue 7 VAL Chi-restraints excluded: chain B3 residue 49 MET Chi-restraints excluded: chain B4 residue 17 VAL Chi-restraints excluded: chain B4 residue 35 GLN Chi-restraints excluded: chain B5 residue -7 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1015 random chunks: chunk 889 optimal weight: 2.9990 chunk 937 optimal weight: 7.9990 chunk 855 optimal weight: 0.6980 chunk 911 optimal weight: 0.9990 chunk 936 optimal weight: 0.9990 chunk 548 optimal weight: 20.0000 chunk 397 optimal weight: 20.0000 chunk 715 optimal weight: 5.9990 chunk 279 optimal weight: 20.0000 chunk 823 optimal weight: 5.9990 chunk 862 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 41 HIS AF 55 HIS AG 130 ASN AG 148 ASN ** AI 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 29 ASN ** AK 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AM 14 HIS ** AN 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 60 GLN AP 18 GLN AP 26 ASN ** AT 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BC 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 41 GLN BF 127 ASN ** BG 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 47 HIS ** BM 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 23 ASN ** BP 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 12 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 159666 Z= 0.168 Angle : 0.681 27.422 239286 Z= 0.346 Chirality : 0.040 2.075 30607 Planarity : 0.006 0.150 12515 Dihedral : 23.650 179.777 80910 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.75 % Favored : 91.54 % Rotamer: Outliers : 4.61 % Allowed : 22.59 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.11), residues: 5522 helix: -0.83 (0.12), residues: 1644 sheet: -2.20 (0.16), residues: 916 loop : -1.90 (0.11), residues: 2962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPAC 22 HIS 0.016 0.001 HISBV 80 PHE 0.030 0.002 PHEBR 5 TYR 0.023 0.002 TYRBJ 75 ARG 0.014 0.001 ARGAK 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 963 time to evaluate : 6.172 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: AB 68 LEU cc_start: 0.5898 (tt) cc_final: 0.5004 (mt) REVERT: AC 102 ASN cc_start: 0.3252 (m110) cc_final: 0.2887 (m-40) REVERT: AC 147 LYS cc_start: 0.5571 (OUTLIER) cc_final: 0.5029 (mmtt) REVERT: AD 136 GLN cc_start: 0.6322 (tp40) cc_final: 0.6094 (tp40) REVERT: AE 11 LEU cc_start: 0.6079 (tp) cc_final: 0.5773 (tp) REVERT: AE 115 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7286 (mm) REVERT: AF 9 MET cc_start: 0.7657 (mmt) cc_final: 0.6801 (mmt) REVERT: AG 26 PHE cc_start: 0.6769 (t80) cc_final: 0.6528 (t80) REVERT: AG 47 LEU cc_start: 0.4650 (OUTLIER) cc_final: 0.4205 (mp) REVERT: AG 74 GLU cc_start: 0.6449 (tp30) cc_final: 0.6133 (tp30) REVERT: AG 76 LYS cc_start: 0.5830 (mttt) cc_final: 0.5186 (mmtp) REVERT: AH 41 LYS cc_start: 0.6688 (tptp) cc_final: 0.6273 (pttt) REVERT: AH 85 ILE cc_start: 0.7516 (mt) cc_final: 0.7306 (mt) REVERT: AH 128 TYR cc_start: 0.7094 (m-80) cc_final: 0.6745 (m-80) REVERT: AI 30 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6291 (mt) REVERT: AI 83 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7479 (mm) REVERT: AL 30 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.6255 (mttt) REVERT: AL 36 ARG cc_start: 0.6183 (ptp-170) cc_final: 0.5623 (ptt180) REVERT: AL 120 LYS cc_start: 0.6885 (mmmt) cc_final: 0.5880 (mmtm) REVERT: AO 59 MET cc_start: 0.7506 (mmm) cc_final: 0.6797 (mmt) REVERT: AP 74 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6442 (tp) REVERT: AS 47 LEU cc_start: 0.7882 (mt) cc_final: 0.7291 (tp) REVERT: AT 26 SER cc_start: 0.7024 (t) cc_final: 0.6200 (p) REVERT: AT 69 LYS cc_start: 0.5486 (pttm) cc_final: 0.5188 (tptt) REVERT: AT 75 HIS cc_start: 0.6480 (OUTLIER) cc_final: 0.5524 (m-70) REVERT: AT 83 ILE cc_start: 0.4964 (pp) cc_final: 0.4552 (pt) REVERT: BC 100 GLU cc_start: 0.6143 (OUTLIER) cc_final: 0.5295 (tp30) REVERT: BC 103 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.7116 (m-10) REVERT: BC 177 ARG cc_start: 0.7115 (tpm170) cc_final: 0.6729 (tpm170) REVERT: BD 88 GLU cc_start: 0.4516 (OUTLIER) cc_final: 0.4297 (pt0) REVERT: BE 25 GLU cc_start: 0.6356 (mp0) cc_final: 0.5673 (mt-10) REVERT: BE 111 GLU cc_start: 0.5890 (tp30) cc_final: 0.5549 (tt0) REVERT: BE 112 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6282 (mt) REVERT: BE 158 PHE cc_start: 0.6180 (t80) cc_final: 0.5545 (m-80) REVERT: BF 48 LYS cc_start: 0.4918 (mmtt) cc_final: 0.4155 (ptpp) REVERT: BF 64 LYS cc_start: 0.4590 (mptt) cc_final: 0.4018 (mmtm) REVERT: BF 103 LEU cc_start: 0.6139 (tp) cc_final: 0.5909 (tp) REVERT: BF 117 LEU cc_start: 0.6289 (mt) cc_final: 0.6083 (mt) REVERT: BF 142 ASP cc_start: 0.3992 (t0) cc_final: 0.2383 (m-30) REVERT: BF 149 VAL cc_start: 0.6791 (m) cc_final: 0.6207 (p) REVERT: BF 152 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5599 (pp) REVERT: BG 143 GLN cc_start: 0.5555 (OUTLIER) cc_final: 0.4977 (tt0) REVERT: BH 33 GLN cc_start: 0.4318 (tt0) cc_final: 0.3915 (tt0) REVERT: BI 136 MET cc_start: 0.2881 (mpp) cc_final: 0.2094 (mpp) REVERT: BJ 41 LYS cc_start: 0.7400 (mttt) cc_final: 0.6481 (tptm) REVERT: BJ 55 ILE cc_start: 0.8560 (mt) cc_final: 0.8201 (tp) REVERT: BJ 71 ASP cc_start: 0.7730 (m-30) cc_final: 0.7391 (m-30) REVERT: BJ 74 TYR cc_start: 0.7295 (m-80) cc_final: 0.7019 (m-10) REVERT: BK 38 ILE cc_start: 0.6844 (mm) cc_final: 0.6446 (tt) REVERT: BK 93 GLN cc_start: 0.7583 (tm-30) cc_final: 0.6781 (pt0) REVERT: BK 106 GLU cc_start: 0.6063 (mp0) cc_final: 0.5186 (mm-30) REVERT: BK 113 MET cc_start: 0.4561 (mmm) cc_final: 0.4286 (mmp) REVERT: BL 55 MET cc_start: 0.7101 (tpp) cc_final: 0.6779 (mmt) REVERT: BN 112 TYR cc_start: 0.7712 (m-80) cc_final: 0.7453 (m-80) REVERT: BO 3 LYS cc_start: 0.5874 (ttmm) cc_final: 0.5399 (mtpp) REVERT: BP 97 LEU cc_start: 0.7684 (mp) cc_final: 0.7466 (mp) REVERT: BQ 57 PHE cc_start: 0.7188 (m-10) cc_final: 0.6978 (m-10) REVERT: BR 23 GLU cc_start: 0.7077 (tp30) cc_final: 0.5460 (pm20) REVERT: BR 84 ARG cc_start: 0.7911 (ptm-80) cc_final: 0.7653 (ptt180) REVERT: BS 84 ARG cc_start: 0.8146 (mmt-90) cc_final: 0.7478 (mmt-90) REVERT: BS 88 ARG cc_start: 0.7102 (mtp85) cc_final: 0.6273 (mmm160) REVERT: BS 107 VAL cc_start: 0.7703 (OUTLIER) cc_final: 0.7495 (p) REVERT: BT 36 LYS cc_start: 0.6671 (tptm) cc_final: 0.6292 (ptmm) REVERT: BV 50 MET cc_start: 0.5772 (tpt) cc_final: 0.4856 (tpt) REVERT: BV 71 LYS cc_start: 0.6754 (mmtm) cc_final: 0.5504 (ptpt) REVERT: BW 32 LEU cc_start: 0.7013 (mt) cc_final: 0.6600 (mp) REVERT: BX 37 ARG cc_start: 0.6940 (ttm110) cc_final: 0.6211 (mtp-110) REVERT: BX 72 ARG cc_start: 0.6104 (mtm110) cc_final: 0.5820 (mtm-85) REVERT: BY 30 MET cc_start: 0.6303 (OUTLIER) cc_final: 0.5917 (mmp) REVERT: BZ 16 ARG cc_start: 0.6104 (mmp80) cc_final: 0.5820 (mmm160) REVERT: BZ 45 ARG cc_start: 0.6416 (tpp-160) cc_final: 0.6046 (ttm-80) REVERT: B0 48 TYR cc_start: 0.6217 (m-10) cc_final: 0.5946 (m-10) REVERT: B2 26 ASN cc_start: 0.6700 (OUTLIER) cc_final: 0.6492 (m110) REVERT: B3 52 LYS cc_start: 0.5606 (ttpt) cc_final: 0.5138 (tppt) REVERT: B4 11 CYS cc_start: 0.5439 (p) cc_final: 0.4499 (m) REVERT: B4 35 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.6859 (mt0) outliers start: 212 outliers final: 156 residues processed: 1094 average time/residue: 1.3445 time to fit residues: 2530.3419 Evaluate side-chains 1085 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 911 time to evaluate : 5.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 41 ILE Chi-restraints excluded: chain AB residue 57 LEU Chi-restraints excluded: chain AB residue 70 VAL Chi-restraints excluded: chain AB residue 183 VAL Chi-restraints excluded: chain AB residue 187 VAL Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AC residue 67 THR Chi-restraints excluded: chain AC residue 119 SER Chi-restraints excluded: chain AC residue 147 LYS Chi-restraints excluded: chain AC residue 151 VAL Chi-restraints excluded: chain AC residue 173 VAL Chi-restraints excluded: chain AC residue 202 ILE Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AD residue 29 ASP Chi-restraints excluded: chain AD residue 67 VAL Chi-restraints excluded: chain AD residue 98 LEU Chi-restraints excluded: chain AD residue 161 LEU Chi-restraints excluded: chain AD residue 191 LEU Chi-restraints excluded: chain AD residue 203 LEU Chi-restraints excluded: chain AE residue 22 SER Chi-restraints excluded: chain AE residue 56 VAL Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AE residue 105 ILE Chi-restraints excluded: chain AE residue 115 LEU Chi-restraints excluded: chain AE residue 120 VAL Chi-restraints excluded: chain AF residue 64 VAL Chi-restraints excluded: chain AF residue 74 LEU Chi-restraints excluded: chain AG residue 6 VAL Chi-restraints excluded: chain AG residue 23 LEU Chi-restraints excluded: chain AG residue 27 VAL Chi-restraints excluded: chain AG residue 30 LEU Chi-restraints excluded: chain AG residue 47 LEU Chi-restraints excluded: chain AG residue 94 VAL Chi-restraints excluded: chain AG residue 104 ILE Chi-restraints excluded: chain AG residue 106 GLU Chi-restraints excluded: chain AH residue 106 THR Chi-restraints excluded: chain AI residue 30 ILE Chi-restraints excluded: chain AI residue 83 ILE Chi-restraints excluded: chain AI residue 104 VAL Chi-restraints excluded: chain AJ residue 53 ILE Chi-restraints excluded: chain AK residue 33 THR Chi-restraints excluded: chain AK residue 35 THR Chi-restraints excluded: chain AK residue 114 THR Chi-restraints excluded: chain AL residue 21 VAL Chi-restraints excluded: chain AL residue 30 LYS Chi-restraints excluded: chain AL residue 65 SER Chi-restraints excluded: chain AL residue 79 VAL Chi-restraints excluded: chain AL residue 82 ILE Chi-restraints excluded: chain AL residue 97 THR Chi-restraints excluded: chain AL residue 104 CYS Chi-restraints excluded: chain AM residue 7 ILE Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AN residue 16 LEU Chi-restraints excluded: chain AN residue 74 LEU Chi-restraints excluded: chain AN residue 82 ILE Chi-restraints excluded: chain AO residue 12 VAL Chi-restraints excluded: chain AO residue 75 VAL Chi-restraints excluded: chain AP residue 4 ILE Chi-restraints excluded: chain AP residue 36 VAL Chi-restraints excluded: chain AP residue 70 ARG Chi-restraints excluded: chain AP residue 74 LEU Chi-restraints excluded: chain AQ residue 13 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AQ residue 76 VAL Chi-restraints excluded: chain AR residue 45 THR Chi-restraints excluded: chain AR residue 55 LEU Chi-restraints excluded: chain AS residue 49 ILE Chi-restraints excluded: chain AS residue 63 THR Chi-restraints excluded: chain AT residue 54 MET Chi-restraints excluded: chain AT residue 75 HIS Chi-restraints excluded: chain BC residue 100 GLU Chi-restraints excluded: chain BC residue 103 TYR Chi-restraints excluded: chain BC residue 141 VAL Chi-restraints excluded: chain BC residue 144 VAL Chi-restraints excluded: chain BC residue 184 VAL Chi-restraints excluded: chain BC residue 192 LEU Chi-restraints excluded: chain BC residue 195 VAL Chi-restraints excluded: chain BC residue 228 VAL Chi-restraints excluded: chain BC residue 263 THR Chi-restraints excluded: chain BD residue 1 MET Chi-restraints excluded: chain BD residue 21 SER Chi-restraints excluded: chain BD residue 50 VAL Chi-restraints excluded: chain BD residue 62 LYS Chi-restraints excluded: chain BD residue 88 GLU Chi-restraints excluded: chain BD residue 92 VAL Chi-restraints excluded: chain BD residue 133 THR Chi-restraints excluded: chain BD residue 145 SER Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BE residue 14 VAL Chi-restraints excluded: chain BE residue 41 GLN Chi-restraints excluded: chain BE residue 53 THR Chi-restraints excluded: chain BE residue 73 ILE Chi-restraints excluded: chain BE residue 112 LEU Chi-restraints excluded: chain BE residue 149 ILE Chi-restraints excluded: chain BE residue 169 VAL Chi-restraints excluded: chain BF residue 51 ASP Chi-restraints excluded: chain BF residue 152 LEU Chi-restraints excluded: chain BF residue 153 ASP Chi-restraints excluded: chain BG residue 10 VAL Chi-restraints excluded: chain BG residue 67 THR Chi-restraints excluded: chain BG residue 90 VAL Chi-restraints excluded: chain BG residue 141 ILE Chi-restraints excluded: chain BG residue 143 GLN Chi-restraints excluded: chain BG residue 168 VAL Chi-restraints excluded: chain BH residue 3 VAL Chi-restraints excluded: chain BI residue 13 VAL Chi-restraints excluded: chain BI residue 49 ILE Chi-restraints excluded: chain BJ residue 57 LEU Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BJ residue 109 LEU Chi-restraints excluded: chain BK residue 1 MET Chi-restraints excluded: chain BK residue 47 ILE Chi-restraints excluded: chain BK residue 57 VAL Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 62 VAL Chi-restraints excluded: chain BK residue 65 THR Chi-restraints excluded: chain BK residue 76 VAL Chi-restraints excluded: chain BK residue 118 LEU Chi-restraints excluded: chain BL residue 78 ARG Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BL residue 116 VAL Chi-restraints excluded: chain BL residue 127 VAL Chi-restraints excluded: chain BM residue 67 VAL Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BM residue 95 LEU Chi-restraints excluded: chain BM residue 126 ILE Chi-restraints excluded: chain BN residue 14 SER Chi-restraints excluded: chain BN residue 59 SER Chi-restraints excluded: chain BN residue 75 ILE Chi-restraints excluded: chain BN residue 76 VAL Chi-restraints excluded: chain BN residue 117 ASP Chi-restraints excluded: chain BO residue 19 GLN Chi-restraints excluded: chain BO residue 65 THR Chi-restraints excluded: chain BP residue 28 VAL Chi-restraints excluded: chain BP residue 32 VAL Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BP residue 102 GLU Chi-restraints excluded: chain BQ residue 6 ARG Chi-restraints excluded: chain BQ residue 98 ILE Chi-restraints excluded: chain BQ residue 110 VAL Chi-restraints excluded: chain BS residue 3 THR Chi-restraints excluded: chain BS residue 25 ARG Chi-restraints excluded: chain BS residue 71 VAL Chi-restraints excluded: chain BS residue 74 ILE Chi-restraints excluded: chain BS residue 96 ILE Chi-restraints excluded: chain BS residue 107 VAL Chi-restraints excluded: chain BT residue 85 VAL Chi-restraints excluded: chain BT residue 86 THR Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BU residue 18 ASP Chi-restraints excluded: chain BU residue 25 VAL Chi-restraints excluded: chain BU residue 42 VAL Chi-restraints excluded: chain BU residue 68 SER Chi-restraints excluded: chain BV residue 47 VAL Chi-restraints excluded: chain BW residue 40 GLN Chi-restraints excluded: chain BW residue 41 ARG Chi-restraints excluded: chain BW residue 67 VAL Chi-restraints excluded: chain BX residue 48 THR Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 58 VAL Chi-restraints excluded: chain BY residue 20 ASN Chi-restraints excluded: chain BY residue 30 MET Chi-restraints excluded: chain BZ residue 23 THR Chi-restraints excluded: chain BZ residue 27 LEU Chi-restraints excluded: chain BZ residue 32 ILE Chi-restraints excluded: chain B1 residue 5 ILE Chi-restraints excluded: chain B1 residue 28 ARG Chi-restraints excluded: chain B2 residue 24 THR Chi-restraints excluded: chain B2 residue 26 ASN Chi-restraints excluded: chain B2 residue 44 VAL Chi-restraints excluded: chain B4 residue 35 GLN Chi-restraints excluded: chain B5 residue -7 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1015 random chunks: chunk 908 optimal weight: 6.9990 chunk 598 optimal weight: 10.0000 chunk 964 optimal weight: 0.0270 chunk 588 optimal weight: 20.0000 chunk 457 optimal weight: 10.0000 chunk 670 optimal weight: 10.0000 chunk 1011 optimal weight: 0.8980 chunk 930 optimal weight: 0.8980 chunk 805 optimal weight: 0.5980 chunk 83 optimal weight: 20.0000 chunk 621 optimal weight: 20.0000 overall best weight: 1.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AE 12 GLN AF 58 HIS AG 130 ASN AG 148 ASN ** AH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 60 GLN ** AT 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 86 ASN BC 260 ASN BE 41 GLN ** BF 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 139 GLN ** BK 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BK 93 GLN BO 34 HIS ** BP 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BU 40 ASN BX 17 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.7350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 159666 Z= 0.151 Angle : 0.631 27.306 239286 Z= 0.320 Chirality : 0.038 2.093 30607 Planarity : 0.006 0.150 12515 Dihedral : 23.475 179.620 80910 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.66 % Favored : 91.67 % Rotamer: Outliers : 3.83 % Allowed : 23.92 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.11), residues: 5522 helix: -0.51 (0.12), residues: 1657 sheet: -1.86 (0.17), residues: 911 loop : -1.74 (0.11), residues: 2954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRPBD 80 HIS 0.018 0.001 HISAK 22 PHE 0.034 0.002 PHEAG 62 TYR 0.033 0.002 TYRBF 128 ARG 0.021 0.001 ARGBE 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11044 Ramachandran restraints generated. 5522 Oldfield, 0 Emsley, 5522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 929 time to evaluate : 8.986 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: AC 102 ASN cc_start: 0.3279 (m110) cc_final: 0.3044 (m-40) REVERT: AC 147 LYS cc_start: 0.5481 (OUTLIER) cc_final: 0.4859 (mmtt) REVERT: AD 136 GLN cc_start: 0.6283 (tp40) cc_final: 0.5522 (tp40) REVERT: AE 11 LEU cc_start: 0.6151 (tp) cc_final: 0.5779 (tp) REVERT: AE 26 LYS cc_start: 0.6317 (ttmm) cc_final: 0.6075 (ttmm) REVERT: AE 115 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6915 (mm) REVERT: AE 147 MET cc_start: 0.4352 (mmm) cc_final: 0.4062 (mmm) REVERT: AF 9 MET cc_start: 0.7452 (mmt) cc_final: 0.6868 (mmt) REVERT: AF 74 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6411 (mm) REVERT: AG 26 PHE cc_start: 0.6785 (t80) cc_final: 0.6446 (t80) REVERT: AG 47 LEU cc_start: 0.5186 (OUTLIER) cc_final: 0.4717 (mp) REVERT: AG 74 GLU cc_start: 0.6455 (tp30) cc_final: 0.6111 (tp30) REVERT: AH 80 ARG cc_start: 0.7743 (mtm110) cc_final: 0.7514 (mtm180) REVERT: AH 128 TYR cc_start: 0.7126 (m-80) cc_final: 0.6763 (m-80) REVERT: AI 30 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6388 (mt) REVERT: AI 83 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7537 (mm) REVERT: AL 30 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.6197 (mttt) REVERT: AL 36 ARG cc_start: 0.6157 (ptp-170) cc_final: 0.5655 (ptt180) REVERT: AL 120 LYS cc_start: 0.7048 (mmmt) cc_final: 0.5904 (mmtm) REVERT: AM 91 HIS cc_start: 0.6472 (m-70) cc_final: 0.6245 (m90) REVERT: AN 83 LYS cc_start: 0.7051 (mmmt) cc_final: 0.6548 (mmtm) REVERT: AO 59 MET cc_start: 0.7584 (mmm) cc_final: 0.7151 (mmt) REVERT: AS 47 LEU cc_start: 0.7906 (mt) cc_final: 0.7241 (tp) REVERT: AT 49 LYS cc_start: 0.7107 (tppt) cc_final: 0.6693 (mmtp) REVERT: AT 68 HIS cc_start: 0.5812 (t-170) cc_final: 0.5605 (t-170) REVERT: AT 69 LYS cc_start: 0.5887 (pttm) cc_final: 0.5245 (tptt) REVERT: AT 75 HIS cc_start: 0.6420 (OUTLIER) cc_final: 0.5525 (m-70) REVERT: AT 83 ILE cc_start: 0.5147 (pp) cc_final: 0.4821 (pt) REVERT: BC 100 GLU cc_start: 0.6126 (OUTLIER) cc_final: 0.5263 (tp30) REVERT: BC 103 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7301 (m-10) REVERT: BC 177 ARG cc_start: 0.6972 (tpm170) cc_final: 0.6626 (tpm170) REVERT: BE 25 GLU cc_start: 0.6170 (mp0) cc_final: 0.5574 (mt-10) REVERT: BE 158 PHE cc_start: 0.6133 (t80) cc_final: 0.5505 (m-80) REVERT: BF 48 LYS cc_start: 0.4657 (mmtt) cc_final: 0.4014 (ptpp) REVERT: BF 64 LYS cc_start: 0.4743 (mptt) cc_final: 0.4239 (mmtm) REVERT: BF 92 ARG cc_start: 0.5864 (ptp90) cc_final: 0.5541 (mtt90) REVERT: BF 117 LEU cc_start: 0.6278 (mt) cc_final: 0.6036 (mt) REVERT: BF 149 VAL cc_start: 0.6584 (m) cc_final: 0.6093 (p) REVERT: BG 143 GLN cc_start: 0.5488 (OUTLIER) cc_final: 0.5205 (tt0) REVERT: BH 27 ARG cc_start: 0.6794 (ttp-110) cc_final: 0.6476 (ttp-110) REVERT: BH 33 GLN cc_start: 0.3446 (tt0) cc_final: 0.3107 (tt0) REVERT: BI 136 MET cc_start: 0.2898 (mpp) cc_final: 0.1755 (mpp) REVERT: BJ 41 LYS cc_start: 0.7351 (mttt) cc_final: 0.6435 (tptm) REVERT: BJ 71 ASP cc_start: 0.7616 (m-30) cc_final: 0.7281 (m-30) REVERT: BJ 74 TYR cc_start: 0.7436 (m-80) cc_final: 0.6893 (m-10) REVERT: BK 38 ILE cc_start: 0.6794 (mm) cc_final: 0.6181 (tt) REVERT: BK 93 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6762 (pt0) REVERT: BK 106 GLU cc_start: 0.6170 (mp0) cc_final: 0.5345 (mm-30) REVERT: BK 113 MET cc_start: 0.4743 (mmm) cc_final: 0.4430 (mmp) REVERT: BL 55 MET cc_start: 0.7199 (tpp) cc_final: 0.6919 (mmt) REVERT: BL 125 LEU cc_start: 0.7355 (mp) cc_final: 0.7098 (mp) REVERT: BL 143 GLU cc_start: 0.5546 (tp30) cc_final: 0.4758 (pt0) REVERT: BM 75 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6413 (mt-10) REVERT: BN 112 TYR cc_start: 0.7845 (m-80) cc_final: 0.7571 (m-80) REVERT: BO 3 LYS cc_start: 0.6025 (ttmm) cc_final: 0.5726 (mtpt) REVERT: BP 15 GLN cc_start: 0.4998 (mt0) cc_final: 0.4476 (mm-40) REVERT: BP 97 LEU cc_start: 0.7702 (mp) cc_final: 0.7446 (mp) REVERT: BR 23 GLU cc_start: 0.7085 (tp30) cc_final: 0.5433 (pm20) REVERT: BR 90 ARG cc_start: 0.7083 (mtm-85) cc_final: 0.6789 (mtm180) REVERT: BU 19 LYS cc_start: 0.6299 (OUTLIER) cc_final: 0.5765 (ptmt) REVERT: BV 45 ASP cc_start: 0.4566 (m-30) cc_final: 0.4363 (t0) REVERT: BV 50 MET cc_start: 0.5767 (tpt) cc_final: 0.5180 (tpt) REVERT: BV 71 LYS cc_start: 0.6725 (mmtm) cc_final: 0.5407 (ptpt) REVERT: BW 32 LEU cc_start: 0.6894 (mt) cc_final: 0.6479 (mp) REVERT: BX 37 ARG cc_start: 0.6998 (ttm110) cc_final: 0.6278 (mtp-110) REVERT: BX 72 ARG cc_start: 0.6122 (mtm110) cc_final: 0.5752 (mtm-85) REVERT: BY 26 PHE cc_start: 0.6199 (t80) cc_final: 0.5930 (t80) REVERT: BY 30 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5986 (mmp) REVERT: BZ 16 ARG cc_start: 0.6035 (mmp80) cc_final: 0.5825 (mmm160) REVERT: B0 4 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7116 (pt0) REVERT: B0 48 TYR cc_start: 0.6168 (m-10) cc_final: 0.5936 (m-10) REVERT: B3 52 LYS cc_start: 0.5648 (ttpt) cc_final: 0.5114 (tppt) REVERT: B4 11 CYS cc_start: 0.5613 (p) cc_final: 0.4686 (m) REVERT: B4 35 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.6862 (mt0) outliers start: 176 outliers final: 130 residues processed: 1044 average time/residue: 1.3377 time to fit residues: 2409.2680 Evaluate side-chains 1036 residues out of total 4597 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 890 time to evaluate : 5.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 41 ILE Chi-restraints excluded: chain AB residue 57 LEU Chi-restraints excluded: chain AB residue 70 VAL Chi-restraints excluded: chain AB residue 93 ASN Chi-restraints excluded: chain AB residue 183 VAL Chi-restraints excluded: chain AB residue 187 VAL Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AC residue 147 LYS Chi-restraints excluded: chain AC residue 151 VAL Chi-restraints excluded: chain AC residue 173 VAL Chi-restraints excluded: chain AC residue 202 ILE Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AD residue 67 VAL Chi-restraints excluded: chain AD residue 161 LEU Chi-restraints excluded: chain AD residue 191 LEU Chi-restraints excluded: chain AD residue 203 LEU Chi-restraints excluded: chain AE residue 22 SER Chi-restraints excluded: chain AE residue 80 THR Chi-restraints excluded: chain AE residue 85 VAL Chi-restraints excluded: chain AE residue 105 ILE Chi-restraints excluded: chain AE residue 115 LEU Chi-restraints excluded: chain AE residue 124 LEU Chi-restraints excluded: chain AF residue 61 LEU Chi-restraints excluded: chain AF residue 74 LEU Chi-restraints excluded: chain AG residue 6 VAL Chi-restraints excluded: chain AG residue 23 LEU Chi-restraints excluded: chain AG residue 30 LEU Chi-restraints excluded: chain AG residue 47 LEU Chi-restraints excluded: chain AG residue 94 VAL Chi-restraints excluded: chain AG residue 104 ILE Chi-restraints excluded: chain AH residue 30 SER Chi-restraints excluded: chain AI residue 30 ILE Chi-restraints excluded: chain AI residue 83 ILE Chi-restraints excluded: chain AI residue 104 VAL Chi-restraints excluded: chain AI residue 116 VAL Chi-restraints excluded: chain AK residue 33 THR Chi-restraints excluded: chain AK residue 35 THR Chi-restraints excluded: chain AK residue 86 VAL Chi-restraints excluded: chain AL residue 21 VAL Chi-restraints excluded: chain AL residue 30 LYS Chi-restraints excluded: chain AL residue 65 SER Chi-restraints excluded: chain AL residue 74 LEU Chi-restraints excluded: chain AL residue 79 VAL Chi-restraints excluded: chain AL residue 82 ILE Chi-restraints excluded: chain AL residue 97 THR Chi-restraints excluded: chain AL residue 104 CYS Chi-restraints excluded: chain AM residue 7 ILE Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 89 LEU Chi-restraints excluded: chain AN residue 16 LEU Chi-restraints excluded: chain AN residue 82 ILE Chi-restraints excluded: chain AO residue 12 VAL Chi-restraints excluded: chain AP residue 70 ARG Chi-restraints excluded: chain AP residue 74 LEU Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AQ residue 76 VAL Chi-restraints excluded: chain AR residue 45 THR Chi-restraints excluded: chain AR residue 55 LEU Chi-restraints excluded: chain AS residue 63 THR Chi-restraints excluded: chain AT residue 54 MET Chi-restraints excluded: chain AT residue 75 HIS Chi-restraints excluded: chain BC residue 100 GLU Chi-restraints excluded: chain BC residue 103 TYR Chi-restraints excluded: chain BC residue 141 VAL Chi-restraints excluded: chain BC residue 144 VAL Chi-restraints excluded: chain BC residue 192 LEU Chi-restraints excluded: chain BC residue 195 VAL Chi-restraints excluded: chain BC residue 228 VAL Chi-restraints excluded: chain BD residue 1 MET Chi-restraints excluded: chain BD residue 21 SER Chi-restraints excluded: chain BD residue 40 LEU Chi-restraints excluded: chain BD residue 50 VAL Chi-restraints excluded: chain BD residue 62 LYS Chi-restraints excluded: chain BD residue 92 VAL Chi-restraints excluded: chain BD residue 109 VAL Chi-restraints excluded: chain BD residue 133 THR Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BE residue 14 VAL Chi-restraints excluded: chain BE residue 149 ILE Chi-restraints excluded: chain BE residue 169 VAL Chi-restraints excluded: chain BF residue 51 ASP Chi-restraints excluded: chain BF residue 61 SER Chi-restraints excluded: chain BF residue 153 ASP Chi-restraints excluded: chain BG residue 67 THR Chi-restraints excluded: chain BG residue 90 VAL Chi-restraints excluded: chain BG residue 132 VAL Chi-restraints excluded: chain BG residue 143 GLN Chi-restraints excluded: chain BG residue 168 VAL Chi-restraints excluded: chain BH residue 3 VAL Chi-restraints excluded: chain BI residue 49 ILE Chi-restraints excluded: chain BJ residue 57 LEU Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BJ residue 109 LEU Chi-restraints excluded: chain BK residue 1 MET Chi-restraints excluded: chain BK residue 47 ILE Chi-restraints excluded: chain BK residue 57 VAL Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 62 VAL Chi-restraints excluded: chain BK residue 65 THR Chi-restraints excluded: chain BK residue 76 VAL Chi-restraints excluded: chain BK residue 93 GLN Chi-restraints excluded: chain BK residue 118 LEU Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BL residue 116 VAL Chi-restraints excluded: chain BL residue 127 VAL Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BM residue 95 LEU Chi-restraints excluded: chain BN residue 59 SER Chi-restraints excluded: chain BN residue 75 ILE Chi-restraints excluded: chain BN residue 76 VAL Chi-restraints excluded: chain BN residue 117 ASP Chi-restraints excluded: chain BP residue 28 VAL Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BQ residue 6 ARG Chi-restraints excluded: chain BS residue 3 THR Chi-restraints excluded: chain BS residue 71 VAL Chi-restraints excluded: chain BS residue 74 ILE Chi-restraints excluded: chain BS residue 96 ILE Chi-restraints excluded: chain BS residue 107 VAL Chi-restraints excluded: chain BT residue 85 VAL Chi-restraints excluded: chain BT residue 86 THR Chi-restraints excluded: chain BU residue 14 LEU Chi-restraints excluded: chain BU residue 18 ASP Chi-restraints excluded: chain BU residue 19 LYS Chi-restraints excluded: chain BU residue 25 VAL Chi-restraints excluded: chain BU residue 42 VAL Chi-restraints excluded: chain BU residue 68 SER Chi-restraints excluded: chain BV residue 47 VAL Chi-restraints excluded: chain BW residue 40 GLN Chi-restraints excluded: chain BW residue 41 ARG Chi-restraints excluded: chain BW residue 67 VAL Chi-restraints excluded: chain BX residue 33 LEU Chi-restraints excluded: chain BX residue 48 THR Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 58 VAL Chi-restraints excluded: chain BY residue 20 ASN Chi-restraints excluded: chain BY residue 30 MET Chi-restraints excluded: chain BZ residue 27 LEU Chi-restraints excluded: chain B0 residue 4 GLN Chi-restraints excluded: chain B1 residue 5 ILE Chi-restraints excluded: chain B1 residue 28 ARG Chi-restraints excluded: chain B2 residue 24 THR Chi-restraints excluded: chain B2 residue 26 ASN Chi-restraints excluded: chain B2 residue 44 VAL Chi-restraints excluded: chain B4 residue 35 GLN Chi-restraints excluded: chain B5 residue -7 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1015 random chunks: chunk 493 optimal weight: 20.0000 chunk 639 optimal weight: 10.0000 chunk 857 optimal weight: 8.9990 chunk 246 optimal weight: 0.0470 chunk 742 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 223 optimal weight: 20.0000 chunk 806 optimal weight: 10.0000 chunk 337 optimal weight: 0.9980 chunk 828 optimal weight: 6.9990 chunk 102 optimal weight: 40.0000 overall best weight: 4.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AG 148 ASN ** AI 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 60 GLN AP 59 HIS ** AT 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 41 GLN BE 90 GLN ** BF 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BJ 128 ASN ** BK 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BK 93 GLN ** BP 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 15 GLN BU 40 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.177306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.161362 restraints weight = 255987.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.158459 restraints weight = 312026.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.155596 restraints weight = 260531.698| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.7363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.275 159666 Z= 0.205 Angle : 0.660 59.183 239286 Z= 0.338 Chirality : 0.039 2.089 30607 Planarity : 0.006 0.150 12515 Dihedral : 23.473 179.595 80910 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.70 % Favored : 91.65 % Rotamer: Outliers : 3.53 % Allowed : 24.31 % Favored : 72.17 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.11), residues: 5522 helix: -0.50 (0.12), residues: 1657 sheet: -1.85 (0.17), residues: 911 loop : -1.73 (0.11), residues: 2954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRPBD 80 HIS 0.056 0.001 HISAL 77 PHE 0.033 0.002 PHEAG 62 TYR 0.022 0.002 TYRAR 23 ARG 0.023 0.001 ARGAU 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36019.88 seconds wall clock time: 632 minutes 25.51 seconds (37945.51 seconds total)