Starting phenix.real_space_refine on Fri Mar 22 03:10:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ju8_8176/03_2024/5ju8_8176_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ju8_8176/03_2024/5ju8_8176.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ju8_8176/03_2024/5ju8_8176_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/5ju8_8176/03_2024/5ju8_8176_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ju8_8176/03_2024/5ju8_8176_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ju8_8176/03_2024/5ju8_8176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ju8_8176/03_2024/5ju8_8176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ju8_8176/03_2024/5ju8_8176_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ju8_8176/03_2024/5ju8_8176_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 4711 5.49 5 S 147 5.16 5 C 72703 2.51 5 N 27029 2.21 5 O 40568 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 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 145158 Number of models: 1 Model: "" Number of chains: 57 Chain: "AA" Number of atoms: 33015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33015 Classifications: {'RNA': 1539} Modifications used: {'rna2p_pur': 119, 'rna2p_pyr': 87, 'rna3p_pur': 755, 'rna3p_pyr': 578} Link IDs: {'rna2p': 206, 'rna3p': 1332} 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: "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': 2, 'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p': 8, 'rna3p_pur': 29, 'rna3p_pyr': 30} Link IDs: {'rna2p': 9, 'rna3p': 67} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 5 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: "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: 55.19, per 1000 atoms: 0.38 Number of scatterers: 145158 At special positions: 0 Unit cell: (267.028, 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 147 16.00 P 4711 15.00 O 40568 8.00 N 27029 7.00 C 72703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 58.71 Conformation dependent library (CDL) restraints added in 7.1 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: 10326 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: 168 helices and 62 sheets defined 37.8% alpha, 16.8% beta 1601 base pairs and 2753 stacking pairs defined. Time for finding SS restraints: 75.25 Creating SS restraints... Processing helix chain 'AB' and resid 24 through 32 removed outlier: 3.636A pdb=" N LYSAB 28 " --> pdb=" O ASNAB 24 " (cutoff:3.500A) Proline residue: AB 29 - end of helix removed outlier: 4.889A 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: 4.434A pdb=" N GLUAB 56 " --> pdb=" O GLUAB 52 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEUAB 57 " --> pdb=" O ALAAB 53 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYSAB 59 " --> pdb=" O ALAAB 55 " (cutoff:3.500A) Processing helix chain 'AB' and resid 76 through 87 removed outlier: 4.207A pdb=" N LYSAB 81 " --> pdb=" O SERAB 77 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASPAB 82 " --> pdb=" O GLUAB 78 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ALAAB 83 " --> pdb=" O ALAAB 79 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALAAB 84 " --> pdb=" O VALAB 80 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEUAB 85 " --> pdb=" O LYSAB 81 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SERAB 86 " --> pdb=" O ASPAB 82 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N CYSAB 87 " --> pdb=" O ALAAB 83 " (cutoff:3.500A) Processing helix chain 'AB' and resid 105 through 123 removed outlier: 4.527A pdb=" N GLNAB 109 " --> pdb=" O LYSAB 105 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SERAB 110 " --> pdb=" O THRAB 106 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THRAB 119 " --> pdb=" O LYSAB 115 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLNAB 120 " --> pdb=" O ASPAB 116 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLNAB 122 " --> pdb=" O GLUAB 118 " (cutoff:3.500A) Processing helix chain 'AB' and resid 130 through 148 removed outlier: 3.618A pdb=" N ALAAB 134 " --> pdb=" O THRAB 130 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARGAB 137 " --> pdb=" O GLUAB 133 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLUAB 140 " --> pdb=" O METAB 136 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEUAB 141 " --> pdb=" O ARGAB 137 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLUAB 142 " --> pdb=" O THRAB 138 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYSAB 143 " --> pdb=" O ARGAB 139 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SERAB 147 " --> pdb=" O LYSAB 143 " (cutoff:3.500A) Processing helix chain 'AB' and resid 150 through 155 removed outlier: 4.177A pdb=" N GLYAB 155 " --> pdb=" O ILEAB 151 " (cutoff:3.500A) Processing helix chain 'AB' and resid 169 through 180 removed outlier: 3.544A pdb=" N GLUAB 175 " --> pdb=" O ILEAB 171 " (cutoff:3.500A) Processing helix chain 'AB' and resid 206 through 223 removed outlier: 3.530A pdb=" N ARGAB 222 " --> pdb=" O ALAAB 218 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLUAB 223 " --> pdb=" O ALAAB 219 " (cutoff:3.500A) Processing helix chain 'AC' and resid 6 through 13 removed outlier: 3.636A pdb=" N ILEAC 10 " --> pdb=" O HISAC 6 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARGAC 11 " --> pdb=" O PROAC 7 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEUAC 12 " --> pdb=" O ASNAC 8 " (cutoff:3.500A) removed outlier: 5.102A 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: 3.757A pdb=" N VALAC 76 " --> pdb=" O ARGAC 72 " (cutoff:3.500A) Processing helix chain 'AC' and resid 81 through 96 removed outlier: 4.400A pdb=" N LYSAC 86 " --> pdb=" O GLUAC 82 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEUAC 87 " --> pdb=" O ASPAC 83 " (cutoff:3.500A) Processing helix chain 'AC' and resid 108 through 113 removed outlier: 4.359A pdb=" N ASPAC 112 " --> pdb=" O LYSAC 108 " (cutoff:3.500A) removed outlier: 5.558A 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: 3.743A pdb=" N GLUAC 125 " --> pdb=" O THRAC 121 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARGAC 126 " --> pdb=" O SERAC 122 " (cutoff:3.500A) Processing helix chain 'AC' and resid 129 through 145 removed outlier: 4.177A pdb=" N ALAAC 141 " --> pdb=" O ALAAC 137 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEUAC 144 " --> pdb=" O ASNAC 140 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLYAC 145 " --> pdb=" O ALAAC 141 " (cutoff:3.500A) Processing helix chain 'AD' and resid 7 through 16 removed outlier: 4.465A pdb=" N LEUAD 11 " --> pdb=" O PROAD 7 " (cutoff:3.500A) Processing helix chain 'AD' and resid 49 through 66 removed outlier: 3.913A pdb=" N LYSAD 58 " --> pdb=" O GLNAD 54 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYRAD 65 " --> pdb=" O VALAD 61 " (cutoff:3.500A) Processing helix chain 'AD' and resid 68 through 83 removed outlier: 5.548A pdb=" N LYSAD 83 " --> pdb=" O ALAAD 79 " (cutoff:3.500A) Processing helix chain 'AD' and resid 85 through 97 removed outlier: 3.817A 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: 3.875A pdb=" N LYSAD 121 " --> pdb=" O LEUAD 117 " (cutoff:3.500A) Processing helix chain 'AD' and resid 152 through 166 removed outlier: 5.329A pdb=" N LYSAD 156 " --> pdb=" O GLNAD 152 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALAAD 157 " --> pdb=" O SERAD 153 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLNAD 164 " --> pdb=" O GLUAD 160 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLUAD 166 " --> pdb=" O ALAAD 162 " (cutoff:3.500A) Processing helix chain 'AD' and resid 187 through 192 removed outlier: 3.952A pdb=" N LEUAD 191 " --> pdb=" O GLUAD 187 " (cutoff:3.500A) removed outlier: 5.112A 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: 4.431A pdb=" N ILEAD 200 " --> pdb=" O ASNAD 196 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VALAD 201 " --> pdb=" O GLUAD 197 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SERAD 205 " --> pdb=" O VALAD 201 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYSAD 206 " --> pdb=" O GLUAD 202 " (cutoff:3.500A) Processing helix chain 'AE' and resid 55 through 71 removed outlier: 3.902A pdb=" N ARGAE 69 " --> pdb=" O GLUAE 65 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ASNAE 70 " --> pdb=" O LYSAE 66 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N METAE 71 " --> pdb=" O ALAAE 67 " (cutoff:3.500A) Processing helix chain 'AE' and resid 109 through 119 removed outlier: 6.209A pdb=" N ALAAE 113 " --> pdb=" O GLYAE 109 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLYAE 119 " --> pdb=" O LEUAE 115 " (cutoff:3.500A) Processing helix chain 'AE' and resid 132 through 154 removed outlier: 4.929A pdb=" N ARGAE 138 " --> pdb=" O ILEAE 134 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILEAE 141 " --> pdb=" O VALAE 137 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLYAE 143 " --> pdb=" O ALAAE 139 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASNAE 146 " --> pdb=" O ASPAE 142 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N METAE 147 " --> pdb=" O GLYAE 143 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ASNAE 148 " --> pdb=" O LEUAE 144 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SERAE 149 " --> pdb=" O GLUAE 145 " (cutoff:3.500A) Proline residue: AE 150 - end of helix removed outlier: 3.810A pdb=" N ALAAE 154 " --> pdb=" O PROAE 150 " (cutoff:3.500A) Processing helix chain 'AF' and resid 14 through 33 removed outlier: 4.493A pdb=" N VALAF 18 " --> pdb=" O GLNAF 14 " (cutoff:3.500A) Proline residue: AF 19 - end of helix removed outlier: 4.006A pdb=" N GLUAF 23 " --> pdb=" O PROAF 19 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARGAF 24 " --> pdb=" O GLYAF 20 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALAAF 28 " --> pdb=" O ARGAF 24 " (cutoff:3.500A) Processing helix chain 'AF' and resid 67 through 82 removed outlier: 3.834A pdb=" N GLUAF 73 " --> pdb=" O GLUAF 69 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASPAF 82 " --> pdb=" O PHEAF 78 " (cutoff:3.500A) Processing helix chain 'AG' and resid 20 through 31 removed outlier: 3.682A pdb=" N ALAAG 24 " --> pdb=" O SERAG 20 " (cutoff:3.500A) Processing helix chain 'AG' and resid 35 through 54 removed outlier: 3.565A pdb=" N ILEAG 42 " --> pdb=" O THRAG 38 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SERAG 45 " --> pdb=" O SERAG 41 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEUAG 50 " --> pdb=" O ALAAG 46 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLNAG 52 " --> pdb=" O GLUAG 48 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARGAG 53 " --> pdb=" O THRAG 49 " (cutoff:3.500A) Processing helix chain 'AG' and resid 57 through 70 removed outlier: 4.716A pdb=" N PHEAG 62 " --> pdb=" O GLUAG 58 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLUAG 63 " --> pdb=" O LEUAG 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALAAG 65 " --> pdb=" O ALAAG 61 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASNAG 68 " --> pdb=" O VALAG 64 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VALAG 69 " --> pdb=" O ALAAG 65 " (cutoff:3.500A) Processing helix chain 'AG' and resid 92 through 112 removed outlier: 3.831A pdb=" N ASNAG 97 " --> pdb=" O PROAG 93 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALAAG 98 " --> pdb=" O VALAG 94 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALAAG 100 " --> pdb=" O ARGAG 96 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLYAG 112 " --> pdb=" O ALAAG 108 " (cutoff:3.500A) Processing helix chain 'AG' and resid 115 through 130 removed outlier: 4.384A pdb=" N GLUAG 129 " --> pdb=" O SERAG 125 " (cutoff:3.500A) Processing helix chain 'AG' and resid 132 through 149 removed outlier: 3.631A pdb=" N LYSAG 136 " --> pdb=" O GLYAG 132 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASNAG 148 " --> pdb=" O METAG 144 " (cutoff:3.500A) Processing helix chain 'AH' and resid 5 through 21 removed outlier: 3.514A pdb=" N ASNAH 21 " --> pdb=" O GLYAH 17 " (cutoff:3.500A) Processing helix chain 'AH' and resid 30 through 44 removed outlier: 3.991A 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: 3.743A pdb=" N TYRAI 38 " --> pdb=" O SERAI 34 " (cutoff:3.500A) Processing helix chain 'AI' and resid 46 through 53 removed outlier: 3.510A 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: 4.824A pdb=" N METAI 88 " --> pdb=" O THRAI 84 " (cutoff:3.500A) Processing helix chain 'AI' and resid 92 through 102 removed outlier: 4.078A pdb=" N SERAI 96 " --> pdb=" O GLUAI 92 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLUAI 97 " --> pdb=" O SERAI 93 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYSAI 100 " --> pdb=" O SERAI 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALAAI 101 " --> pdb=" O GLUAI 97 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 14 through 33 removed outlier: 3.682A pdb=" N ASPAJ 19 " --> pdb=" O HISAJ 15 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLNAJ 20 " --> pdb=" O ARGAJ 16 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLUAJ 24 " --> pdb=" O GLNAJ 20 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILEAJ 25 " --> pdb=" O ALAAJ 21 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 80 through 89 removed outlier: 3.551A pdb=" N ALAAJ 86 " --> pdb=" O LYSAJ 82 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ARGAJ 89 " --> pdb=" O ASPAJ 85 " (cutoff:3.500A) Processing helix chain 'AK' and resid 46 through 51 removed outlier: 3.926A pdb=" N GLYAK 51 " --> pdb=" O ALAAK 47 " (cutoff:3.500A) Processing helix chain 'AK' and resid 54 through 59 removed outlier: 4.642A pdb=" N SERAK 58 " --> pdb=" O GLYAK 54 " (cutoff:3.500A) removed outlier: 4.670A 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: 5.074A pdb=" N ALAAK 73 " --> pdb=" O ARGAK 69 " (cutoff:3.500A) Processing helix chain 'AK' and resid 92 through 104 removed outlier: 4.324A pdb=" N THRAK 96 " --> pdb=" O GLYAK 92 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILEAK 97 " --> pdb=" O ARGAK 93 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALAAK 99 " --> pdb=" O SERAK 95 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEUAK 100 " --> pdb=" O THRAK 96 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASNAK 101 " --> pdb=" O ILEAK 97 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALAAK 102 " --> pdb=" O ARGAK 98 " (cutoff:3.500A) Processing helix chain 'AL' and resid 3 through 10 removed outlier: 3.618A pdb=" N LEUAL 7 " --> pdb=" O THRAL 3 " (cutoff:3.500A) Processing helix chain 'AL' and resid 113 through 118 removed outlier: 4.313A pdb=" N TYRAL 117 " --> pdb=" O ALAAL 113 " (cutoff:3.500A) Processing helix chain 'AM' and resid 14 through 22 removed outlier: 4.252A pdb=" N THRAM 20 " --> pdb=" O VALAM 16 " (cutoff:3.500A) removed outlier: 4.253A 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: 4.218A pdb=" N ASPAM 54 " --> pdb=" O GLUAM 50 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THRAM 55 " --> pdb=" O GLYAM 51 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEUAM 56 " --> pdb=" O GLNAM 52 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLUAM 59 " --> pdb=" O THRAM 55 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHEAM 63 " --> pdb=" O GLUAM 59 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VALAM 64 " --> pdb=" O VALAM 60 " (cutoff:3.500A) Processing helix chain 'AM' and resid 66 through 84 removed outlier: 3.606A pdb=" N ARGAM 70 " --> pdb=" O GLUAM 66 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SERAM 76 " --> pdb=" O GLUAM 72 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASPAM 82 " --> pdb=" O LYSAM 78 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLYAM 84 " --> pdb=" O LEUAM 80 " (cutoff:3.500A) Processing helix chain 'AM' and resid 85 through 94 removed outlier: 3.659A pdb=" N ARGAM 93 " --> pdb=" O LEUAM 89 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLYAM 94 " --> pdb=" O ARGAM 90 " (cutoff:3.500A) Processing helix chain 'AN' and resid 3 through 25 removed outlier: 3.535A pdb=" N ARGAN 13 " --> pdb=" O ARGAN 9 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASPAN 18 " --> pdb=" O VALAN 14 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYSAN 19 " --> pdb=" O ALAAN 15 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHEAN 21 " --> pdb=" O ALAAN 17 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ALAAN 22 " --> pdb=" O ASPAN 18 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYSAN 23 " --> pdb=" O LYSAN 19 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARGAN 24 " --> pdb=" O TYRAN 20 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALAAN 25 " --> pdb=" O PHEAN 21 " (cutoff:3.500A) Processing helix chain 'AN' and resid 26 through 34 removed outlier: 3.895A pdb=" N ILEAN 30 " --> pdb=" O GLUAN 26 " (cutoff:3.500A) removed outlier: 4.280A 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: 4.342A pdb=" N ASPAN 33 " --> pdb=" O ALAAN 29 " (cutoff:3.500A) removed outlier: 5.500A 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: 5.420A pdb=" N LYSAN 47 " --> pdb=" O ASNAN 43 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEUAN 48 " --> pdb=" O ALAAN 44 " (cutoff:3.500A) removed outlier: 5.470A 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: 3.572A 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: 4.216A pdb=" N GLYAO 41 " --> pdb=" O ASNAO 37 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N HISAO 42 " --> pdb=" O HISAO 38 " (cutoff:3.500A) Processing helix chain 'AO' and resid 49 through 74 removed outlier: 3.974A pdb=" N GLYAO 55 " --> pdb=" O HISAO 51 " (cutoff:3.500A) removed outlier: 3.535A 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: 3.701A 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: 4.064A pdb=" N ASNAR 31 " --> pdb=" O ALAAR 27 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYRAR 32 " --> pdb=" O THRAR 28 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILEAR 33 " --> pdb=" O LEUAR 29 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N THRAR 34 " --> pdb=" O LYSAR 30 " (cutoff:3.500A) Processing helix chain 'AR' and resid 41 through 46 removed outlier: 3.663A 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: 3.716A pdb=" N LYSAS 18 " --> pdb=" O HISAS 14 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLUAS 24 " --> pdb=" O GLUAS 20 " (cutoff:3.500A) Processing helix chain 'AS' and resid 70 through 76 removed outlier: 4.714A pdb=" N PHEAS 74 " --> pdb=" O LYSAS 70 " (cutoff:3.500A) removed outlier: 4.447A 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: 4.091A pdb=" N VALAS 67 " --> pdb=" O ASPAS 64 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLYAS 68 " --> pdb=" O GLUAS 65 " (cutoff:3.500A) Processing helix chain 'AT' and resid 6 through 42 removed outlier: 4.025A pdb=" N ARGAT 10 " --> pdb=" O SERAT 6 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILEAT 12 " --> pdb=" O LYSAT 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLUAT 15 " --> pdb=" O ALAAT 11 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SERAT 23 " --> pdb=" O LYSAT 19 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N METAT 28 " --> pdb=" O ARGAT 24 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VALAT 35 " --> pdb=" O PHEAT 31 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALAAT 37 " --> pdb=" O LYSAT 33 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALAAT 38 " --> pdb=" O LYSAT 34 " (cutoff:3.500A) removed outlier: 3.700A 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: 4.610A pdb=" N ALAAT 72 " --> pdb=" O HISAT 68 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALAAT 73 " --> pdb=" O LYSAT 69 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASNAT 78 " --> pdb=" O ARGAT 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASNAT 84 " --> pdb=" O THRAT 80 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYSAT 85 " --> pdb=" O ALAAT 81 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEUAT 86 " --> pdb=" O GLNAT 82 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALAAT 87 " --> pdb=" O ILEAT 83 " (cutoff:3.500A) Processing helix chain 'AU' and resid 18 through 24 removed outlier: 3.741A pdb=" N GLUAU 24 " --> pdb=" O LYSAU 20 " (cutoff:3.500A) Processing helix chain 'AU' and resid 27 through 34 removed outlier: 5.588A pdb=" N GLUAU 31 " --> pdb=" O GLYAU 27 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARGAU 34 " --> pdb=" O ALAAU 30 " (cutoff:3.500A) Processing helix chain 'AU' and resid 39 through 53 removed outlier: 6.638A pdb=" N THRAU 43 " --> pdb=" O GLUAU 39 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VALAU 53 " --> pdb=" O LYSAU 49 " (cutoff:3.500A) Processing helix chain 'BC' and resid 10 through 17 removed outlier: 3.830A pdb=" N ARGBC 14 " --> pdb=" O SERBC 10 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N HISBC 15 " --> pdb=" O PROBC 11 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N VALBC 16 " --> pdb=" O GLYBC 12 " (cutoff:3.500A) removed outlier: 5.891A 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: 3.954A pdb=" N LEUBC 34 " --> pdb=" O PHEBC 30 " (cutoff:3.500A) removed outlier: 5.569A 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: 3.913A 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: 4.363A pdb=" N TRPBC 213 " --> pdb=" O GLYBC 209 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARGBC 214 " --> pdb=" O ALABC 210 " (cutoff:3.500A) removed outlier: 3.530A 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: 4.577A 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: 6.061A pdb=" N ASPBC 264 " --> pdb=" O ASNBC 260 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYSBC 265 " --> pdb=" O LYSBC 261 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N PHEBC 266 " --> pdb=" O ARGBC 262 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILEBC 267 " --> pdb=" O THRBC 263 " (cutoff:3.500A) removed outlier: 5.145A 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: 3.592A pdb=" N HISBC 200 " --> pdb=" O ASNBC 197 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N METBC 201 " --> pdb=" O ALABC 198 " (cutoff:3.500A) Processing helix chain 'BD' and resid 61 through 72 removed outlier: 3.717A pdb=" N HISBD 67 " --> pdb=" O PROBD 63 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALABD 71 " --> pdb=" O HISBD 67 " (cutoff:3.500A) Processing helix chain 'BD' and resid 98 through 105 removed outlier: 4.275A pdb=" N ALABD 102 " --> pdb=" O VALBD 98 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASPBD 103 " --> pdb=" O GLUBD 99 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VALBD 104 " --> pdb=" O LEUBD 100 " (cutoff:3.500A) removed outlier: 4.912A 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: 3.700A pdb=" N PHEBE 19 " --> pdb=" O SERBE 15 " (cutoff:3.500A) removed outlier: 3.785A 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: 3.695A pdb=" N GLNBE 30 " --> pdb=" O ALABE 26 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLNBE 41 " --> pdb=" O ALABE 37 " (cutoff:3.500A) Processing helix chain 'BE' and resid 48 through 53 removed outlier: 5.872A pdb=" N THRBE 53 " --> pdb=" O ARGBE 49 " (cutoff:3.500A) Processing helix chain 'BE' and resid 97 through 116 removed outlier: 3.745A pdb=" N GLUBE 111 " --> pdb=" O SERBE 107 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEUBE 112 " --> pdb=" O ILEBE 108 " (cutoff:3.500A) Processing helix chain 'BE' and resid 130 through 142 removed outlier: 3.691A pdb=" N LEUBE 134 " --> pdb=" O LYSBE 130 " (cutoff:3.500A) Processing helix chain 'BE' and resid 154 through 163 removed outlier: 3.671A pdb=" N LEUBE 159 " --> pdb=" O GLUBE 155 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALABE 160 " --> pdb=" O ASNBE 156 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALABE 161 " --> pdb=" O LEUBE 157 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASNBE 163 " --> pdb=" O LEUBE 159 " (cutoff:3.500A) Processing helix chain 'BE' and resid 176 through 182 removed outlier: 3.623A pdb=" N LEUBE 180 " --> pdb=" O ASPBE 176 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILEBE 181 " --> pdb=" O PROBE 177 " (cutoff:3.500A) Processing helix chain 'BE' and resid 189 through 201 removed outlier: 4.194A pdb=" N LYSBE 194 " --> pdb=" O ALABE 190 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLNBE 195 " --> pdb=" O ASPBE 191 " (cutoff:3.500A) Processing helix chain 'BF' and resid 2 through 21 removed outlier: 3.689A pdb=" N LYSBF 9 " --> pdb=" O HISBF 5 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASPBF 10 " --> pdb=" O ASPBF 6 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLUBF 11 " --> pdb=" O TYRBF 7 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VALBF 12 " --> pdb=" O TYRBF 8 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VALBF 13 " --> pdb=" O LYSBF 9 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYSBF 14 " --> pdb=" O ASPBF 10 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLUBF 19 " --> pdb=" O LYSBF 15 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHEBF 20 " --> pdb=" O LEUBF 16 " (cutoff:3.500A) Processing helix chain 'BF' and resid 46 through 61 removed outlier: 4.184A pdb=" N LEUBF 50 " --> pdb=" O ASPBF 46 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASPBF 51 " --> pdb=" O LYSBF 47 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEUBF 57 " --> pdb=" O ALABF 53 " (cutoff:3.500A) Processing helix chain 'BF' and resid 93 through 111 removed outlier: 3.581A pdb=" N TRPBF 97 " --> pdb=" O GLYBF 93 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THRBF 105 " --> pdb=" O GLUBF 101 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILEBF 106 " --> pdb=" O ARGBF 102 " (cutoff:3.500A) removed outlier: 4.726A 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: 3.506A pdb=" N GLYBF 166 " --> pdb=" O SERBF 162 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALABF 168 " --> pdb=" O GLUBF 164 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUBF 170 " --> pdb=" O GLYBF 166 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALABF 171 " --> pdb=" O ARGBF 167 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALABF 172 " --> pdb=" O ALABF 168 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHEBF 173 " --> pdb=" O LEUBF 169 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASPBF 174 " --> pdb=" O LEUBF 170 " (cutoff:3.500A) Processing helix chain 'BF' and resid 40 through 45 removed outlier: 4.413A pdb=" N ALABF 43 " --> pdb=" O VALBF 40 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILEBF 44 " --> pdb=" O GLYBF 41 " (cutoff:3.500A) Processing helix chain 'BF' and resid 134 through 139 removed outlier: 3.843A 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: 3.589A pdb=" N LYSBG 6 " --> pdb=" O SERBG 2 " (cutoff:3.500A) removed outlier: 3.974A 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: 3.739A pdb=" N GLNBG 64 " --> pdb=" O ASPBG 60 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLYBG 66 " --> pdb=" O TRPBG 62 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASNBG 73 " --> pdb=" O ARGBG 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THRBG 80 " --> pdb=" O VALBG 76 " (cutoff:3.500A) Processing helix chain 'BG' and resid 137 through 153 removed outlier: 3.782A pdb=" N ARGBG 152 " --> pdb=" O LEUBG 148 " (cutoff:3.500A) Processing helix chain 'BH' and resid 22 through 29 removed outlier: 3.528A pdb=" N ASNBH 28 " --> pdb=" O GLYBH 24 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHEBH 29 " --> pdb=" O TYRBH 25 " (cutoff:3.500A) Processing helix chain 'BH' and resid 40 through 47 removed outlier: 6.001A pdb=" N ILEBH 44 " --> pdb=" O THRBH 40 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLUBH 45 " --> pdb=" O LYSBH 41 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHEBH 46 " --> pdb=" O LYSBH 42 " (cutoff:3.500A) Processing helix chain 'BI' and resid 34 through 50 removed outlier: 4.649A pdb=" N PHEBI 38 " --> pdb=" O ASNBI 34 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N CYSBI 39 " --> pdb=" O ILEBI 35 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N PHEBI 42 " --> pdb=" O PHEBI 38 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASNBI 43 " --> pdb=" O CYSBI 39 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALABI 44 " --> pdb=" O LYSBI 40 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYSBI 45 " --> pdb=" O ALABI 41 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N SERBI 48 " --> pdb=" O ALABI 44 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILEBI 49 " --> pdb=" O LYSBI 45 " (cutoff:3.500A) Processing helix chain 'BI' and resid 75 through 84 removed outlier: 3.716A pdb=" N LEUBI 79 " --> pdb=" O PROBI 75 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEUBI 80 " --> pdb=" O ALABI 76 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LYSBI 81 " --> pdb=" O ALABI 77 " (cutoff:3.500A) removed outlier: 4.538A 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: 4.242A pdb=" N LEUBI 106 " --> pdb=" O SERBI 102 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLUBI 108 " --> pdb=" O ALABI 104 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILEBI 109 " --> pdb=" O GLNBI 105 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THRBI 112 " --> pdb=" O GLUBI 108 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALABI 114 " --> pdb=" O ALABI 110 " (cutoff:3.500A) Processing helix chain 'BI' and resid 121 through 135 removed outlier: 3.773A pdb=" N METBI 125 " --> pdb=" O ASPBI 121 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARGBI 127 " --> pdb=" O GLUBI 123 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SERBI 128 " --> pdb=" O ALABI 124 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILEBI 129 " --> pdb=" O METBI 125 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLUBI 130 " --> pdb=" O THRBI 126 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THRBI 132 " --> pdb=" O SERBI 128 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALABI 133 " --> pdb=" O ILEBI 129 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SERBI 135 " --> pdb=" O GLYBI 131 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 24 through 38 removed outlier: 3.901A pdb=" N GLUBJ 31 " --> pdb=" O ARGBJ 27 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 88 through 96 removed outlier: 3.902A pdb=" N ILEBJ 93 " --> pdb=" O PHEBJ 89 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALABJ 94 " --> pdb=" O GLUBJ 90 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 97 through 110 removed outlier: 4.130A pdb=" N ILEBJ 101 " --> pdb=" O PROBJ 97 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALABJ 104 " --> pdb=" O VALBJ 100 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLYBJ 107 " --> pdb=" O ILEBJ 103 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N METBJ 108 " --> pdb=" O ALABJ 104 " (cutoff:3.500A) Proline residue: BJ 110 - end of helix Processing helix chain 'BJ' and resid 112 through 122 removed outlier: 3.850A pdb=" N LYSBJ 121 " --> pdb=" O ALABJ 117 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEUBJ 122 " --> pdb=" O METBJ 118 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 130 through 135 removed outlier: 3.944A pdb=" N ALABJ 133 " --> pdb=" O HISBJ 130 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALABJ 134 " --> pdb=" O ASNBJ 131 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 67 through 72 removed outlier: 4.164A 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: 5.541A pdb=" N METBK 113 " --> pdb=" O SERBK 109 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LYSBK 114 " --> pdb=" O GLUBK 110 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILEBK 115 " --> pdb=" O LYSBK 111 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEUBK 118 " --> pdb=" O LYSBK 114 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALABK 119 " --> pdb=" O ILEBK 115 " (cutoff:3.500A) Processing helix chain 'BL' and resid 37 through 42 removed outlier: 3.634A pdb=" N ARGBL 41 " --> pdb=" O GLYBL 37 " (cutoff:3.500A) removed outlier: 5.748A 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: 3.579A pdb=" N THRBL 74 " --> pdb=" O LYSBL 70 " (cutoff:3.500A) removed outlier: 5.092A 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: 6.056A pdb=" N VALBL 85 " --> pdb=" O ASPBL 81 " (cutoff:3.500A) removed outlier: 5.178A 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: 5.460A pdb=" N ALABL 97 " --> pdb=" O ASNBL 93 " (cutoff:3.500A) Processing helix chain 'BL' and resid 128 through 139 removed outlier: 3.786A pdb=" N ALABL 133 " --> pdb=" O LYSBL 129 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALABL 134 " --> pdb=" O GLYBL 130 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALABL 138 " --> pdb=" O ALABL 134 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLYBL 139 " --> pdb=" O ILEBL 135 " (cutoff:3.500A) Processing helix chain 'BM' and resid 42 through 58 removed outlier: 3.535A pdb=" N ARGBM 51 " --> pdb=" O GLUBM 47 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALABM 56 " --> pdb=" O ALABM 52 " (cutoff:3.500A) Processing helix chain 'BM' and resid 109 through 125 removed outlier: 3.653A pdb=" N GLUBM 115 " --> pdb=" O GLUBM 111 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALABM 120 " --> pdb=" O ALABM 116 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALABM 122 " --> pdb=" O LYSBM 118 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYSBM 123 " --> pdb=" O LEUBM 119 " (cutoff:3.500A) removed outlier: 3.730A 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: 3.751A pdb=" N ALABN 19 " --> pdb=" O SERBN 15 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHEBN 21 " --> pdb=" O ARGBN 17 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARGBN 22 " --> pdb=" O GLNBN 18 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLYBN 26 " --> pdb=" O ARGBN 22 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HISBN 31 " --> pdb=" O SERBN 27 " (cutoff:3.500A) Processing helix chain 'BN' and resid 38 through 57 removed outlier: 3.997A pdb=" N ARGBN 46 " --> pdb=" O LYSBN 42 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VALBN 47 " --> pdb=" O GLUBN 43 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLUBN 49 " --> pdb=" O ARGBN 45 " (cutoff:3.500A) Proline residue: BN 50 - end of helix removed outlier: 4.600A pdb=" N THRBN 57 " --> pdb=" O THRBN 53 " (cutoff:3.500A) Processing helix chain 'BN' and resid 59 through 71 removed outlier: 3.806A pdb=" N ARGBN 64 " --> pdb=" O VALBN 60 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARGBN 69 " --> pdb=" O LEUBN 65 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THRBN 70 " --> pdb=" O ALABN 66 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARGBN 71 " --> pdb=" O PHEBN 67 " (cutoff:3.500A) Processing helix chain 'BN' and resid 72 through 81 removed outlier: 4.463A pdb=" N PHEBN 80 " --> pdb=" O VALBN 76 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASNBN 81 " --> pdb=" O ALABN 77 " (cutoff:3.500A) Processing helix chain 'BN' and resid 82 through 88 removed outlier: 3.606A pdb=" N ARGBN 86 " --> pdb=" O GLUBN 82 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHEBN 87 " --> pdb=" O LEUBN 83 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALABN 88 " --> pdb=" O GLYBN 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'BN' and resid 82 through 88' Processing helix chain 'BO' and resid 2 through 22 removed outlier: 3.902A pdb=" N ALABO 6 " --> pdb=" O ASPBO 2 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARGBO 7 " --> pdb=" O LYSBO 3 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILEBO 8 " --> pdb=" O LYSBO 4 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARGBO 9 " --> pdb=" O SERBO 5 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALABO 11 " --> pdb=" O ARGBO 7 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARGBO 13 " --> pdb=" O ARGBO 9 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ALABO 14 " --> pdb=" O ARGBO 10 " (cutoff:3.500A) removed outlier: 3.771A 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: 4.036A pdb=" N GLUBO 60 " --> pdb=" O LYSBO 56 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLNBO 61 " --> pdb=" O ALABO 57 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LYSBO 63 " --> pdb=" O ALABO 59 " (cutoff:3.500A) Processing helix chain 'BO' and resid 67 through 86 removed outlier: 3.571A pdb=" N ALABO 79 " --> pdb=" O GLYBO 75 " (cutoff:3.500A) Processing helix chain 'BO' and resid 101 through 114 removed outlier: 3.753A pdb=" N ALABO 105 " --> pdb=" O GLYBO 101 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLYBO 114 " --> pdb=" O ALABO 110 " (cutoff:3.500A) Processing helix chain 'BP' and resid 2 through 14 removed outlier: 3.547A pdb=" N GLUBP 11 " --> pdb=" O GLNBP 7 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLNBP 12 " --> pdb=" O LEUBP 8 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LYSBP 14 " --> pdb=" O GLNBP 10 " (cutoff:3.500A) Processing helix chain 'BP' and resid 97 through 104 removed outlier: 4.266A pdb=" N ARGBP 101 " --> pdb=" O LEUBP 97 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLUBP 102 " --> pdb=" O TYRBP 98 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARGBP 103 " --> pdb=" O TYRBP 99 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N THRBP 104 " --> pdb=" O LEUBP 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'BP' and resid 97 through 104' Processing helix chain 'BQ' and resid 6 through 22 removed outlier: 3.773A pdb=" N ARGBQ 11 " --> pdb=" O GLYBQ 7 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALABQ 12 " --> pdb=" O VALBQ 8 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILEBQ 17 " --> pdb=" O ARGBQ 13 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 26 through 31 removed outlier: 3.935A pdb=" N ARGBQ 30 " --> pdb=" O GLYBQ 26 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 39 through 73 removed outlier: 3.941A pdb=" N ARGBQ 51 " --> pdb=" O TYRBQ 47 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYSBQ 54 " --> pdb=" O ARGBQ 50 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARGBQ 55 " --> pdb=" O ARGBQ 51 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHEBQ 57 " --> pdb=" O ARGBQ 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARGBQ 58 " --> pdb=" O LYSBQ 54 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLNBQ 71 " --> pdb=" O ALABQ 67 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASNBQ 72 " --> pdb=" O ALABQ 68 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 75 through 87 Processing helix chain 'BQ' and resid 91 through 102 removed outlier: 3.574A pdb=" N LEUBQ 95 " --> pdb=" O ASPBQ 91 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 103 through 118 removed outlier: 3.547A pdb=" N THRBQ 107 " --> pdb=" O LYSBQ 103 " (cutoff:3.500A) Processing helix chain 'BS' and resid 15 through 25 removed outlier: 4.380A pdb=" N LEUBS 19 " --> pdb=" O GLNBS 15 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VALBS 20 " --> pdb=" O LYSBS 16 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEUBS 23 " --> pdb=" O LEUBS 19 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILEBS 24 " --> pdb=" O VALBS 20 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARGBS 25 " --> pdb=" O ALABS 21 " (cutoff:3.500A) Processing helix chain 'BS' and resid 28 through 39 removed outlier: 5.253A pdb=" N ALABS 32 " --> pdb=" O LYSBS 28 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASPBS 34 " --> pdb=" O SERBS 30 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILEBS 35 " --> pdb=" O GLNBS 31 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYRBS 38 " --> pdb=" O ASPBS 34 " (cutoff:3.500A) Processing helix chain 'BS' and resid 41 through 61 removed outlier: 3.761A pdb=" N VALBS 45 " --> pdb=" O LYSBS 41 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEUBS 46 " --> pdb=" O LYSBS 42 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYSBS 49 " --> pdb=" O VALBS 45 " (cutoff:3.500A) Processing helix chain 'BT' and resid 3 through 12 removed outlier: 3.649A pdb=" N LEUBT 7 " --> pdb=" O ARGBT 3 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYSBT 9 " --> pdb=" O GLUBT 5 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VALBT 10 " --> pdb=" O ARGBT 6 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEUBT 11 " --> pdb=" O LEUBT 7 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ARGBT 12 " --> pdb=" O LEUBT 8 " (cutoff:3.500A) Processing helix chain 'BT' and resid 17 through 26 removed outlier: 3.623A pdb=" N THRBT 22 " --> pdb=" O GLUBT 18 " (cutoff:3.500A) Processing helix chain 'BT' and resid 39 through 50 removed outlier: 3.530A pdb=" N VALBT 47 " --> pdb=" O ILEBT 43 " (cutoff:3.500A) Processing helix chain 'BU' and resid 66 through 71 removed outlier: 3.915A pdb=" N VALBU 70 " --> pdb=" O GLNBU 66 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ALABU 71 " --> pdb=" O VALBU 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'BU' and resid 66 through 71' Processing helix chain 'BV' and resid 13 through 24 removed outlier: 3.810A pdb=" N ARGBV 19 " --> pdb=" O GLYBV 15 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASNBV 24 " --> pdb=" O LEUBV 20 " (cutoff:3.500A) Processing helix chain 'BV' and resid 43 through 53 removed outlier: 3.810A pdb=" N VALBV 47 " --> pdb=" O ASPBV 43 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASNBV 49 " --> pdb=" O ASPBV 45 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALABV 52 " --> pdb=" O METBV 48 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYSBV 53 " --> pdb=" O ASNBV 49 " (cutoff:3.500A) Processing helix chain 'BV' and resid 54 through 59 Processing helix chain 'BX' and resid 52 through 63 removed outlier: 4.132A pdb=" N ARGBX 57 " --> pdb=" O ALABX 53 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VALBX 58 " --> pdb=" O LYSBX 54 " (cutoff:3.500A) Processing helix chain 'BX' and resid 64 through 75 removed outlier: 3.600A pdb=" N ALABX 69 " --> pdb=" O ASPBX 65 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARGBX 74 " --> pdb=" O GLUBX 70 " (cutoff:3.500A) Processing helix chain 'BY' and resid 1 through 7 removed outlier: 5.472A pdb=" N GLUBY 5 " --> pdb=" O METBY 1 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEUBY 6 " --> pdb=" O LYSBY 2 " (cutoff:3.500A) removed outlier: 4.323A 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 35 removed outlier: 3.693A pdb=" N GLUBY 13 " --> pdb=" O LYSBY 9 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLNBY 25 " --> pdb=" O LEUBY 21 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHEBY 26 " --> pdb=" O LEUBY 22 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASNBY 27 " --> pdb=" O ARGBY 23 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARGBY 29 " --> pdb=" O GLNBY 25 " (cutoff:3.500A) Processing helix chain 'BY' and resid 39 through 61 removed outlier: 4.514A pdb=" N LEUBY 43 " --> pdb=" O GLNBY 39 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYSBY 44 " --> pdb=" O SERBY 40 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VALBY 46 " --> pdb=" O LEUBY 42 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARGBY 47 " --> pdb=" O LEUBY 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEUBY 57 " --> pdb=" O VALBY 53 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLUBY 59 " --> pdb=" O THRBY 55 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 17 through 28 Processing helix chain 'BZ' and resid 41 through 52 removed outlier: 3.703A pdb=" N VALBZ 51 " --> pdb=" O METBZ 47 " (cutoff:3.500A) Processing helix chain 'B0' and resid 9 through 21 removed outlier: 4.529A pdb=" N HISB0 19 " --> pdb=" O METB0 15 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASPB0 20 " --> pdb=" O ARGB0 16 " (cutoff:3.500A) removed outlier: 4.041A 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 Processing helix chain 'B2' and resid 17 through 25 removed outlier: 4.223A pdb=" N THRB2 24 " --> pdb=" O ALAB2 20 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYSB2 25 " --> pdb=" O ARGB2 21 " (cutoff:3.500A) Processing helix chain 'B2' and resid 26 through 38 Processing helix chain 'B3' and resid 7 through 14 removed outlier: 3.544A pdb=" N ALAB3 11 " --> pdb=" O VALB3 7 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYSB3 12 " --> pdb=" O ARGB3 8 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARGB3 13 " --> pdb=" O GLYB3 9 " (cutoff:3.500A) Processing helix chain 'B3' and resid 37 through 46 removed outlier: 3.868A pdb=" N HISB3 43 " --> pdb=" O LYSB3 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEUB3 44 " --> pdb=" O ARGB3 40 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARGB3 45 " --> pdb=" O LYSB3 41 " (cutoff:3.500A) Proline residue: B3 46 - end of helix Processing helix chain 'B3' and resid 52 through 63 removed outlier: 3.986A pdb=" N GLYB3 56 " --> pdb=" O LYSB3 52 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEUB3 57 " --> pdb=" O GLYB3 53 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILEB3 59 " --> pdb=" O LEUB3 55 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ALAB3 60 " --> pdb=" O GLYB3 56 " (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: 6.739A pdb=" N PHEAB 90 " --> pdb=" O ILEAB 67 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEUAB 68 " --> pdb=" O ALAAB 160 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHEAB 162 " --> pdb=" O LEUAB 68 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILEAB 164 " --> pdb=" O VALAB 70 " (cutoff:3.500A) removed outlier: 3.519A 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: 3.520A pdb=" N ARGAC 54 " --> pdb=" O HISAC 69 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILEAC 64 " --> pdb=" O PROAC 98 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VALAC 66 " --> pdb=" O GLNAC 100 " (cutoff:3.500A) removed outlier: 3.745A 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: 3.574A pdb=" N THRAC 191 " --> pdb=" O GLYAC 194 " (cutoff:3.500A) removed outlier: 5.940A 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: 4.106A 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: 3.667A pdb=" N ALAAE 17 " --> pdb=" O LEUAE 36 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEUAE 36 " --> pdb=" O ALAAE 17 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILEAE 30 " --> pdb=" O LYSAE 23 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALAAE 35 " --> pdb=" O GLYAE 51 " (cutoff:3.500A) removed outlier: 4.336A 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: 7.566A 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: 3.955A pdb=" N GLUAF 40 " --> pdb=" O LEUAF 61 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYRAF 59 " --> pdb=" O TRPAF 42 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VALAF 60 " --> pdb=" O PHEAF 8 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHEAF 8 " --> pdb=" O VALAF 60 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N METAF 62 " --> pdb=" O ILEAF 6 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILEAF 6 " --> pdb=" O METAF 62 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N HISAF 3 " --> pdb=" O THRAF 92 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THRAF 92 " --> pdb=" O HISAF 3 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VALAF 7 " --> pdb=" O METAF 88 " (cutoff:3.500A) removed outlier: 5.379A 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: 6.327A 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: 6.016A pdb=" N ALAAH 23 " --> pdb=" O LEUAH 63 " (cutoff:3.500A) removed outlier: 4.779A 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: 3.779A pdb=" N CYSAH 127 " --> pdb=" O VALAH 103 " (cutoff:3.500A) removed outlier: 3.879A 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: 4.371A 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: 6.652A pdb=" N ILEAJ 8 " --> pdb=" O VALAJ 74 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILEAJ 6 " --> pdb=" O ILEAJ 76 " (cutoff:3.500A) removed outlier: 4.074A 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: 3.537A pdb=" N ILEAK 23 " --> pdb=" O METAK 85 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASNAK 109 " --> pdb=" O LEUAK 82 " (cutoff:3.500A) removed outlier: 5.955A 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: 4.788A pdb=" N LEUAL 81 " --> pdb=" O VALAL 98 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N HISAL 96 " --> pdb=" O ARGAL 83 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'AL' and resid 36 through 41 removed outlier: 3.690A pdb=" N ARGAL 36 " --> pdb=" O ARGAL 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THRAL 40 " --> pdb=" O ARGAL 50 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARGAL 50 " --> pdb=" O THRAL 40 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYSAL 51 " --> pdb=" O ILEAL 67 " (cutoff:3.500A) removed outlier: 4.035A 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: 5.514A 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: 5.639A 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: 5.222A pdb=" N LYSAQ 19 " --> pdb=" O ASPAQ 48 " (cutoff:3.500A) removed outlier: 4.203A 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: 4.234A 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: 3.754A pdb=" N ARGBC 80 " --> pdb=" O LEUBC 93 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEUBC 93 " --> pdb=" O GLUBC 79 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILEBC 74 " --> pdb=" O SERBC 118 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N SERBC 118 " --> pdb=" O ILEBC 74 " (cutoff:3.500A) removed outlier: 5.041A 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: 4.159A 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: 4.584A pdb=" N SERBD 199 " --> pdb=" O LYSBD 8 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ASPBD 200 " --> pdb=" O THRBD 112 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THRBD 112 " --> pdb=" O ASPBD 200 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VALBD 109 " --> pdb=" O VALBD 172 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VALBD 172 " --> pdb=" O VALBD 109 " (cutoff:3.500A) removed outlier: 4.059A 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: 3.946A pdb=" N ILEBD 22 " --> pdb=" O ILEBD 14 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THRBD 16 " --> pdb=" O VALBD 20 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VALBD 20 " --> pdb=" O THRBD 16 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VALBD 189 " --> pdb=" O THRBD 25 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILEBD 27 " --> pdb=" O LEUBD 187 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASPBD 181 " --> pdb=" O LEUBD 186 " (cutoff:3.500A) removed outlier: 4.031A 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: 6.873A pdb=" N GLNBD 49 " --> pdb=" O THRBD 35 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLNBD 94 " --> pdb=" O VALBD 34 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'BE' and resid 1 through 6 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'BE' and resid 117 through 120 removed outlier: 5.842A pdb=" N ARGBE 117 " --> pdb=" O ASPBE 184 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ILEBE 149 " --> pdb=" O VALBE 187 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASPBE 168 " --> pdb=" O VALBE 146 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'BF' and resid 65 through 68 removed outlier: 3.725A pdb=" N GLYBF 86 " --> pdb=" O THRBF 68 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYSBF 87 " --> pdb=" O METBF 38 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VALBF 89 " --> pdb=" O LEUBF 36 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYSBF 33 " --> pdb=" O THRBF 157 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASNBF 37 " --> pdb=" O ASPBF 153 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLYBF 39 " --> pdb=" O GLYBF 151 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLYBF 151 " --> pdb=" O GLYBF 39 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEUBF 152 " --> pdb=" O VALBF 132 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYRBF 128 " --> pdb=" O ILEBF 156 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'BG' and resid 16 through 19 removed outlier: 3.688A pdb=" N ASPBG 16 " --> pdb=" O LYSBG 27 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYSBG 18 " --> pdb=" O THRBG 25 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THRBG 25 " --> pdb=" O LYSBG 18 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'BG' and resid 41 through 45 Processing sheet with id= 32, first strand: chain 'BG' and resid 83 through 89 removed outlier: 3.622A pdb=" N PHEBG 83 " --> pdb=" O GLYBG 135 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLYBG 135 " --> pdb=" O PHEBG 83 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYSBG 85 " --> pdb=" O LEUBG 133 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEUBG 133 " --> pdb=" O LYSBG 85 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N THRBG 129 " --> pdb=" O LEUBG 89 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'BG' and resid 94 through 98 removed outlier: 3.716A pdb=" N ALABG 97 " --> pdb=" O ASNBG 104 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILEBG 103 " --> pdb=" O HISBG 115 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HISBG 115 " --> pdb=" O ILEBG 103 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'BH' and resid 3 through 6 removed outlier: 5.747A pdb=" N LYSBH 35 " --> pdb=" O LEUBH 6 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'BJ' and resid 52 through 57 removed outlier: 3.579A pdb=" N LEUBJ 57 " --> pdb=" O VALBJ 18 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLNBJ 138 " --> pdb=" O TRPBJ 15 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASPBJ 19 " --> pdb=" O LEUBJ 140 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'BJ' and resid 74 through 78 removed outlier: 3.557A pdb=" N LYSBJ 85 " --> pdb=" O HISBJ 76 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLYBJ 83 " --> pdb=" O THRBJ 78 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'BK' and resid 6 through 10 removed outlier: 3.991A pdb=" N THRBK 6 " --> pdb=" O CYSBK 21 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ARGBK 17 " --> pdb=" O VALBK 10 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'BK' and resid 38 through 42 removed outlier: 4.539A pdb=" N LYSBK 59 " --> pdb=" O LEUBK 87 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'BL' and resid 88 through 91 removed outlier: 3.520A pdb=" N LYSBL 141 " --> pdb=" O VALBL 120 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'BM' and resid 63 through 66 removed outlier: 7.176A pdb=" N LEUBM 102 " --> pdb=" O ARGBM 66 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYRBM 103 " --> pdb=" O LEUBM 33 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N SERBM 30 " --> pdb=" O LYSBM 133 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VALBM 131 " --> pdb=" O GLYBM 32 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYSBM 34 " --> pdb=" O THRBM 129 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYSBM 127 " --> pdb=" O VALBM 36 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'BN' and resid 33 through 37 removed outlier: 5.733A pdb=" N METBN 110 " --> pdb=" O CYSBN 100 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N TYRBN 94 " --> pdb=" O VALBN 116 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'BO' and resid 49 through 53 removed outlier: 3.777A pdb=" N VALBO 49 " --> pdb=" O VALBO 39 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALABO 51 " --> pdb=" O ALABO 37 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALABO 37 " --> pdb=" O ALABO 51 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THRBO 53 " --> pdb=" O ILEBO 35 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILEBO 35 " --> pdb=" O THRBO 53 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLNBO 38 " --> pdb=" O VALBO 27 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VALBO 27 " --> pdb=" O GLNBO 38 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARGBO 25 " --> pdb=" O ILEBO 40 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'BP' and resid 40 through 45 removed outlier: 6.794A pdb=" N THRBP 25 " --> pdb=" O LYSBP 87 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SERBP 85 " --> pdb=" O GLUBP 27 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SERBP 83 " --> pdb=" O LYSBP 29 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'BP' and resid 57 through 64 removed outlier: 7.933A pdb=" N SERBP 57 " --> pdb=" O THRBP 76 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'BR' and resid 3 through 6 removed outlier: 3.849A pdb=" N VALBR 14 " --> pdb=" O ALABR 3 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHEBR 5 " --> pdb=" O HISBR 12 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'BR' and resid 19 through 23 removed outlier: 3.571A pdb=" N VALBR 96 " --> pdb=" O VALBR 20 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEUBR 22 " --> pdb=" O THRBR 94 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASPBR 95 " --> pdb=" O VALBR 64 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LYSBR 60 " --> pdb=" O THRBR 99 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'BR' and resid 39 through 42 removed outlier: 8.464A pdb=" N LEUBR 39 " --> pdb=" O ILEBR 49 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILEBR 41 " --> pdb=" O VALBR 47 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'BR' and resid 57 through 60 removed outlier: 3.905A pdb=" N SERBR 102 " --> pdb=" O VALBR 58 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLYBR 100 " --> pdb=" O LYSBR 60 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'BR' and resid 67 through 78 No H-bonds generated for sheet with id= 49 Processing sheet with id= 50, first strand: chain 'BS' and resid 2 through 8 removed outlier: 4.159A pdb=" N VALBS 107 " --> pdb=" O THRBS 3 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'BT' and resid 28 through 33 removed outlier: 6.081A pdb=" N ASNBT 28 " --> pdb=" O LEUBT 87 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARGBT 77 " --> pdb=" O LYSBT 66 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYSBT 66 " --> pdb=" O ARGBT 77 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASPBT 79 " --> pdb=" O LYSBT 64 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LYSBT 64 " --> pdb=" O ASPBT 79 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYSBT 81 " --> pdb=" O VALBT 62 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VALBT 62 " --> pdb=" O LYSBT 81 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALABT 83 " --> pdb=" O THRBT 60 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THRBT 60 " --> pdb=" O ALABT 83 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VALBT 85 " --> pdb=" O VALBT 58 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VALBT 58 " --> pdb=" O VALBT 85 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'BU' and resid 40 through 43 removed outlier: 4.802A pdb=" N ASNBU 40 " --> pdb=" O ALABU 63 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'BU' and resid 82 through 87 removed outlier: 6.008A pdb=" N ARGBU 82 " --> pdb=" O LYSBU 97 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'BV' and resid 69 through 73 removed outlier: 5.112A pdb=" N PHEBV 2 " --> pdb=" O VALBV 60 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLUBV 7 " --> pdb=" O GLUBV 41 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALABV 39 " --> pdb=" O ARGBV 9 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILEBV 30 " --> pdb=" O LEUBV 38 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILEBV 89 " --> pdb=" O PROBV 27 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILEBV 29 " --> pdb=" O ILEBV 89 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASPBV 76 " --> pdb=" O ASPBV 90 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'BW' and resid 51 through 54 removed outlier: 6.683A pdb=" N GLYBW 52 " --> pdb=" O LEUBW 59 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEUBW 59 " --> pdb=" O GLYBW 52 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLYBW 54 " --> pdb=" O HISBW 57 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'BW' and resid 65 through 71 Processing sheet with id= 57, first strand: chain 'BX' and resid 12 through 17 removed outlier: 4.082A pdb=" N VALBX 13 " --> pdb=" O PHEBX 29 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THRBX 25 " --> pdb=" O ASNBX 17 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'BZ' and resid 35 through 40 removed outlier: 6.163A pdb=" N ASPBZ 40 " --> pdb=" O LYSBZ 3 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LYSBZ 3 " --> pdb=" O ASPBZ 40 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYSBZ 6 " --> pdb=" O GLUBZ 58 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLUBZ 58 " --> pdb=" O LYSBZ 6 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N METBZ 54 " --> pdb=" O THRBZ 10 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'B0' and resid 28 through 31 removed outlier: 6.264A pdb=" N SERB0 29 " --> pdb=" O LYSB0 37 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYSB0 37 " --> pdb=" O SERB0 29 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASPB0 31 " --> pdb=" O GLYB0 35 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'B1' and resid 7 through 12 removed outlier: 3.509A pdb=" N GLUB1 7 " --> pdb=" O LYSB1 25 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'B1' and resid 33 through 39 removed outlier: 5.801A pdb=" N LEUB1 34 " --> pdb=" O GLUB1 51 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLUB1 51 " --> pdb=" O LEUB1 34 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEUB1 36 " --> pdb=" O TYRB1 49 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYRB1 49 " --> pdb=" O LEUB1 36 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'B4' and resid 14 through 19 removed outlier: 3.629A pdb=" N GLNB4 35 " --> pdb=" O VALB4 25 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N CYSB4 27 " --> pdb=" O HISB4 33 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N HISB4 33 " --> pdb=" O CYSB4 27 " (cutoff:3.500A) 1417 hydrogen bonds defined for protein. 4188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4009 hydrogen bonds 6218 hydrogen bond angles 0 basepair planarities 1601 basepair parallelities 2753 stacking parallelities Total time for adding SS restraints: 270.33 Time building geometry restraints manager: 63.67 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: 22731 1.33 - 1.45: 64536 1.45 - 1.57: 60934 1.57 - 1.69: 9419 1.69 - 1.81: 262 Bond restraints: 157882 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 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 1.380 0.255 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 bond pdb=" N3 5MUAY 54 " pdb=" C4 5MUAY 54 " ideal model delta sigma weight residual 1.182 1.403 -0.221 2.00e-02 2.50e+03 1.23e+02 ... (remaining 157877 not shown) Histogram of bond angle deviations from ideal: 100.08 - 107.12: 25128 107.12 - 114.17: 103880 114.17 - 121.21: 68489 121.21 - 128.25: 30719 128.25 - 135.30: 8304 Bond angle restraints: 236520 Sorted by residual: angle pdb=" C1' 2MAAX 37 " pdb=" N9 2MAAX 37 " pdb=" C8 2MAAX 37 " ideal model delta sigma weight residual 106.32 128.58 -22.26 3.00e+00 1.11e-01 5.51e+01 angle pdb=" C VALAL 21 " pdb=" N PROAL 22 " pdb=" CA PROAL 22 " ideal model delta sigma weight residual 119.28 126.18 -6.90 1.10e+00 8.26e-01 3.94e+01 angle pdb=" C THRBI 73 " pdb=" N PROBI 74 " pdb=" CA PROBI 74 " ideal model delta sigma weight residual 119.66 124.11 -4.45 7.30e-01 1.88e+00 3.72e+01 angle pdb=" C ILEBC 135 " pdb=" N PROBC 136 " pdb=" CA PROBC 136 " ideal model delta sigma weight residual 119.78 125.83 -6.05 1.03e+00 9.43e-01 3.45e+01 angle pdb=" N ILEBC 135 " pdb=" CA ILEBC 135 " pdb=" C ILEBC 135 " ideal model delta sigma weight residual 108.63 113.65 -5.02 8.60e-01 1.35e+00 3.40e+01 ... (remaining 236515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 89500 35.96 - 71.92: 10342 71.92 - 107.89: 1293 107.89 - 143.85: 10 143.85 - 179.81: 29 Dihedral angle restraints: 101174 sinusoidal: 85165 harmonic: 16009 Sorted by residual: dihedral pdb=" C4' AAA1493 " pdb=" C3' AAA1493 " pdb=" C2' AAA1493 " pdb=" C1' AAA1493 " ideal model delta sinusoidal sigma weight residual -35.00 35.87 -70.87 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' UBA2506 " pdb=" C3' UBA2506 " pdb=" C2' UBA2506 " pdb=" C1' UBA2506 " ideal model delta sinusoidal sigma weight residual -35.00 34.42 -69.42 1 8.00e+00 1.56e-02 9.73e+01 dihedral pdb=" O4' AAA1493 " pdb=" C2' AAA1493 " pdb=" C1' AAA1493 " pdb=" C3' AAA1493 " ideal model delta sinusoidal sigma weight residual -35.00 33.57 -68.57 1 8.00e+00 1.56e-02 9.52e+01 ... (remaining 101171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.120: 30231 1.120 - 2.240: 0 2.240 - 3.360: 0 3.360 - 4.481: 0 4.481 - 5.601: 4 Chirality restraints: 30235 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 2.86 -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 -5.50 2.00e-01 2.50e+01 7.57e+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 -2.70 5.38 2.00e-01 2.50e+01 7.24e+02 ... (remaining 30232 not shown) Planarity restraints: 12439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' H2UAX 19 " -0.864 2.00e-02 2.50e+03 5.78e-01 7.52e+03 pdb=" C4' H2UAX 19 " 0.216 2.00e-02 2.50e+03 pdb=" O4' H2UAX 19 " 0.708 2.00e-02 2.50e+03 pdb=" C3' H2UAX 19 " -0.226 2.00e-02 2.50e+03 pdb=" O3' H2UAX 19 " 0.881 2.00e-02 2.50e+03 pdb=" C2' H2UAX 19 " -0.602 2.00e-02 2.50e+03 pdb=" O2' H2UAX 19 " -0.568 2.00e-02 2.50e+03 pdb=" C1' H2UAX 19 " 0.448 2.00e-02 2.50e+03 pdb=" N1 H2UAX 19 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MGAY 46 " -0.854 2.00e-02 2.50e+03 5.76e-01 7.46e+03 pdb=" C4' 7MGAY 46 " 0.221 2.00e-02 2.50e+03 pdb=" O4' 7MGAY 46 " 0.683 2.00e-02 2.50e+03 pdb=" C3' 7MGAY 46 " -0.220 2.00e-02 2.50e+03 pdb=" O3' 7MGAY 46 " 0.893 2.00e-02 2.50e+03 pdb=" C2' 7MGAY 46 " -0.606 2.00e-02 2.50e+03 pdb=" O2' 7MGAY 46 " -0.574 2.00e-02 2.50e+03 pdb=" C1' 7MGAY 46 " 0.443 2.00e-02 2.50e+03 pdb=" N9 7MGAY 46 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MUAX 54 " 0.034 2.00e-02 2.50e+03 5.69e-01 7.27e+03 pdb=" C4' 5MUAX 54 " 0.433 2.00e-02 2.50e+03 pdb=" O4' 5MUAX 54 " 0.618 2.00e-02 2.50e+03 pdb=" C3' 5MUAX 54 " -0.589 2.00e-02 2.50e+03 pdb=" O3' 5MUAX 54 " -0.570 2.00e-02 2.50e+03 pdb=" C2' 5MUAX 54 " -0.208 2.00e-02 2.50e+03 pdb=" O2' 5MUAX 54 " 0.912 2.00e-02 2.50e+03 pdb=" C1' 5MUAX 54 " 0.231 2.00e-02 2.50e+03 pdb=" N1 5MUAX 54 " -0.860 2.00e-02 2.50e+03 ... (remaining 12436 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 6 2.13 - 2.82: 39545 2.82 - 3.51: 187038 3.51 - 4.21: 469747 4.21 - 4.90: 612453 Nonbonded interactions: 1308789 Sorted by model distance: nonbonded pdb=" O3' AAX 76 " pdb=" C ASPB5 0 " model vdw 1.433 3.270 nonbonded pdb=" O2' AAA1493 " pdb=" OP1 GAA1494 " model vdw 1.913 2.440 nonbonded pdb=" O2 CAA1409 " pdb=" N6 AAA1492 " model vdw 2.002 2.520 nonbonded pdb=" O3' AAA1493 " pdb=" N1 ABA1913 " model vdw 2.021 3.120 nonbonded pdb=" O2' AAA1492 " pdb=" N7 AAA1493 " model vdw 2.078 2.520 ... (remaining 1308784 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: 2.300 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: 0.160 Extract box with map and model: 15.810 Check model and map are aligned: 1.570 Set scattering table: 0.980 Process input model: 561.300 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 588.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 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 157882 Z= 0.884 Angle : 1.742 22.260 236520 Z= 0.669 Chirality : 0.067 5.601 30235 Planarity : 0.014 0.578 12439 Dihedral : 22.170 179.811 90848 Min Nonbonded Distance : 1.433 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 2.68 % Allowed : 7.33 % Favored : 89.99 % 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: -1.92 (0.11), residues: 5522 helix: -3.03 (0.07), residues: 1588 sheet: -3.24 (0.14), residues: 873 loop : 0.63 (0.12), residues: 3061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRPBC 213 HIS 0.004 0.001 HISBZ 34 PHE 0.017 0.001 PHEBC 30 TYR 0.016 0.001 TYRAD 75 ARG 0.010 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 2000 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2000 time to evaluate : 5.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 43 LEU cc_start: 0.6428 (pp) cc_final: 0.6188 (tp) REVERT: AB 105 LYS cc_start: 0.7092 (tttt) cc_final: 0.6799 (pttt) REVERT: AC 36 ASP cc_start: 0.6052 (m-30) cc_final: 0.5684 (t0) REVERT: AD 192 SER cc_start: 0.3061 (t) cc_final: 0.2849 (t) REVERT: AD 198 HIS cc_start: 0.6434 (p90) cc_final: 0.5765 (p90) REVERT: AE 83 HIS cc_start: 0.7466 (p90) cc_final: 0.7262 (p90) REVERT: AE 89 HIS cc_start: 0.5595 (t70) cc_final: 0.4868 (t70) REVERT: AE 141 ILE cc_start: 0.8297 (mp) cc_final: 0.7972 (mt) REVERT: AF 59 TYR cc_start: 0.5090 (m-10) cc_final: 0.4821 (m-10) REVERT: AI 19 VAL cc_start: 0.6289 (t) cc_final: 0.6014 (p) REVERT: AK 24 HIS cc_start: 0.5358 (t70) cc_final: 0.5077 (t-90) REVERT: AN 11 VAL cc_start: 0.7415 (t) cc_final: 0.7177 (t) REVERT: AN 96 LEU cc_start: 0.7292 (tp) cc_final: 0.7006 (tp) REVERT: AP 21 VAL cc_start: 0.8157 (t) cc_final: 0.7946 (p) REVERT: AS 62 VAL cc_start: 0.5597 (t) cc_final: 0.5296 (t) REVERT: BC 146 MET cc_start: 0.4785 (mtp) cc_final: 0.4364 (ttm) REVERT: BD 67 HIS cc_start: 0.6111 (t70) cc_final: 0.5796 (t-90) REVERT: BD 110 THR cc_start: 0.8037 (m) cc_final: 0.7771 (m) REVERT: BD 151 THR cc_start: 0.7627 (m) cc_final: 0.7150 (p) REVERT: BD 171 THR cc_start: 0.7196 (m) cc_final: 0.6896 (p) REVERT: BE 136 GLN cc_start: 0.6811 (mm-40) cc_final: 0.6477 (mt0) REVERT: BE 187 VAL cc_start: 0.6062 (t) cc_final: 0.5845 (m) REVERT: BE 189 THR cc_start: 0.5078 (m) cc_final: 0.4421 (p) REVERT: BF 17 MET cc_start: 0.5495 (mmm) cc_final: 0.4496 (tpt) REVERT: BI 136 MET cc_start: 0.1975 (mtm) cc_final: 0.1550 (ttm) REVERT: BJ 1 MET cc_start: 0.2956 (ptp) cc_final: 0.2664 (mtt) REVERT: BJ 67 ASN cc_start: 0.7036 (m-40) cc_final: 0.6558 (m-40) REVERT: BK 2 ILE cc_start: 0.8481 (mm) cc_final: 0.8057 (mm) REVERT: BK 39 ILE cc_start: 0.8910 (pt) cc_final: 0.8429 (pt) REVERT: BK 77 ILE cc_start: 0.8373 (mt) cc_final: 0.8152 (mt) REVERT: BK 111 LYS cc_start: 0.6962 (ptpt) cc_final: 0.6747 (ptpp) REVERT: BM 53 MET cc_start: 0.7245 (mtt) cc_final: 0.6884 (mtm) REVERT: BM 115 GLU cc_start: 0.6460 (mm-30) cc_final: 0.6054 (mm-30) REVERT: BM 134 THR cc_start: 0.4537 (p) cc_final: 0.4207 (m) REVERT: BN 58 ASP cc_start: 0.4510 (t0) cc_final: 0.3918 (p0) REVERT: BN 102 PHE cc_start: 0.7320 (m-10) cc_final: 0.7084 (m-10) REVERT: BN 107 ASN cc_start: 0.7059 (t0) cc_final: 0.6462 (t0) REVERT: BO 49 VAL cc_start: 0.6144 (t) cc_final: 0.5877 (t) REVERT: BQ 74 ILE cc_start: 0.7116 (tt) cc_final: 0.6892 (tt) REVERT: BS 38 TYR cc_start: 0.6235 (m-80) cc_final: 0.5872 (m-80) REVERT: BS 71 VAL cc_start: 0.6758 (t) cc_final: 0.6547 (t) REVERT: BS 104 THR cc_start: 0.6580 (m) cc_final: 0.5837 (p) REVERT: BS 106 VAL cc_start: 0.7670 (t) cc_final: 0.7380 (t) REVERT: BT 14 PRO cc_start: 0.4671 (Cg_endo) cc_final: 0.4415 (Cg_exo) REVERT: B0 12 LYS cc_start: 0.7752 (tptt) cc_final: 0.7325 (tppt) REVERT: B3 29 LEU cc_start: 0.7157 (tp) cc_final: 0.6876 (tp) REVERT: B4 18 LYS cc_start: 0.7127 (ttmt) cc_final: 0.6781 (pttm) outliers start: 0 outliers final: 0 residues processed: 2000 average time/residue: 1.4292 time to fit residues: 4691.7927 Evaluate side-chains 1206 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1206 time to evaluate : 5.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 851 optimal weight: 20.0000 chunk 764 optimal weight: 5.9990 chunk 423 optimal weight: 5.9990 chunk 260 optimal weight: 8.9990 chunk 515 optimal weight: 0.9990 chunk 408 optimal weight: 0.9990 chunk 790 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 480 optimal weight: 0.9990 chunk 588 optimal weight: 0.9990 chunk 915 optimal weight: 5.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 15 HIS ** AB 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 32 ASN AC 102 ASN AC 176 HIS AD 40 GLN AD 100 ASN AD 136 GLN AG 28 ASN AG 142 HIS ** AG 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 4 GLN ** AH 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 126 GLN AJ 56 HIS ** AK 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 5 ASN AM 12 HIS ** AQ 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AS 57 HIS ** AT 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 46 ASN BC 58 HIS BC 90 ASN BC 134 ASN BC 163 GLN BC 200 HIS BC 260 ASN ** BD 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 49 GLN BD 164 GLN BE 30 GLN BE 41 GLN BE 163 ASN BF 127 ASN ** BG 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 116 GLN BI 12 GLN BJ 130 HIS BJ 131 ASN BK 3 GLN BK 29 HIS ** BM 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 31 HIS BO 104 GLN BQ 37 GLN BQ 52 GLN BS 40 ASN BS 61 ASN ** BU 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BU 69 ASN BU 74 ASN ** BV 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 87 GLN BX 16 ASN BX 17 ASN ** BX 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 36 HIS ** BY 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B0 19 HIS B0 38 HIS B0 42 HIS B1 46 HIS ** B3 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4 35 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 157882 Z= 0.162 Angle : 0.615 26.661 236520 Z= 0.314 Chirality : 0.038 2.337 30235 Planarity : 0.006 0.145 12439 Dihedral : 23.050 179.477 79768 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 1.03 % Allowed : 6.95 % Favored : 92.01 % Rotamer: Outliers : 3.42 % Allowed : 14.39 % Favored : 82.19 % 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: -1.52 (0.11), residues: 5522 helix: -1.21 (0.11), residues: 1657 sheet: -2.84 (0.14), residues: 922 loop : -0.04 (0.12), residues: 2943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPBQ 61 HIS 0.010 0.001 HISAM 12 PHE 0.035 0.002 PHEAS 74 TYR 0.036 0.002 TYRBP 98 ARG 0.021 0.001 ARGBF 148 *********************** 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 1487 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1330 time to evaluate : 6.068 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: AB 38 VAL cc_start: 0.5027 (t) cc_final: 0.4745 (t) REVERT: AB 43 LEU cc_start: 0.6657 (pp) cc_final: 0.6280 (tp) REVERT: AB 118 GLU cc_start: 0.4703 (pt0) cc_final: 0.4481 (pt0) REVERT: AC 23 PHE cc_start: 0.7289 (t80) cc_final: 0.7048 (t80) REVERT: AD 33 LYS cc_start: 0.5919 (mttt) cc_final: 0.5450 (pttt) REVERT: AE 45 ARG cc_start: 0.5800 (tpt-90) cc_final: 0.5552 (tpp-160) REVERT: AE 83 HIS cc_start: 0.7469 (p90) cc_final: 0.6858 (p90) REVERT: AG 116 MET cc_start: 0.4878 (tpp) cc_final: 0.4656 (tpp) REVERT: AG 144 MET cc_start: 0.4834 (mmm) cc_final: 0.3791 (ttm) REVERT: AJ 66 GLU cc_start: 0.5187 (mt-10) cc_final: 0.4174 (mt-10) REVERT: AM 11 ASP cc_start: 0.6779 (t0) cc_final: 0.5601 (m-30) REVERT: AM 12 HIS cc_start: 0.5792 (t-90) cc_final: 0.5096 (t-170) REVERT: AM 97 VAL cc_start: 0.8619 (t) cc_final: 0.8383 (p) REVERT: AN 96 LEU cc_start: 0.7451 (tp) cc_final: 0.7163 (tp) REVERT: AP 56 ARG cc_start: 0.6052 (mmm160) cc_final: 0.5759 (tpm170) REVERT: AT 27 MET cc_start: 0.6720 (ppp) cc_final: 0.6181 (ttm) REVERT: AT 31 PHE cc_start: 0.6060 (m-80) cc_final: 0.5758 (m-80) REVERT: AT 74 ARG cc_start: 0.6103 (ttp80) cc_final: 0.5825 (ttm170) REVERT: AT 79 LEU cc_start: 0.7298 (mt) cc_final: 0.6314 (mt) REVERT: BC 146 MET cc_start: 0.5073 (mtp) cc_final: 0.4684 (ttm) REVERT: BD 40 LEU cc_start: 0.6153 (mp) cc_final: 0.5693 (mp) REVERT: BD 151 THR cc_start: 0.7297 (OUTLIER) cc_final: 0.6832 (p) REVERT: BE 136 GLN cc_start: 0.7059 (mm-40) cc_final: 0.6470 (mt0) REVERT: BE 195 GLN cc_start: 0.5221 (tm-30) cc_final: 0.4908 (tm-30) REVERT: BF 17 MET cc_start: 0.5136 (mmm) cc_final: 0.4317 (tpt) REVERT: BF 123 ASP cc_start: 0.4486 (p0) cc_final: 0.4065 (p0) REVERT: BF 144 ASP cc_start: 0.3973 (m-30) cc_final: 0.2733 (t0) REVERT: BG 17 VAL cc_start: 0.6010 (t) cc_final: 0.5743 (m) REVERT: BI 117 MET cc_start: 0.1222 (mmm) cc_final: -0.0426 (ppp) REVERT: BI 136 MET cc_start: 0.1669 (mtm) cc_final: 0.1239 (ttm) REVERT: BJ 1 MET cc_start: 0.2994 (ptp) cc_final: 0.2741 (mtt) REVERT: BJ 23 LYS cc_start: 0.7167 (mtpp) cc_final: 0.6910 (mtmm) REVERT: BJ 119 PHE cc_start: 0.6008 (t80) cc_final: 0.5734 (t80) REVERT: BK 2 ILE cc_start: 0.8063 (mm) cc_final: 0.7779 (mm) REVERT: BK 9 ASN cc_start: 0.7733 (m-40) cc_final: 0.7517 (m-40) REVERT: BK 106 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: BM 73 ILE cc_start: 0.8738 (mp) cc_final: 0.8499 (tp) REVERT: BM 101 VAL cc_start: 0.6486 (t) cc_final: 0.6159 (p) REVERT: BM 115 GLU cc_start: 0.6549 (mm-30) cc_final: 0.6227 (mm-30) REVERT: BN 24 MET cc_start: 0.5447 (ttp) cc_final: 0.5172 (ttt) REVERT: BN 37 THR cc_start: 0.8558 (p) cc_final: 0.7975 (m) REVERT: BN 58 ASP cc_start: 0.4500 (t0) cc_final: 0.3897 (p0) REVERT: BN 102 PHE cc_start: 0.7342 (m-10) cc_final: 0.7081 (m-10) REVERT: BN 107 ASN cc_start: 0.6810 (t0) cc_final: 0.6309 (t0) REVERT: BO 83 LEU cc_start: 0.5117 (mt) cc_final: 0.4028 (tp) REVERT: BO 95 SER cc_start: 0.7599 (m) cc_final: 0.7135 (p) REVERT: BP 72 ARG cc_start: 0.7432 (mtp180) cc_final: 0.6879 (ttm170) REVERT: BP 96 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.6097 (tptp) REVERT: BQ 20 GLN cc_start: 0.8335 (mp10) cc_final: 0.8053 (mp10) REVERT: BQ 74 ILE cc_start: 0.6876 (tt) cc_final: 0.6642 (tt) REVERT: BR 10 LYS cc_start: 0.5888 (mtmm) cc_final: 0.5426 (mtmm) REVERT: BR 62 GLU cc_start: 0.5668 (tp30) cc_final: 0.5244 (tp30) REVERT: BR 80 ARG cc_start: 0.8034 (ttp-110) cc_final: 0.7831 (ttp-110) REVERT: BS 38 TYR cc_start: 0.6798 (m-80) cc_final: 0.6508 (m-80) REVERT: BS 48 LYS cc_start: 0.8213 (tttp) cc_final: 0.7959 (tttp) REVERT: BS 104 THR cc_start: 0.6505 (m) cc_final: 0.5967 (p) REVERT: BT 7 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.5851 (tp) REVERT: BT 24 MET cc_start: 0.5598 (tpt) cc_final: 0.5319 (tpt) REVERT: BV 26 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.6919 (p90) REVERT: BV 51 GLN cc_start: 0.6220 (pp30) cc_final: 0.5559 (pt0) REVERT: BV 56 PHE cc_start: 0.6705 (t80) cc_final: 0.6369 (t80) REVERT: B0 12 LYS cc_start: 0.7654 (tptt) cc_final: 0.7116 (tppt) REVERT: B3 29 LEU cc_start: 0.7224 (tp) cc_final: 0.6953 (tp) outliers start: 157 outliers final: 84 residues processed: 1393 average time/residue: 1.3213 time to fit residues: 3144.8737 Evaluate side-chains 1231 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1142 time to evaluate : 5.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 167 ASP Chi-restraints excluded: chain AB residue 168 HIS Chi-restraints excluded: chain AB residue 181 ILE Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 40 GLN Chi-restraints excluded: chain AD residue 67 VAL Chi-restraints excluded: chain AD residue 81 ARG Chi-restraints excluded: chain AD residue 134 SER Chi-restraints excluded: chain AD residue 142 VAL Chi-restraints excluded: chain AD residue 181 THR Chi-restraints excluded: chain AE residue 90 THR Chi-restraints excluded: chain AF residue 85 ILE Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AG residue 6 VAL Chi-restraints excluded: chain AG residue 22 LEU Chi-restraints excluded: chain AG residue 27 VAL Chi-restraints excluded: chain AG residue 35 LYS Chi-restraints excluded: chain AH residue 12 THR Chi-restraints excluded: chain AH residue 30 SER Chi-restraints excluded: chain AH residue 51 VAL Chi-restraints excluded: chain AH residue 106 THR Chi-restraints excluded: chain AH residue 112 THR Chi-restraints excluded: chain AI residue 116 VAL Chi-restraints excluded: chain AK residue 26 SER Chi-restraints excluded: chain AL residue 3 THR Chi-restraints excluded: chain AL residue 8 VAL Chi-restraints excluded: chain AL residue 41 THR Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 66 GLU Chi-restraints excluded: chain AM residue 74 SER Chi-restraints excluded: chain AN residue 79 LEU Chi-restraints excluded: chain AO residue 24 SER Chi-restraints excluded: chain AP residue 19 VAL Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AQ residue 70 THR Chi-restraints excluded: chain AS residue 79 THR Chi-restraints excluded: chain AT residue 39 ILE Chi-restraints excluded: chain BC residue 65 VAL Chi-restraints excluded: chain BC residue 144 VAL Chi-restraints excluded: chain BD residue 29 VAL Chi-restraints excluded: chain BD residue 100 LEU Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 183 GLU Chi-restraints excluded: chain BE residue 1 MET Chi-restraints excluded: chain BE residue 12 LEU Chi-restraints excluded: chain BF residue 35 THR Chi-restraints excluded: chain BF residue 113 ASP Chi-restraints excluded: chain BJ residue 52 ASP Chi-restraints excluded: chain BK residue 57 VAL Chi-restraints excluded: chain BK residue 61 VAL Chi-restraints excluded: chain BK residue 103 VAL Chi-restraints excluded: chain BK residue 106 GLU Chi-restraints excluded: chain BM residue 106 ASP Chi-restraints excluded: chain BM residue 136 MET Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 33 ILE Chi-restraints excluded: chain BN residue 116 VAL Chi-restraints excluded: chain BO residue 43 ASN Chi-restraints excluded: chain BO residue 48 LEU Chi-restraints excluded: chain BP residue 40 LEU Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BP residue 96 LYS Chi-restraints excluded: chain BQ residue 17 ILE Chi-restraints excluded: chain BQ residue 22 LYS Chi-restraints excluded: chain BQ residue 75 SER Chi-restraints excluded: chain BQ residue 77 SER Chi-restraints excluded: chain BQ residue 110 VAL Chi-restraints excluded: chain BR residue 43 ASN Chi-restraints excluded: chain BR residue 64 VAL Chi-restraints excluded: chain BS residue 12 SER Chi-restraints excluded: chain BS residue 85 ILE Chi-restraints excluded: chain BS residue 99 ARG Chi-restraints excluded: chain BS residue 107 VAL Chi-restraints excluded: chain BT residue 7 LEU Chi-restraints excluded: chain BT residue 17 SER Chi-restraints excluded: chain BT residue 60 THR Chi-restraints excluded: chain BT residue 63 VAL Chi-restraints excluded: chain BU residue 15 THR Chi-restraints excluded: chain BU residue 83 VAL Chi-restraints excluded: chain BV residue 7 GLU Chi-restraints excluded: chain BV residue 26 PHE Chi-restraints excluded: chain BV residue 65 VAL Chi-restraints excluded: chain BV residue 86 LEU Chi-restraints excluded: chain BW residue 38 VAL Chi-restraints excluded: chain BY residue 55 THR Chi-restraints excluded: chain BZ residue 48 ILE Chi-restraints excluded: chain B1 residue 23 THR Chi-restraints excluded: chain B4 residue 17 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 508 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 761 optimal weight: 6.9990 chunk 623 optimal weight: 20.0000 chunk 252 optimal weight: 0.9990 chunk 917 optimal weight: 30.0000 chunk 990 optimal weight: 20.0000 chunk 816 optimal weight: 0.9980 chunk 909 optimal weight: 5.9990 chunk 312 optimal weight: 8.9990 chunk 735 optimal weight: 8.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 19 GLN AC 102 ASN AD 40 GLN AD 196 ASN AG 142 HIS AG 148 ASN AH 4 GLN AI 31 ASN ** AI 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 64 GLN ** AK 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AM 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 43 ASN AO 40 GLN AQ 9 GLN AT 3 ASN ** AT 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 134 ASN BC 260 ASN BD 36 GLN BD 150 GLN BD 167 ASN BG 45 HIS BI 43 ASN BJ 40 HIS BJ 131 ASN BL 38 GLN BM 97 GLN BN 3 HIS BO 29 HIS BP 56 HIS BQ 14 HIS BQ 52 GLN BS 7 HIS BS 40 ASN BT 59 ASN BT 72 GLN ** BU 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BV 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 87 GLN ** BX 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BY 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 157882 Z= 0.287 Angle : 0.752 28.381 236520 Z= 0.383 Chirality : 0.043 2.223 30235 Planarity : 0.007 0.191 12439 Dihedral : 23.147 179.765 79768 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.98 % Allowed : 7.30 % Favored : 91.72 % Rotamer: Outliers : 5.77 % Allowed : 15.37 % Favored : 78.86 % 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: -1.60 (0.11), residues: 5522 helix: -0.62 (0.12), residues: 1679 sheet: -2.55 (0.15), residues: 908 loop : -0.69 (0.11), residues: 2935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRPBC 213 HIS 0.017 0.002 HISBR 82 PHE 0.053 0.003 PHEAS 74 TYR 0.042 0.003 TYRBP 98 ARG 0.019 0.001 ARGAP 51 *********************** 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 1588 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1323 time to evaluate : 7.960 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 43 LEU cc_start: 0.6678 (pp) cc_final: 0.6255 (tp) REVERT: AB 93 ASN cc_start: 0.4242 (OUTLIER) cc_final: 0.3567 (p0) REVERT: AC 37 PHE cc_start: 0.7329 (t80) cc_final: 0.7078 (t80) REVERT: AE 82 GLN cc_start: 0.6246 (mt0) cc_final: 0.6029 (mp10) REVERT: AF 42 TRP cc_start: 0.4649 (m-10) cc_final: 0.4412 (m-10) REVERT: AG 64 VAL cc_start: 0.6186 (m) cc_final: 0.5860 (t) REVERT: AG 144 MET cc_start: 0.5120 (mmm) cc_final: 0.4546 (ttp) REVERT: AH 111 MET cc_start: 0.6922 (OUTLIER) cc_final: 0.6721 (mtt) REVERT: AJ 58 ASN cc_start: 0.6190 (m110) cc_final: 0.5904 (m-40) REVERT: AL 36 ARG cc_start: 0.5636 (OUTLIER) cc_final: 0.4890 (tmm-80) REVERT: AM 97 VAL cc_start: 0.8697 (t) cc_final: 0.8436 (p) REVERT: AN 4 GLN cc_start: 0.7111 (tp40) cc_final: 0.6586 (tp-100) REVERT: AN 77 PHE cc_start: 0.7716 (m-80) cc_final: 0.7456 (m-10) REVERT: AN 84 VAL cc_start: 0.8566 (t) cc_final: 0.8320 (t) REVERT: AO 35 GLN cc_start: 0.6888 (tt0) cc_final: 0.6683 (tt0) REVERT: AO 49 ASP cc_start: 0.7623 (t0) cc_final: 0.7300 (t0) REVERT: AP 17 TYR cc_start: 0.6261 (m-80) cc_final: 0.5869 (m-10) REVERT: AQ 17 MET cc_start: 0.5228 (pmm) cc_final: 0.4662 (ppp) REVERT: AT 74 ARG cc_start: 0.6415 (ttp80) cc_final: 0.6175 (ttp-170) REVERT: AU 34 ARG cc_start: 0.4455 (ttt-90) cc_final: 0.4199 (ttt-90) REVERT: BD 126 ASN cc_start: 0.7989 (m110) cc_final: 0.7621 (t0) REVERT: BE 60 TRP cc_start: 0.7970 (p90) cc_final: 0.7528 (p90) REVERT: BE 136 GLN cc_start: 0.7206 (mm-40) cc_final: 0.6483 (mt0) REVERT: BE 195 GLN cc_start: 0.5540 (tm-30) cc_final: 0.3340 (tm-30) REVERT: BF 17 MET cc_start: 0.4795 (mmm) cc_final: 0.4372 (tpt) REVERT: BF 85 ILE cc_start: 0.7128 (mm) cc_final: 0.6794 (tt) REVERT: BF 123 ASP cc_start: 0.4648 (p0) cc_final: 0.4163 (p0) REVERT: BF 130 MET cc_start: 0.6713 (ppp) cc_final: 0.6499 (ppp) REVERT: BF 144 ASP cc_start: 0.3910 (m-30) cc_final: 0.3560 (t0) REVERT: BG 17 VAL cc_start: 0.6444 (t) cc_final: 0.5913 (m) REVERT: BG 151 TYR cc_start: 0.6308 (m-80) cc_final: 0.6008 (m-80) REVERT: BI 136 MET cc_start: 0.2087 (mtm) cc_final: 0.1547 (ttm) REVERT: BJ 44 TYR cc_start: 0.7719 (t80) cc_final: 0.6848 (t80) REVERT: BK 9 ASN cc_start: 0.7713 (m-40) cc_final: 0.7475 (m-40) REVERT: BK 78 ARG cc_start: 0.7902 (mtm110) cc_final: 0.7681 (mtm110) REVERT: BM 115 GLU cc_start: 0.6721 (mm-30) cc_final: 0.6253 (mm-30) REVERT: BM 136 MET cc_start: 0.1534 (ttp) cc_final: 0.1144 (mmt) REVERT: BN 24 MET cc_start: 0.5792 (ttp) cc_final: 0.5581 (ttt) REVERT: BN 58 ASP cc_start: 0.4343 (t0) cc_final: 0.3703 (p0) REVERT: BN 102 PHE cc_start: 0.7679 (m-10) cc_final: 0.7335 (m-10) REVERT: BN 107 ASN cc_start: 0.7708 (t0) cc_final: 0.7289 (t0) REVERT: BN 110 MET cc_start: 0.7474 (tpp) cc_final: 0.7161 (tpt) REVERT: BO 3 LYS cc_start: 0.5224 (ttpt) cc_final: 0.4895 (ttmm) REVERT: BO 88 LYS cc_start: 0.4402 (tppt) cc_final: 0.4162 (mmmt) REVERT: BO 95 SER cc_start: 0.8131 (m) cc_final: 0.7467 (p) REVERT: BP 12 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6032 (mm-40) REVERT: BP 96 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6698 (tptp) REVERT: BQ 20 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: BR 62 GLU cc_start: 0.5786 (tp30) cc_final: 0.5345 (tp30) REVERT: BS 38 TYR cc_start: 0.6668 (m-80) cc_final: 0.6363 (m-80) REVERT: BS 98 LYS cc_start: 0.7841 (mtpp) cc_final: 0.7488 (mttt) REVERT: BT 11 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6977 (mm) REVERT: BT 39 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7382 (m) REVERT: BV 2 PHE cc_start: 0.2869 (m-80) cc_final: 0.2661 (m-80) REVERT: BV 26 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7697 (p90) REVERT: BV 51 GLN cc_start: 0.6526 (pp30) cc_final: 0.6036 (pt0) REVERT: BX 32 ASN cc_start: 0.7313 (t0) cc_final: 0.7029 (t0) REVERT: B0 12 LYS cc_start: 0.7719 (tptt) cc_final: 0.7328 (tppt) REVERT: B1 8 LYS cc_start: 0.5804 (OUTLIER) cc_final: 0.5596 (mtmt) REVERT: B2 37 LYS cc_start: 0.6489 (tttt) cc_final: 0.6261 (ttmt) REVERT: B3 29 LEU cc_start: 0.7710 (tp) cc_final: 0.7380 (tp) outliers start: 265 outliers final: 162 residues processed: 1466 average time/residue: 1.3761 time to fit residues: 3489.6277 Evaluate side-chains 1306 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1135 time to evaluate : 5.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 93 ASN Chi-restraints excluded: chain AB residue 168 HIS Chi-restraints excluded: chain AC residue 12 LEU Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AC residue 191 THR Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 67 VAL Chi-restraints excluded: chain AD residue 81 ARG Chi-restraints excluded: chain AD residue 102 VAL Chi-restraints excluded: chain AD residue 138 SER Chi-restraints excluded: chain AD residue 142 VAL Chi-restraints excluded: chain AD residue 144 SER Chi-restraints excluded: chain AD residue 200 ILE Chi-restraints excluded: chain AE residue 90 THR Chi-restraints excluded: chain AE residue 106 ILE Chi-restraints excluded: chain AE residue 131 THR Chi-restraints excluded: chain AF residue 3 HIS Chi-restraints excluded: chain AF residue 51 ILE Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AG residue 27 VAL Chi-restraints excluded: chain AG residue 32 VAL Chi-restraints excluded: chain AG residue 35 LYS Chi-restraints excluded: chain AG residue 38 THR Chi-restraints excluded: chain AG residue 89 VAL Chi-restraints excluded: chain AG residue 141 VAL Chi-restraints excluded: chain AH residue 12 THR Chi-restraints excluded: chain AH residue 14 ILE Chi-restraints excluded: chain AH residue 30 SER Chi-restraints excluded: chain AH residue 40 LEU Chi-restraints excluded: chain AH residue 51 VAL Chi-restraints excluded: chain AH residue 111 MET Chi-restraints excluded: chain AH residue 112 THR Chi-restraints excluded: chain AI residue 111 VAL Chi-restraints excluded: chain AI residue 116 VAL Chi-restraints excluded: chain AJ residue 64 GLN Chi-restraints excluded: chain AJ residue 71 LEU Chi-restraints excluded: chain AK residue 26 SER Chi-restraints excluded: chain AK residue 59 THR Chi-restraints excluded: chain AK residue 105 PHE Chi-restraints excluded: chain AL residue 3 THR Chi-restraints excluded: chain AL residue 8 VAL Chi-restraints excluded: chain AL residue 36 ARG Chi-restraints excluded: chain AL residue 41 THR Chi-restraints excluded: chain AL residue 53 CYS Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 28 THR Chi-restraints excluded: chain AM residue 49 SER Chi-restraints excluded: chain AM residue 66 GLU Chi-restraints excluded: chain AM residue 74 SER Chi-restraints excluded: chain AO residue 24 SER Chi-restraints excluded: chain AO residue 61 SER Chi-restraints excluded: chain AP residue 19 VAL Chi-restraints excluded: chain AP residue 36 VAL Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AP residue 68 SER Chi-restraints excluded: chain AQ residue 58 VAL Chi-restraints excluded: chain AQ residue 67 LEU Chi-restraints excluded: chain AQ residue 70 THR Chi-restraints excluded: chain AS residue 15 LEU Chi-restraints excluded: chain AS residue 79 THR Chi-restraints excluded: chain BC residue 130 LEU Chi-restraints excluded: chain BC residue 260 ASN Chi-restraints excluded: chain BD residue 25 THR Chi-restraints excluded: chain BD residue 26 VAL Chi-restraints excluded: chain BD residue 29 VAL Chi-restraints excluded: chain BD residue 110 THR Chi-restraints excluded: chain BD residue 112 THR Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 155 VAL Chi-restraints excluded: chain BD residue 171 THR Chi-restraints excluded: chain BD residue 183 GLU Chi-restraints excluded: chain BE residue 12 LEU Chi-restraints excluded: chain BE residue 55 SER Chi-restraints excluded: chain BE residue 97 ASN Chi-restraints excluded: chain BE residue 126 VAL Chi-restraints excluded: chain BE residue 133 LEU Chi-restraints excluded: chain BE residue 144 GLU Chi-restraints excluded: chain BE residue 149 ILE Chi-restraints excluded: chain BE residue 187 VAL Chi-restraints excluded: chain BF residue 11 GLU Chi-restraints excluded: chain BF residue 35 THR Chi-restraints excluded: chain BF residue 61 SER Chi-restraints excluded: chain BF residue 97 TRP Chi-restraints excluded: chain BF residue 113 ASP Chi-restraints excluded: chain BF residue 121 SER Chi-restraints excluded: chain BF residue 152 LEU Chi-restraints excluded: chain BG residue 51 THR Chi-restraints excluded: chain BG residue 71 LEU Chi-restraints excluded: chain BG residue 106 SER Chi-restraints excluded: chain BG residue 111 HIS Chi-restraints excluded: chain BG residue 129 THR Chi-restraints excluded: chain BG residue 133 LEU Chi-restraints excluded: chain BG residue 171 THR Chi-restraints excluded: chain BI residue 49 ILE Chi-restraints excluded: chain BJ residue 30 THR Chi-restraints excluded: chain BJ residue 45 THR Chi-restraints excluded: chain BJ residue 65 THR Chi-restraints excluded: chain BJ residue 70 THR Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BJ residue 105 VAL Chi-restraints excluded: chain BK residue 10 VAL Chi-restraints excluded: chain BK residue 38 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 76 VAL Chi-restraints excluded: chain BK residue 103 VAL Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BL residue 116 VAL Chi-restraints excluded: chain BL residue 118 THR Chi-restraints excluded: chain BM residue 62 LYS Chi-restraints excluded: chain BM residue 80 VAL Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BM residue 106 ASP Chi-restraints excluded: chain BM residue 126 ILE Chi-restraints excluded: chain BM residue 134 THR Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 29 VAL Chi-restraints excluded: chain BN residue 33 ILE Chi-restraints excluded: chain BN residue 34 ILE Chi-restraints excluded: chain BN residue 52 ILE Chi-restraints excluded: chain BN residue 116 VAL Chi-restraints excluded: chain BO residue 13 ARG Chi-restraints excluded: chain BO residue 43 ASN Chi-restraints excluded: chain BO residue 48 LEU Chi-restraints excluded: chain BO residue 53 THR Chi-restraints excluded: chain BO residue 91 SER Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BP residue 60 THR Chi-restraints excluded: chain BP residue 96 LYS Chi-restraints excluded: chain BQ residue 17 ILE Chi-restraints excluded: chain BQ residue 20 GLN Chi-restraints excluded: chain BQ residue 77 SER Chi-restraints excluded: chain BQ residue 80 ILE Chi-restraints excluded: chain BQ residue 110 VAL Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 20 VAL Chi-restraints excluded: chain BR residue 58 VAL Chi-restraints excluded: chain BR residue 64 VAL Chi-restraints excluded: chain BS residue 12 SER Chi-restraints excluded: chain BS residue 39 THR Chi-restraints excluded: chain BS residue 85 ILE Chi-restraints excluded: chain BS residue 106 VAL Chi-restraints excluded: chain BS residue 107 VAL Chi-restraints excluded: chain BT residue 11 LEU Chi-restraints excluded: chain BT residue 16 VAL Chi-restraints excluded: chain BT residue 22 THR Chi-restraints excluded: chain BT residue 39 THR Chi-restraints excluded: chain BT residue 60 THR Chi-restraints excluded: chain BT residue 63 VAL Chi-restraints excluded: chain BU residue 15 THR Chi-restraints excluded: chain BU residue 58 ILE Chi-restraints excluded: chain BU residue 59 VAL Chi-restraints excluded: chain BU residue 83 VAL Chi-restraints excluded: chain BV residue 26 PHE Chi-restraints excluded: chain BV residue 63 ILE Chi-restraints excluded: chain BV residue 65 VAL Chi-restraints excluded: chain BV residue 86 LEU Chi-restraints excluded: chain BW residue 38 VAL Chi-restraints excluded: chain BX residue 44 LYS Chi-restraints excluded: chain BX residue 48 THR Chi-restraints excluded: chain BX residue 66 THR Chi-restraints excluded: chain BY residue 19 LEU Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B1 residue 8 LYS Chi-restraints excluded: chain B1 residue 23 THR Chi-restraints excluded: chain B1 residue 48 ILE Chi-restraints excluded: chain B3 residue 6 THR Chi-restraints excluded: chain B4 residue 17 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 906 optimal weight: 0.9990 chunk 689 optimal weight: 20.0000 chunk 475 optimal weight: 10.0000 chunk 101 optimal weight: 30.0000 chunk 437 optimal weight: 10.0000 chunk 615 optimal weight: 10.0000 chunk 920 optimal weight: 9.9990 chunk 974 optimal weight: 0.0570 chunk 480 optimal weight: 10.0000 chunk 872 optimal weight: 5.9990 chunk 262 optimal weight: 0.9980 overall best weight: 3.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AC 102 ASN ** AD 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 19 ASN ** AE 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 97 GLN AF 55 HIS AG 142 HIS ** AH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AM 12 HIS AO 40 GLN AQ 31 HIS ** AT 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 68 HIS AT 84 ASN BC 134 ASN BD 130 GLN BD 167 ASN ** BF 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BG 139 GLN BJ 136 GLN BK 3 GLN ** BM 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 66 ASN BQ 52 GLN BS 7 HIS BS 40 ASN ** BU 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BU 74 ASN BV 87 GLN BW 46 HIS ** BX 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BY 15 ASN BY 20 ASN B2 29 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 157882 Z= 0.203 Angle : 0.634 27.614 236520 Z= 0.326 Chirality : 0.039 2.152 30235 Planarity : 0.006 0.151 12439 Dihedral : 23.126 179.738 79768 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.87 % Allowed : 7.10 % Favored : 92.03 % Rotamer: Outliers : 4.96 % Allowed : 19.35 % Favored : 75.69 % 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: -1.36 (0.11), residues: 5522 helix: -0.18 (0.13), residues: 1659 sheet: -2.16 (0.15), residues: 896 loop : -0.82 (0.11), residues: 2967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPBC 213 HIS 0.015 0.001 HISBM 13 PHE 0.034 0.002 PHEAI 127 TYR 0.031 0.002 TYRAI 38 ARG 0.012 0.001 ARGAP 51 *********************** 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 1433 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1205 time to evaluate : 5.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 21 ARG cc_start: 0.4764 (tpm170) cc_final: 0.2482 (mtp180) REVERT: AB 43 LEU cc_start: 0.6659 (pp) cc_final: 0.6271 (tp) REVERT: AB 179 LEU cc_start: 0.4938 (mp) cc_final: 0.4666 (mt) REVERT: AC 125 GLU cc_start: 0.5494 (mm-30) cc_final: 0.5161 (mm-30) REVERT: AE 30 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7196 (tt) REVERT: AE 105 ILE cc_start: 0.7330 (tp) cc_final: 0.6955 (tp) REVERT: AG 144 MET cc_start: 0.5083 (mmm) cc_final: 0.4636 (ttp) REVERT: AH 111 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6617 (mtt) REVERT: AJ 58 ASN cc_start: 0.6345 (m110) cc_final: 0.6041 (m-40) REVERT: AK 46 THR cc_start: 0.8361 (p) cc_final: 0.8126 (p) REVERT: AM 97 VAL cc_start: 0.8483 (t) cc_final: 0.8134 (p) REVERT: AN 86 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7097 (tp30) REVERT: AP 17 TYR cc_start: 0.6306 (m-80) cc_final: 0.5909 (m-10) REVERT: AS 20 GLU cc_start: 0.6017 (pt0) cc_final: 0.5811 (pt0) REVERT: AS 62 VAL cc_start: 0.5529 (OUTLIER) cc_final: 0.5196 (t) REVERT: AT 68 HIS cc_start: 0.6485 (t-90) cc_final: 0.6115 (t70) REVERT: AT 74 ARG cc_start: 0.6412 (ttp80) cc_final: 0.5827 (ttm170) REVERT: BC 201 MET cc_start: 0.6349 (ttp) cc_final: 0.5948 (ttm) REVERT: BD 126 ASN cc_start: 0.8114 (m110) cc_final: 0.7719 (t0) REVERT: BE 119 ILE cc_start: 0.6270 (mp) cc_final: 0.5804 (mt) REVERT: BE 195 GLN cc_start: 0.5454 (tm-30) cc_final: 0.4481 (tm-30) REVERT: BE 197 GLU cc_start: 0.5670 (tt0) cc_final: 0.5448 (tt0) REVERT: BF 17 MET cc_start: 0.4945 (mmm) cc_final: 0.4512 (tpt) REVERT: BF 123 ASP cc_start: 0.4711 (p0) cc_final: 0.4152 (p0) REVERT: BF 144 ASP cc_start: 0.3869 (m-30) cc_final: 0.3116 (t0) REVERT: BG 17 VAL cc_start: 0.6526 (t) cc_final: 0.6256 (m) REVERT: BG 151 TYR cc_start: 0.6508 (m-80) cc_final: 0.6172 (m-80) REVERT: BI 136 MET cc_start: 0.2475 (mtm) cc_final: 0.1867 (ttm) REVERT: BJ 44 TYR cc_start: 0.7880 (t80) cc_final: 0.7187 (t80) REVERT: BJ 96 ARG cc_start: 0.7528 (ttm110) cc_final: 0.7273 (tpp80) REVERT: BJ 106 LYS cc_start: 0.7252 (ttmm) cc_final: 0.6987 (tttt) REVERT: BK 9 ASN cc_start: 0.7790 (m-40) cc_final: 0.7504 (m-40) REVERT: BM 17 ASN cc_start: 0.8213 (t0) cc_final: 0.8002 (t0) REVERT: BM 82 MET cc_start: 0.7944 (mtm) cc_final: 0.7509 (mtp) REVERT: BM 128 THR cc_start: 0.6927 (OUTLIER) cc_final: 0.6623 (m) REVERT: BM 136 MET cc_start: 0.1699 (ttp) cc_final: 0.1159 (mmt) REVERT: BN 58 ASP cc_start: 0.4554 (t0) cc_final: 0.3853 (p0) REVERT: BN 110 MET cc_start: 0.7460 (tpp) cc_final: 0.7194 (mmt) REVERT: BO 3 LYS cc_start: 0.5333 (ttpt) cc_final: 0.4966 (ttmm) REVERT: BO 95 SER cc_start: 0.8155 (m) cc_final: 0.7583 (p) REVERT: BP 72 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7604 (ttm170) REVERT: BP 96 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6849 (mmmt) REVERT: BQ 20 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7905 (mp10) REVERT: BR 62 GLU cc_start: 0.5883 (tp30) cc_final: 0.5625 (tp30) REVERT: BS 38 TYR cc_start: 0.6803 (m-80) cc_final: 0.6437 (m-80) REVERT: BS 48 LYS cc_start: 0.8411 (tttp) cc_final: 0.8155 (tttp) REVERT: BS 98 LYS cc_start: 0.7690 (mtpp) cc_final: 0.7352 (mttt) REVERT: BT 56 GLU cc_start: 0.5735 (mt-10) cc_final: 0.5533 (mt-10) REVERT: BV 51 GLN cc_start: 0.6424 (pp30) cc_final: 0.6167 (pt0) REVERT: BW 36 ILE cc_start: 0.8629 (tp) cc_final: 0.8388 (tt) REVERT: BX 32 ASN cc_start: 0.7065 (t0) cc_final: 0.6692 (t0) REVERT: BY 19 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7234 (mm) REVERT: B0 12 LYS cc_start: 0.7692 (tptt) cc_final: 0.7364 (tppt) REVERT: B2 37 LYS cc_start: 0.6619 (tttt) cc_final: 0.6224 (ttmt) outliers start: 228 outliers final: 159 residues processed: 1330 average time/residue: 1.2471 time to fit residues: 2863.9978 Evaluate side-chains 1261 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1095 time to evaluate : 6.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AC residue 18 TRP Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AC residue 82 GLU Chi-restraints excluded: chain AC residue 175 LEU Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 55 LEU Chi-restraints excluded: chain AD residue 67 VAL Chi-restraints excluded: chain AD residue 81 ARG Chi-restraints excluded: chain AD residue 85 ASN Chi-restraints excluded: chain AD residue 138 SER Chi-restraints excluded: chain AD residue 142 VAL Chi-restraints excluded: chain AD residue 152 GLN Chi-restraints excluded: chain AD residue 200 ILE Chi-restraints excluded: chain AE residue 30 ILE Chi-restraints excluded: chain AE residue 90 THR Chi-restraints excluded: chain AE residue 103 THR Chi-restraints excluded: chain AE residue 106 ILE Chi-restraints excluded: chain AE residue 131 THR Chi-restraints excluded: chain AE residue 148 ASN Chi-restraints excluded: chain AF residue 3 HIS Chi-restraints excluded: chain AF residue 5 GLU Chi-restraints excluded: chain AF residue 60 VAL Chi-restraints excluded: chain AG residue 27 VAL Chi-restraints excluded: chain AG residue 35 LYS Chi-restraints excluded: chain AG residue 83 SER Chi-restraints excluded: chain AG residue 89 VAL Chi-restraints excluded: chain AG residue 141 VAL Chi-restraints excluded: chain AH residue 12 THR Chi-restraints excluded: chain AH residue 30 SER Chi-restraints excluded: chain AH residue 40 LEU Chi-restraints excluded: chain AH residue 51 VAL Chi-restraints excluded: chain AH residue 111 MET Chi-restraints excluded: chain AH residue 112 THR Chi-restraints excluded: chain AI residue 111 VAL Chi-restraints excluded: chain AI residue 116 VAL Chi-restraints excluded: chain AJ residue 10 LEU Chi-restraints excluded: chain AJ residue 71 LEU Chi-restraints excluded: chain AK residue 26 SER Chi-restraints excluded: chain AK residue 85 MET Chi-restraints excluded: chain AL residue 3 THR Chi-restraints excluded: chain AL residue 8 VAL Chi-restraints excluded: chain AL residue 41 THR Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 28 THR Chi-restraints excluded: chain AM residue 49 SER Chi-restraints excluded: chain AM residue 65 VAL Chi-restraints excluded: chain AM residue 66 GLU Chi-restraints excluded: chain AO residue 24 SER Chi-restraints excluded: chain AO residue 66 LEU Chi-restraints excluded: chain AP residue 19 VAL Chi-restraints excluded: chain AP residue 29 ASN Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AP residue 68 SER Chi-restraints excluded: chain AQ residue 58 VAL Chi-restraints excluded: chain AQ residue 64 CYS Chi-restraints excluded: chain AQ residue 67 LEU Chi-restraints excluded: chain AQ residue 70 THR Chi-restraints excluded: chain AR residue 36 SER Chi-restraints excluded: chain AS residue 62 VAL Chi-restraints excluded: chain AS residue 79 THR Chi-restraints excluded: chain BC residue 130 LEU Chi-restraints excluded: chain BC residue 183 LYS Chi-restraints excluded: chain BC residue 187 ASP Chi-restraints excluded: chain BC residue 195 VAL Chi-restraints excluded: chain BC residue 232 HIS Chi-restraints excluded: chain BD residue 29 VAL Chi-restraints excluded: chain BD residue 113 SER Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 167 ASN Chi-restraints excluded: chain BD residue 170 VAL Chi-restraints excluded: chain BD residue 171 THR Chi-restraints excluded: chain BD residue 183 GLU Chi-restraints excluded: chain BE residue 12 LEU Chi-restraints excluded: chain BE residue 55 SER Chi-restraints excluded: chain BE residue 126 VAL Chi-restraints excluded: chain BE residue 144 GLU Chi-restraints excluded: chain BE residue 149 ILE Chi-restraints excluded: chain BE residue 187 VAL Chi-restraints excluded: chain BF residue 11 GLU Chi-restraints excluded: chain BF residue 56 ASP Chi-restraints excluded: chain BF residue 61 SER Chi-restraints excluded: chain BF residue 113 ASP Chi-restraints excluded: chain BF residue 121 SER Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 51 THR Chi-restraints excluded: chain BG residue 72 LEU Chi-restraints excluded: chain BG residue 106 SER Chi-restraints excluded: chain BG residue 111 HIS Chi-restraints excluded: chain BG residue 133 LEU Chi-restraints excluded: chain BJ residue 30 THR Chi-restraints excluded: chain BJ residue 45 THR Chi-restraints excluded: chain BJ residue 65 THR Chi-restraints excluded: chain BJ residue 70 THR Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BK residue 10 VAL Chi-restraints excluded: chain BK residue 38 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 76 VAL Chi-restraints excluded: chain BK residue 103 VAL Chi-restraints excluded: chain BK residue 106 GLU Chi-restraints excluded: chain BL residue 25 SER Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BL residue 129 LYS Chi-restraints excluded: chain BM residue 5 LYS Chi-restraints excluded: chain BM residue 42 THR Chi-restraints excluded: chain BM residue 54 THR Chi-restraints excluded: chain BM residue 62 LYS Chi-restraints excluded: chain BM residue 88 ASN Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BM residue 106 ASP Chi-restraints excluded: chain BM residue 126 ILE Chi-restraints excluded: chain BM residue 128 THR Chi-restraints excluded: chain BM residue 134 THR Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 29 VAL Chi-restraints excluded: chain BN residue 33 ILE Chi-restraints excluded: chain BN residue 76 VAL Chi-restraints excluded: chain BN residue 116 VAL Chi-restraints excluded: chain BO residue 43 ASN Chi-restraints excluded: chain BO residue 48 LEU Chi-restraints excluded: chain BO residue 53 THR Chi-restraints excluded: chain BO residue 91 SER Chi-restraints excluded: chain BO residue 103 VAL Chi-restraints excluded: chain BP residue 32 VAL Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BP residue 96 LYS Chi-restraints excluded: chain BQ residue 17 ILE Chi-restraints excluded: chain BQ residue 20 GLN Chi-restraints excluded: chain BQ residue 75 SER Chi-restraints excluded: chain BQ residue 77 SER Chi-restraints excluded: chain BQ residue 80 ILE Chi-restraints excluded: chain BQ residue 110 VAL Chi-restraints excluded: chain BR residue 58 VAL Chi-restraints excluded: chain BR residue 64 VAL Chi-restraints excluded: chain BS residue 12 SER Chi-restraints excluded: chain BS residue 39 THR Chi-restraints excluded: chain BS residue 76 VAL Chi-restraints excluded: chain BS residue 85 ILE Chi-restraints excluded: chain BS residue 107 VAL Chi-restraints excluded: chain BT residue 1 MET Chi-restraints excluded: chain BT residue 7 LEU Chi-restraints excluded: chain BT residue 17 SER Chi-restraints excluded: chain BT residue 63 VAL Chi-restraints excluded: chain BU residue 15 THR Chi-restraints excluded: chain BU residue 59 VAL Chi-restraints excluded: chain BU residue 102 THR Chi-restraints excluded: chain BV residue 63 ILE Chi-restraints excluded: chain BV residue 64 VAL Chi-restraints excluded: chain BV residue 65 VAL Chi-restraints excluded: chain BV residue 86 LEU Chi-restraints excluded: chain BW residue 15 ASP Chi-restraints excluded: chain BW residue 38 VAL Chi-restraints excluded: chain BX residue 19 SER Chi-restraints excluded: chain BX residue 44 LYS Chi-restraints excluded: chain BX residue 48 THR Chi-restraints excluded: chain BY residue 19 LEU Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B1 residue 23 THR Chi-restraints excluded: chain B1 residue 48 ILE Chi-restraints excluded: chain B2 residue 44 VAL Chi-restraints excluded: chain B3 residue 6 THR Chi-restraints excluded: chain B4 residue 17 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 811 optimal weight: 9.9990 chunk 553 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 725 optimal weight: 20.0000 chunk 402 optimal weight: 20.0000 chunk 831 optimal weight: 10.0000 chunk 673 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 497 optimal weight: 20.0000 chunk 874 optimal weight: 8.9990 chunk 245 optimal weight: 4.9990 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 177 ASN ** AC 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AG 130 ASN AG 142 HIS ** AH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AK 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 20 ASN AM 12 HIS AN 4 GLN AO 28 GLN ** AO 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 40 GLN AP 79 ASN AQ 47 HIS ** AT 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 75 HIS BC 134 ASN BE 30 GLN BF 52 ASN ** BG 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 115 HIS BK 3 GLN BM 13 HIS ** BP 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 52 ASN ** BP 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 52 GLN BQ 71 GLN ** BU 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY 15 ASN B0 6 ASN B2 13 ASN B2 29 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6656 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.171 157882 Z= 0.448 Angle : 0.923 30.112 236520 Z= 0.457 Chirality : 0.050 2.156 30235 Planarity : 0.008 0.158 12439 Dihedral : 23.570 178.815 79768 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.62 % Favored : 90.51 % Rotamer: Outliers : 7.21 % Allowed : 20.18 % Favored : 72.62 % 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: -2.15 (0.11), residues: 5522 helix: -0.72 (0.12), residues: 1673 sheet: -2.32 (0.15), residues: 891 loop : -1.50 (0.11), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.004 TRPBF 97 HIS 0.019 0.003 HISBF 5 PHE 0.045 0.004 PHEAK 52 TYR 0.036 0.003 TYRB1 49 ARG 0.016 0.001 ARGBK 78 *********************** 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 1533 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1202 time to evaluate : 6.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 43 LEU cc_start: 0.6563 (pp) cc_final: 0.6251 (tp) REVERT: AB 78 GLU cc_start: 0.3509 (tp30) cc_final: 0.3205 (tp30) REVERT: AB 167 ASP cc_start: 0.4368 (p0) cc_final: 0.4110 (p0) REVERT: AB 179 LEU cc_start: 0.5339 (mp) cc_final: 0.5086 (mt) REVERT: AC 121 THR cc_start: 0.6527 (m) cc_final: 0.6166 (p) REVERT: AD 121 LYS cc_start: 0.7305 (mttt) cc_final: 0.6945 (mttt) REVERT: AD 136 GLN cc_start: 0.7250 (tp-100) cc_final: 0.6973 (mm-40) REVERT: AF 16 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.5695 (pm20) REVERT: AG 31 MET cc_start: 0.5955 (ttp) cc_final: 0.5700 (ttp) REVERT: AG 120 LEU cc_start: 0.8072 (tp) cc_final: 0.7719 (tp) REVERT: AK 46 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8309 (p) REVERT: AM 97 VAL cc_start: 0.8498 (t) cc_final: 0.8265 (p) REVERT: AN 4 GLN cc_start: 0.7199 (tp-100) cc_final: 0.6977 (tp40) REVERT: AN 53 ARG cc_start: 0.4881 (OUTLIER) cc_final: 0.3174 (mtp180) REVERT: AN 66 GLN cc_start: 0.7225 (pm20) cc_final: 0.6316 (pm20) REVERT: AN 75 ARG cc_start: 0.7367 (mmt90) cc_final: 0.6941 (mtp85) REVERT: AN 96 LEU cc_start: 0.7773 (tp) cc_final: 0.7399 (tt) REVERT: AO 84 ARG cc_start: 0.6680 (ttt180) cc_final: 0.6432 (ttt180) REVERT: AP 17 TYR cc_start: 0.6512 (m-80) cc_final: 0.6222 (m-10) REVERT: AP 21 VAL cc_start: 0.8438 (m) cc_final: 0.8110 (p) REVERT: AS 71 LEU cc_start: 0.6457 (mt) cc_final: 0.6185 (mt) REVERT: BC 93 LEU cc_start: 0.7656 (tp) cc_final: 0.7305 (pp) REVERT: BD 126 ASN cc_start: 0.8265 (m110) cc_final: 0.7972 (t0) REVERT: BE 69 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7699 (ptp-170) REVERT: BF 17 MET cc_start: 0.5299 (mmm) cc_final: 0.4639 (tpt) REVERT: BF 77 PHE cc_start: 0.6143 (m-10) cc_final: 0.5290 (m-10) REVERT: BG 11 VAL cc_start: 0.5034 (OUTLIER) cc_final: 0.4774 (p) REVERT: BG 17 VAL cc_start: 0.7276 (t) cc_final: 0.6941 (m) REVERT: BG 104 ASN cc_start: 0.6670 (t0) cc_final: 0.6330 (t0) REVERT: BG 133 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6677 (pp) REVERT: BG 149 ARG cc_start: 0.6807 (mmm-85) cc_final: 0.6538 (mmm160) REVERT: BI 49 ILE cc_start: -0.0680 (OUTLIER) cc_final: -0.1201 (tp) REVERT: BI 136 MET cc_start: 0.2001 (mtm) cc_final: 0.1356 (ttm) REVERT: BJ 44 TYR cc_start: 0.8069 (t80) cc_final: 0.7268 (t80) REVERT: BJ 53 TYR cc_start: 0.8334 (m-10) cc_final: 0.8130 (m-80) REVERT: BJ 60 ASP cc_start: 0.6495 (p0) cc_final: 0.6265 (p0) REVERT: BJ 84 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7834 (tt) REVERT: BK 9 ASN cc_start: 0.8060 (m-40) cc_final: 0.7847 (m110) REVERT: BM 17 ASN cc_start: 0.8172 (t0) cc_final: 0.7923 (t0) REVERT: BM 82 MET cc_start: 0.7918 (mtm) cc_final: 0.7594 (mtp) REVERT: BM 136 MET cc_start: 0.1994 (ttp) cc_final: 0.1410 (mmm) REVERT: BN 58 ASP cc_start: 0.4636 (t0) cc_final: 0.3900 (p0) REVERT: BN 112 TYR cc_start: 0.6143 (m-10) cc_final: 0.5783 (m-10) REVERT: BO 95 SER cc_start: 0.8287 (m) cc_final: 0.7880 (p) REVERT: BP 12 GLN cc_start: 0.6531 (mm-40) cc_final: 0.6150 (tm-30) REVERT: BQ 20 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: BQ 109 LEU cc_start: 0.8052 (mm) cc_final: 0.7782 (tp) REVERT: BR 62 GLU cc_start: 0.5922 (tp30) cc_final: 0.5481 (tp30) REVERT: BR 84 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.8029 (mtm110) REVERT: BS 76 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8507 (p) REVERT: BS 84 ARG cc_start: 0.7351 (mpt180) cc_final: 0.7046 (mmt180) REVERT: BS 98 LYS cc_start: 0.7734 (mtpp) cc_final: 0.7253 (mttt) REVERT: BV 51 GLN cc_start: 0.6628 (pp30) cc_final: 0.6357 (pt0) REVERT: BW 36 ILE cc_start: 0.8667 (tp) cc_final: 0.8298 (tt) REVERT: BW 75 LYS cc_start: 0.7667 (mttt) cc_final: 0.7093 (mmmt) REVERT: BX 32 ASN cc_start: 0.7182 (t0) cc_final: 0.6780 (t0) REVERT: B0 12 LYS cc_start: 0.7524 (tptt) cc_final: 0.7222 (tppt) REVERT: B1 47 VAL cc_start: 0.7748 (t) cc_final: 0.7523 (m) REVERT: B2 37 LYS cc_start: 0.6617 (tttt) cc_final: 0.6340 (ttpp) REVERT: B4 16 ILE cc_start: 0.7074 (mm) cc_final: 0.6722 (mm) outliers start: 331 outliers final: 226 residues processed: 1377 average time/residue: 1.2939 time to fit residues: 3075.4407 Evaluate side-chains 1311 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1075 time to evaluate : 5.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 50 PHE Chi-restraints excluded: chain AB residue 93 ASN Chi-restraints excluded: chain AB residue 199 VAL Chi-restraints excluded: chain AB residue 217 VAL Chi-restraints excluded: chain AC residue 18 TRP Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AC residue 69 HIS Chi-restraints excluded: chain AC residue 82 GLU Chi-restraints excluded: chain AC residue 144 LEU Chi-restraints excluded: chain AC residue 191 THR Chi-restraints excluded: chain AD residue 11 LEU Chi-restraints excluded: chain AD residue 12 SER Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 55 LEU Chi-restraints excluded: chain AD residue 67 VAL Chi-restraints excluded: chain AD residue 85 ASN Chi-restraints excluded: chain AD residue 101 VAL Chi-restraints excluded: chain AD residue 138 SER Chi-restraints excluded: chain AD residue 142 VAL Chi-restraints excluded: chain AD residue 152 GLN Chi-restraints excluded: chain AD residue 200 ILE Chi-restraints excluded: chain AE residue 30 ILE Chi-restraints excluded: chain AE residue 38 VAL Chi-restraints excluded: chain AE residue 90 THR Chi-restraints excluded: chain AE residue 103 THR Chi-restraints excluded: chain AE residue 115 LEU Chi-restraints excluded: chain AE residue 131 THR Chi-restraints excluded: chain AF residue 3 HIS Chi-restraints excluded: chain AF residue 10 VAL Chi-restraints excluded: chain AF residue 16 GLU Chi-restraints excluded: chain AF residue 49 TYR Chi-restraints excluded: chain AF residue 60 VAL Chi-restraints excluded: chain AG residue 29 ILE Chi-restraints excluded: chain AG residue 35 LYS Chi-restraints excluded: chain AG residue 83 SER Chi-restraints excluded: chain AG residue 87 VAL Chi-restraints excluded: chain AG residue 89 VAL Chi-restraints excluded: chain AG residue 115 SER Chi-restraints excluded: chain AG residue 141 VAL Chi-restraints excluded: chain AG residue 142 HIS Chi-restraints excluded: chain AH residue 12 THR Chi-restraints excluded: chain AH residue 15 ARG Chi-restraints excluded: chain AH residue 30 SER Chi-restraints excluded: chain AH residue 40 LEU Chi-restraints excluded: chain AH residue 51 VAL Chi-restraints excluded: chain AH residue 63 LEU Chi-restraints excluded: chain AH residue 112 THR Chi-restraints excluded: chain AH residue 121 LEU Chi-restraints excluded: chain AI residue 111 VAL Chi-restraints excluded: chain AI residue 116 VAL Chi-restraints excluded: chain AI residue 120 LYS Chi-restraints excluded: chain AI residue 127 PHE Chi-restraints excluded: chain AJ residue 10 LEU Chi-restraints excluded: chain AJ residue 71 LEU Chi-restraints excluded: chain AK residue 26 SER Chi-restraints excluded: chain AK residue 35 THR Chi-restraints excluded: chain AK residue 46 THR Chi-restraints excluded: chain AK residue 59 THR Chi-restraints excluded: chain AK residue 84 VAL Chi-restraints excluded: chain AL residue 3 THR Chi-restraints excluded: chain AL residue 4 VAL Chi-restraints excluded: chain AL residue 8 VAL Chi-restraints excluded: chain AL residue 41 THR Chi-restraints excluded: chain AL residue 52 VAL Chi-restraints excluded: chain AL residue 53 CYS Chi-restraints excluded: chain AL residue 55 VAL Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 28 THR Chi-restraints excluded: chain AM residue 63 PHE Chi-restraints excluded: chain AM residue 65 VAL Chi-restraints excluded: chain AM residue 66 GLU Chi-restraints excluded: chain AN residue 48 LEU Chi-restraints excluded: chain AN residue 53 ARG Chi-restraints excluded: chain AN residue 84 VAL Chi-restraints excluded: chain AO residue 24 SER Chi-restraints excluded: chain AO residue 61 SER Chi-restraints excluded: chain AO residue 66 LEU Chi-restraints excluded: chain AP residue 19 VAL Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AQ residue 22 VAL Chi-restraints excluded: chain AQ residue 41 THR Chi-restraints excluded: chain AQ residue 58 VAL Chi-restraints excluded: chain AQ residue 64 CYS Chi-restraints excluded: chain AR residue 34 THR Chi-restraints excluded: chain AR residue 51 TYR Chi-restraints excluded: chain AS residue 13 LEU Chi-restraints excluded: chain AS residue 79 THR Chi-restraints excluded: chain BC residue 35 GLU Chi-restraints excluded: chain BC residue 38 SER Chi-restraints excluded: chain BC residue 130 LEU Chi-restraints excluded: chain BC residue 154 LEU Chi-restraints excluded: chain BC residue 174 LEU Chi-restraints excluded: chain BC residue 183 LYS Chi-restraints excluded: chain BC residue 187 ASP Chi-restraints excluded: chain BC residue 195 VAL Chi-restraints excluded: chain BC residue 228 VAL Chi-restraints excluded: chain BC residue 232 HIS Chi-restraints excluded: chain BD residue 25 THR Chi-restraints excluded: chain BD residue 26 VAL Chi-restraints excluded: chain BD residue 29 VAL Chi-restraints excluded: chain BD residue 109 VAL Chi-restraints excluded: chain BD residue 112 THR Chi-restraints excluded: chain BD residue 113 SER Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 155 VAL Chi-restraints excluded: chain BD residue 171 THR Chi-restraints excluded: chain BD residue 180 VAL Chi-restraints excluded: chain BD residue 201 LEU Chi-restraints excluded: chain BE residue 12 LEU Chi-restraints excluded: chain BE residue 43 THR Chi-restraints excluded: chain BE residue 48 THR Chi-restraints excluded: chain BE residue 55 SER Chi-restraints excluded: chain BE residue 69 ARG Chi-restraints excluded: chain BE residue 113 VAL Chi-restraints excluded: chain BE residue 126 VAL Chi-restraints excluded: chain BE residue 133 LEU Chi-restraints excluded: chain BE residue 149 ILE Chi-restraints excluded: chain BE residue 165 HIS Chi-restraints excluded: chain BE residue 187 VAL Chi-restraints excluded: chain BF residue 25 VAL Chi-restraints excluded: chain BF residue 56 ASP Chi-restraints excluded: chain BF residue 61 SER Chi-restraints excluded: chain BF residue 81 GLN Chi-restraints excluded: chain BF residue 113 ASP Chi-restraints excluded: chain BF residue 121 SER Chi-restraints excluded: chain BF residue 132 VAL Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 26 ILE Chi-restraints excluded: chain BG residue 51 THR Chi-restraints excluded: chain BG residue 71 LEU Chi-restraints excluded: chain BG residue 92 VAL Chi-restraints excluded: chain BG residue 106 SER Chi-restraints excluded: chain BG residue 129 THR Chi-restraints excluded: chain BG residue 133 LEU Chi-restraints excluded: chain BG residue 148 LEU Chi-restraints excluded: chain BI residue 49 ILE Chi-restraints excluded: chain BJ residue 30 THR Chi-restraints excluded: chain BJ residue 41 LYS Chi-restraints excluded: chain BJ residue 45 THR Chi-restraints excluded: chain BJ residue 62 VAL Chi-restraints excluded: chain BJ residue 70 THR Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BJ residue 80 HIS Chi-restraints excluded: chain BJ residue 84 ILE Chi-restraints excluded: chain BJ residue 105 VAL Chi-restraints excluded: chain BJ residue 139 VAL Chi-restraints excluded: chain BK residue 10 VAL Chi-restraints excluded: chain BK residue 29 HIS Chi-restraints excluded: chain BK residue 38 ILE Chi-restraints excluded: chain BK residue 39 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 76 VAL Chi-restraints excluded: chain BK residue 103 VAL Chi-restraints excluded: chain BL residue 25 SER Chi-restraints excluded: chain BL residue 61 LEU Chi-restraints excluded: chain BL residue 77 ILE Chi-restraints excluded: chain BL residue 107 PHE Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BL residue 116 VAL Chi-restraints excluded: chain BL residue 118 THR Chi-restraints excluded: chain BL residue 129 LYS Chi-restraints excluded: chain BM residue 42 THR Chi-restraints excluded: chain BM residue 54 THR Chi-restraints excluded: chain BM residue 62 LYS Chi-restraints excluded: chain BM residue 80 VAL Chi-restraints excluded: chain BM residue 88 ASN Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BM residue 126 ILE Chi-restraints excluded: chain BM residue 134 THR Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 29 VAL Chi-restraints excluded: chain BN residue 31 HIS Chi-restraints excluded: chain BN residue 34 ILE Chi-restraints excluded: chain BN residue 36 THR Chi-restraints excluded: chain BN residue 42 LYS Chi-restraints excluded: chain BN residue 52 ILE Chi-restraints excluded: chain BN residue 76 VAL Chi-restraints excluded: chain BN residue 116 VAL Chi-restraints excluded: chain BO residue 43 ASN Chi-restraints excluded: chain BO residue 48 LEU Chi-restraints excluded: chain BO residue 53 THR Chi-restraints excluded: chain BO residue 64 TYR Chi-restraints excluded: chain BO residue 91 SER Chi-restraints excluded: chain BO residue 100 HIS Chi-restraints excluded: chain BO residue 103 VAL Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BQ residue 17 ILE Chi-restraints excluded: chain BQ residue 20 GLN Chi-restraints excluded: chain BQ residue 77 SER Chi-restraints excluded: chain BQ residue 80 ILE Chi-restraints excluded: chain BQ residue 104 VAL Chi-restraints excluded: chain BQ residue 110 VAL Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 34 GLU Chi-restraints excluded: chain BR residue 58 VAL Chi-restraints excluded: chain BR residue 64 VAL Chi-restraints excluded: chain BS residue 12 SER Chi-restraints excluded: chain BS residue 39 THR Chi-restraints excluded: chain BS residue 47 VAL Chi-restraints excluded: chain BS residue 76 VAL Chi-restraints excluded: chain BS residue 85 ILE Chi-restraints excluded: chain BS residue 101 SER Chi-restraints excluded: chain BS residue 105 VAL Chi-restraints excluded: chain BS residue 107 VAL Chi-restraints excluded: chain BT residue 1 MET Chi-restraints excluded: chain BT residue 11 LEU Chi-restraints excluded: chain BT residue 17 SER Chi-restraints excluded: chain BT residue 22 THR Chi-restraints excluded: chain BT residue 60 THR Chi-restraints excluded: chain BT residue 63 VAL Chi-restraints excluded: chain BU residue 15 THR Chi-restraints excluded: chain BU residue 49 VAL Chi-restraints excluded: chain BU residue 102 THR Chi-restraints excluded: chain BV residue 63 ILE Chi-restraints excluded: chain BV residue 86 LEU Chi-restraints excluded: chain BW residue 15 ASP Chi-restraints excluded: chain BW residue 17 GLU Chi-restraints excluded: chain BW residue 38 VAL Chi-restraints excluded: chain BX residue 19 SER Chi-restraints excluded: chain BX residue 48 THR Chi-restraints excluded: chain BX residue 60 ASP Chi-restraints excluded: chain BY residue 36 GLN Chi-restraints excluded: chain BY residue 49 ASP Chi-restraints excluded: chain BZ residue 8 THR Chi-restraints excluded: chain BZ residue 32 ILE Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B0 residue 26 THR Chi-restraints excluded: chain B1 residue 23 THR Chi-restraints excluded: chain B1 residue 25 LYS Chi-restraints excluded: chain B1 residue 48 ILE Chi-restraints excluded: chain B2 residue 44 VAL Chi-restraints excluded: chain B3 residue 28 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 327 optimal weight: 0.9980 chunk 877 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 572 optimal weight: 3.9990 chunk 240 optimal weight: 30.0000 chunk 975 optimal weight: 3.9990 chunk 809 optimal weight: 0.9990 chunk 451 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 322 optimal weight: 9.9990 chunk 512 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 177 ASN ** AC 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 41 HIS AF 17 GLN AG 28 ASN AK 22 HIS AM 12 HIS ** AO 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 40 GLN ** AP 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AP 29 ASN AR 52 GLN ** AT 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 68 HIS AT 70 ASN BC 239 ASN BC 251 GLN BD 42 ASN ** BF 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BL 38 GLN BN 107 ASN ** BO 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BU 74 ASN ** BV 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BW 76 ASN ** BX 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BY 15 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 157882 Z= 0.173 Angle : 0.653 26.960 236520 Z= 0.336 Chirality : 0.039 2.129 30235 Planarity : 0.006 0.153 12439 Dihedral : 23.389 178.943 79768 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.80 % Allowed : 7.23 % Favored : 91.98 % Rotamer: Outliers : 4.88 % Allowed : 23.68 % Favored : 71.44 % 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: -1.70 (0.11), residues: 5522 helix: -0.24 (0.13), residues: 1671 sheet: -2.00 (0.16), residues: 901 loop : -1.33 (0.11), residues: 2950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRPBF 97 HIS 0.011 0.001 HISAM 12 PHE 0.034 0.002 PHEAI 127 TYR 0.027 0.002 TYRBP 98 ARG 0.014 0.001 ARGAQ 62 *********************** 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 1401 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1177 time to evaluate : 5.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AB 21 ARG cc_start: 0.4737 (tpm170) cc_final: 0.2633 (mtp180) REVERT: AB 43 LEU cc_start: 0.6492 (pp) cc_final: 0.6278 (tp) REVERT: AB 78 GLU cc_start: 0.3661 (tp30) cc_final: 0.3398 (tp30) REVERT: AB 204 ASP cc_start: 0.5272 (p0) cc_final: 0.4054 (p0) REVERT: AC 37 PHE cc_start: 0.7259 (t80) cc_final: 0.6479 (t80) REVERT: AD 136 GLN cc_start: 0.7101 (tp-100) cc_final: 0.6786 (mm-40) REVERT: AE 45 ARG cc_start: 0.6602 (tpp-160) cc_final: 0.6371 (tpp-160) REVERT: AF 5 GLU cc_start: 0.5337 (OUTLIER) cc_final: 0.5081 (mt-10) REVERT: AK 46 THR cc_start: 0.8376 (p) cc_final: 0.8169 (p) REVERT: AK 113 VAL cc_start: 0.6760 (OUTLIER) cc_final: 0.6430 (t) REVERT: AL 36 ARG cc_start: 0.5951 (OUTLIER) cc_final: 0.4847 (tmm-80) REVERT: AM 81 MET cc_start: 0.7037 (tmm) cc_final: 0.6689 (tmm) REVERT: AM 97 VAL cc_start: 0.8357 (t) cc_final: 0.8147 (p) REVERT: AN 74 LEU cc_start: 0.8545 (mt) cc_final: 0.8294 (mt) REVERT: AN 75 ARG cc_start: 0.7234 (mmt90) cc_final: 0.6603 (ttm170) REVERT: AP 17 TYR cc_start: 0.6292 (m-80) cc_final: 0.5989 (m-10) REVERT: AP 21 VAL cc_start: 0.8384 (m) cc_final: 0.8072 (p) REVERT: AQ 57 ASP cc_start: 0.4140 (m-30) cc_final: 0.3760 (p0) REVERT: AT 28 MET cc_start: 0.7096 (tmm) cc_final: 0.6587 (tmm) REVERT: BC 93 LEU cc_start: 0.7558 (tp) cc_final: 0.7349 (pp) REVERT: BC 195 VAL cc_start: 0.7147 (OUTLIER) cc_final: 0.6845 (t) REVERT: BC 201 MET cc_start: 0.6495 (ttp) cc_final: 0.6143 (ttm) REVERT: BD 126 ASN cc_start: 0.8086 (m110) cc_final: 0.7834 (t0) REVERT: BE 119 ILE cc_start: 0.6341 (mp) cc_final: 0.5854 (mt) REVERT: BE 141 MET cc_start: 0.4699 (ptp) cc_final: 0.4381 (ptp) REVERT: BF 17 MET cc_start: 0.5028 (mmm) cc_final: 0.4762 (tpt) REVERT: BG 11 VAL cc_start: 0.4990 (OUTLIER) cc_final: 0.4742 (p) REVERT: BG 17 VAL cc_start: 0.7284 (t) cc_final: 0.6938 (m) REVERT: BG 133 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6688 (pp) REVERT: BH 1 MET cc_start: 0.4989 (tpp) cc_final: 0.4735 (tpp) REVERT: BI 49 ILE cc_start: -0.0830 (OUTLIER) cc_final: -0.1569 (tp) REVERT: BI 117 MET cc_start: 0.2734 (mmt) cc_final: -0.0721 (tpp) REVERT: BI 136 MET cc_start: 0.2041 (mtm) cc_final: 0.1477 (ttm) REVERT: BJ 39 LYS cc_start: 0.6762 (mmmt) cc_final: 0.6462 (ttmm) REVERT: BJ 44 TYR cc_start: 0.8120 (t80) cc_final: 0.7225 (t80) REVERT: BJ 60 ASP cc_start: 0.6548 (p0) cc_final: 0.6334 (p0) REVERT: BJ 106 LYS cc_start: 0.7360 (ttmm) cc_final: 0.7134 (tttt) REVERT: BM 17 ASN cc_start: 0.8152 (t0) cc_final: 0.7901 (t0) REVERT: BM 82 MET cc_start: 0.7877 (mtm) cc_final: 0.7632 (mtp) REVERT: BM 129 THR cc_start: 0.6894 (p) cc_final: 0.6436 (t) REVERT: BM 136 MET cc_start: 0.2231 (ttp) cc_final: 0.1430 (mmt) REVERT: BN 11 ASN cc_start: 0.7938 (m-40) cc_final: 0.7575 (m-40) REVERT: BN 42 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7660 (mttp) REVERT: BN 58 ASP cc_start: 0.4509 (t0) cc_final: 0.3808 (p0) REVERT: BN 107 ASN cc_start: 0.8468 (t0) cc_final: 0.7832 (t0) REVERT: BO 95 SER cc_start: 0.8276 (m) cc_final: 0.7807 (p) REVERT: BQ 20 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: BR 62 GLU cc_start: 0.6012 (tp30) cc_final: 0.5518 (mm-30) REVERT: BS 38 TYR cc_start: 0.7039 (m-80) cc_final: 0.6605 (m-80) REVERT: BS 48 LYS cc_start: 0.8395 (tttp) cc_final: 0.8113 (tttp) REVERT: BS 84 ARG cc_start: 0.7259 (mpt180) cc_final: 0.6974 (mmt180) REVERT: BS 101 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8639 (m) REVERT: BT 1 MET cc_start: 0.4843 (OUTLIER) cc_final: 0.3428 (pmm) REVERT: BV 53 LYS cc_start: 0.5701 (OUTLIER) cc_final: 0.5345 (ptpp) REVERT: BW 36 ILE cc_start: 0.8535 (tp) cc_final: 0.8225 (tt) REVERT: BW 62 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.6924 (mmmm) REVERT: BY 1 MET cc_start: 0.5215 (pmm) cc_final: 0.4949 (tpp) REVERT: B1 47 VAL cc_start: 0.7717 (t) cc_final: 0.7299 (m) outliers start: 224 outliers final: 152 residues processed: 1293 average time/residue: 1.2657 time to fit residues: 2832.5178 Evaluate side-chains 1260 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1095 time to evaluate : 6.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 50 PHE Chi-restraints excluded: chain AB residue 186 ILE Chi-restraints excluded: chain AB residue 199 VAL Chi-restraints excluded: chain AC residue 18 TRP Chi-restraints excluded: chain AC residue 34 ASP Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AC residue 82 GLU Chi-restraints excluded: chain AC residue 191 THR Chi-restraints excluded: chain AD residue 12 SER Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 55 LEU Chi-restraints excluded: chain AD residue 81 ARG Chi-restraints excluded: chain AD residue 94 LEU Chi-restraints excluded: chain AD residue 138 SER Chi-restraints excluded: chain AD residue 142 VAL Chi-restraints excluded: chain AD residue 152 GLN Chi-restraints excluded: chain AD residue 200 ILE Chi-restraints excluded: chain AE residue 30 ILE Chi-restraints excluded: chain AE residue 90 THR Chi-restraints excluded: chain AE residue 103 THR Chi-restraints excluded: chain AE residue 131 THR Chi-restraints excluded: chain AE residue 151 GLU Chi-restraints excluded: chain AF residue 3 HIS Chi-restraints excluded: chain AF residue 5 GLU Chi-restraints excluded: chain AF residue 9 MET Chi-restraints excluded: chain AF residue 60 VAL Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AG residue 83 SER Chi-restraints excluded: chain AG residue 89 VAL Chi-restraints excluded: chain AG residue 115 SER Chi-restraints excluded: chain AH residue 30 SER Chi-restraints excluded: chain AH residue 40 LEU Chi-restraints excluded: chain AH residue 51 VAL Chi-restraints excluded: chain AH residue 83 LEU Chi-restraints excluded: chain AH residue 112 THR Chi-restraints excluded: chain AI residue 29 VAL Chi-restraints excluded: chain AJ residue 10 LEU Chi-restraints excluded: chain AJ residue 71 LEU Chi-restraints excluded: chain AK residue 26 SER Chi-restraints excluded: chain AK residue 35 THR Chi-restraints excluded: chain AK residue 113 VAL Chi-restraints excluded: chain AL residue 3 THR Chi-restraints excluded: chain AL residue 36 ARG Chi-restraints excluded: chain AL residue 55 VAL Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 28 THR Chi-restraints excluded: chain AM residue 65 VAL Chi-restraints excluded: chain AM residue 66 GLU Chi-restraints excluded: chain AM residue 102 THR Chi-restraints excluded: chain AO residue 24 SER Chi-restraints excluded: chain AO residue 36 ILE Chi-restraints excluded: chain AP residue 19 VAL Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AP residue 59 HIS Chi-restraints excluded: chain AQ residue 17 MET Chi-restraints excluded: chain AQ residue 22 VAL Chi-restraints excluded: chain AQ residue 41 THR Chi-restraints excluded: chain AQ residue 42 THR Chi-restraints excluded: chain AQ residue 81 LYS Chi-restraints excluded: chain AT residue 36 TYR Chi-restraints excluded: chain BC residue 116 ILE Chi-restraints excluded: chain BC residue 187 ASP Chi-restraints excluded: chain BC residue 195 VAL Chi-restraints excluded: chain BC residue 202 LEU Chi-restraints excluded: chain BC residue 228 VAL Chi-restraints excluded: chain BD residue 29 VAL Chi-restraints excluded: chain BD residue 92 VAL Chi-restraints excluded: chain BD residue 113 SER Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BE residue 1 MET Chi-restraints excluded: chain BE residue 12 LEU Chi-restraints excluded: chain BE residue 43 THR Chi-restraints excluded: chain BE residue 55 SER Chi-restraints excluded: chain BE residue 113 VAL Chi-restraints excluded: chain BE residue 115 GLN Chi-restraints excluded: chain BE residue 149 ILE Chi-restraints excluded: chain BE residue 165 HIS Chi-restraints excluded: chain BE residue 187 VAL Chi-restraints excluded: chain BF residue 56 ASP Chi-restraints excluded: chain BF residue 81 GLN Chi-restraints excluded: chain BF residue 103 LEU Chi-restraints excluded: chain BF residue 113 ASP Chi-restraints excluded: chain BG residue 11 VAL Chi-restraints excluded: chain BG residue 26 ILE Chi-restraints excluded: chain BG residue 92 VAL Chi-restraints excluded: chain BG residue 102 VAL Chi-restraints excluded: chain BG residue 106 SER Chi-restraints excluded: chain BG residue 129 THR Chi-restraints excluded: chain BG residue 133 LEU Chi-restraints excluded: chain BH residue 19 VAL Chi-restraints excluded: chain BI residue 49 ILE Chi-restraints excluded: chain BJ residue 30 THR Chi-restraints excluded: chain BJ residue 41 LYS Chi-restraints excluded: chain BJ residue 70 THR Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BK residue 10 VAL Chi-restraints excluded: chain BK residue 29 HIS Chi-restraints excluded: chain BK residue 38 ILE Chi-restraints excluded: chain BK residue 39 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 103 VAL Chi-restraints excluded: chain BL residue 25 SER Chi-restraints excluded: chain BL residue 42 SER Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BM residue 42 THR Chi-restraints excluded: chain BM residue 62 LYS Chi-restraints excluded: chain BM residue 88 ASN Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BM residue 105 MET Chi-restraints excluded: chain BM residue 106 ASP Chi-restraints excluded: chain BM residue 126 ILE Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 29 VAL Chi-restraints excluded: chain BN residue 36 THR Chi-restraints excluded: chain BN residue 42 LYS Chi-restraints excluded: chain BN residue 76 VAL Chi-restraints excluded: chain BN residue 116 VAL Chi-restraints excluded: chain BO residue 43 ASN Chi-restraints excluded: chain BO residue 48 LEU Chi-restraints excluded: chain BO residue 53 THR Chi-restraints excluded: chain BO residue 103 VAL Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BQ residue 20 GLN Chi-restraints excluded: chain BQ residue 62 ILE Chi-restraints excluded: chain BQ residue 77 SER Chi-restraints excluded: chain BQ residue 80 ILE Chi-restraints excluded: chain BQ residue 110 VAL Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 64 VAL Chi-restraints excluded: chain BS residue 12 SER Chi-restraints excluded: chain BS residue 101 SER Chi-restraints excluded: chain BT residue 1 MET Chi-restraints excluded: chain BT residue 11 LEU Chi-restraints excluded: chain BT residue 57 VAL Chi-restraints excluded: chain BU residue 15 THR Chi-restraints excluded: chain BU residue 36 VAL Chi-restraints excluded: chain BU residue 49 VAL Chi-restraints excluded: chain BU residue 58 ILE Chi-restraints excluded: chain BU residue 59 VAL Chi-restraints excluded: chain BV residue 53 LYS Chi-restraints excluded: chain BV residue 60 VAL Chi-restraints excluded: chain BV residue 63 ILE Chi-restraints excluded: chain BV residue 64 VAL Chi-restraints excluded: chain BV residue 86 LEU Chi-restraints excluded: chain BW residue 17 GLU Chi-restraints excluded: chain BW residue 38 VAL Chi-restraints excluded: chain BW residue 62 LYS Chi-restraints excluded: chain BX residue 19 SER Chi-restraints excluded: chain BX residue 46 PHE Chi-restraints excluded: chain BX residue 59 ILE Chi-restraints excluded: chain BX residue 60 ASP Chi-restraints excluded: chain BX residue 67 VAL Chi-restraints excluded: chain BY residue 14 LEU Chi-restraints excluded: chain BY residue 36 GLN Chi-restraints excluded: chain BY residue 49 ASP Chi-restraints excluded: chain BZ residue 8 THR Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B0 residue 26 THR Chi-restraints excluded: chain B1 residue 23 THR Chi-restraints excluded: chain B1 residue 48 ILE Chi-restraints excluded: chain B2 residue 44 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 940 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 555 optimal weight: 10.0000 chunk 712 optimal weight: 6.9990 chunk 551 optimal weight: 30.0000 chunk 820 optimal weight: 10.0000 chunk 544 optimal weight: 20.0000 chunk 971 optimal weight: 0.0570 chunk 608 optimal weight: 40.0000 chunk 592 optimal weight: 10.0000 chunk 448 optimal weight: 20.0000 overall best weight: 6.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 177 ASN ** AC 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AG 28 ASN ** AG 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 142 HIS ** AH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AK 22 HIS AK 40 ASN ** AO 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 40 GLN ** AT 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 68 HIS AT 70 ASN ** BC 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 163 GLN BC 251 GLN BD 42 ASN ** BF 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BH 2 GLN BK 3 GLN BK 9 ASN ** BO 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 72 ASN BS 31 GLN ** BU 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BU 69 ASN BW 76 ASN ** BX 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BY 15 ASN ** B5 -2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.6381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 157882 Z= 0.331 Angle : 0.778 28.710 236520 Z= 0.390 Chirality : 0.044 2.126 30235 Planarity : 0.007 0.156 12439 Dihedral : 23.495 179.997 79768 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.86 % Favored : 90.40 % Rotamer: Outliers : 6.40 % Allowed : 23.49 % Favored : 70.11 % 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: -1.95 (0.11), residues: 5522 helix: -0.41 (0.12), residues: 1660 sheet: -1.96 (0.16), residues: 880 loop : -1.57 (0.11), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPBF 97 HIS 0.027 0.002 HISAJ 70 PHE 0.036 0.003 PHEAU 37 TYR 0.032 0.002 TYRB1 49 ARG 0.014 0.001 ARGAJ 68 *********************** 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 1443 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 294 poor density : 1149 time to evaluate : 6.076 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 21 ARG cc_start: 0.4810 (tpm170) cc_final: 0.2666 (mtp180) REVERT: AB 43 LEU cc_start: 0.6540 (pp) cc_final: 0.6292 (tp) REVERT: AB 170 HIS cc_start: 0.6721 (p-80) cc_final: 0.6433 (p-80) REVERT: AD 71 GLN cc_start: 0.7664 (tm-30) cc_final: 0.7146 (tm-30) REVERT: AD 136 GLN cc_start: 0.7169 (tp-100) cc_final: 0.6960 (mm-40) REVERT: AE 60 ILE cc_start: 0.7976 (pp) cc_final: 0.7533 (mp) REVERT: AF 5 GLU cc_start: 0.5407 (OUTLIER) cc_final: 0.4919 (mt-10) REVERT: AF 16 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5895 (pm20) REVERT: AF 17 GLN cc_start: 0.5369 (tp40) cc_final: 0.5119 (tp-100) REVERT: AH 111 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6043 (mtt) REVERT: AK 98 ARG cc_start: 0.6431 (OUTLIER) cc_final: 0.6170 (tpt170) REVERT: AM 81 MET cc_start: 0.7042 (tmm) cc_final: 0.6343 (tmm) REVERT: AN 75 ARG cc_start: 0.7322 (mmt90) cc_final: 0.7060 (mtp85) REVERT: AP 17 TYR cc_start: 0.6380 (m-80) cc_final: 0.6123 (m-10) REVERT: AP 21 VAL cc_start: 0.8449 (m) cc_final: 0.8157 (p) REVERT: AQ 57 ASP cc_start: 0.4111 (m-30) cc_final: 0.3560 (p0) REVERT: BC 14 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7016 (mtp85) REVERT: BD 126 ASN cc_start: 0.8198 (m110) cc_final: 0.7958 (t0) REVERT: BE 40 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.5987 (ttm-80) REVERT: BE 69 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7497 (ptp-170) REVERT: BE 141 MET cc_start: 0.4792 (ptp) cc_final: 0.4517 (ptp) REVERT: BF 17 MET cc_start: 0.5056 (mmm) cc_final: 0.4692 (tpt) REVERT: BG 17 VAL cc_start: 0.7417 (t) cc_final: 0.7044 (m) REVERT: BG 133 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6688 (pp) REVERT: BG 149 ARG cc_start: 0.6729 (mmm-85) cc_final: 0.6169 (mmm160) REVERT: BI 49 ILE cc_start: -0.0779 (OUTLIER) cc_final: -0.1950 (tp) REVERT: BI 117 MET cc_start: 0.2929 (mmt) cc_final: 0.2591 (mmt) REVERT: BJ 44 TYR cc_start: 0.8121 (t80) cc_final: 0.7418 (t80) REVERT: BJ 106 LYS cc_start: 0.7341 (ttmm) cc_final: 0.7113 (tttt) REVERT: BM 17 ASN cc_start: 0.8154 (t0) cc_final: 0.7872 (t0) REVERT: BM 136 MET cc_start: 0.2416 (ttp) cc_final: 0.1415 (mmm) REVERT: BN 42 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7732 (mttp) REVERT: BN 58 ASP cc_start: 0.4620 (t0) cc_final: 0.3853 (p0) REVERT: BO 95 SER cc_start: 0.8289 (m) cc_final: 0.7898 (p) REVERT: BP 39 ARG cc_start: 0.4941 (tpp-160) cc_final: 0.4545 (tpp-160) REVERT: BP 62 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7150 (tpt170) REVERT: BQ 20 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: BQ 89 GLU cc_start: 0.7366 (tp30) cc_final: 0.7164 (pt0) REVERT: BQ 109 LEU cc_start: 0.8005 (mm) cc_final: 0.7793 (tp) REVERT: BS 76 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8427 (p) REVERT: BS 84 ARG cc_start: 0.7226 (mpt180) cc_final: 0.6895 (mmt180) REVERT: BT 1 MET cc_start: 0.5470 (OUTLIER) cc_final: 0.3921 (pmm) REVERT: BU 74 ASN cc_start: 0.4932 (t0) cc_final: 0.3804 (p0) REVERT: BW 36 ILE cc_start: 0.8623 (tp) cc_final: 0.8313 (tt) REVERT: BW 62 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.6923 (mmmm) REVERT: B1 47 VAL cc_start: 0.7880 (t) cc_final: 0.7548 (m) REVERT: B3 49 MET cc_start: 0.6347 (OUTLIER) cc_final: 0.6134 (tpt) REVERT: B4 34 LYS cc_start: 0.8450 (tppt) cc_final: 0.8120 (mmmt) outliers start: 294 outliers final: 219 residues processed: 1305 average time/residue: 1.2591 time to fit residues: 2849.1912 Evaluate side-chains 1327 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1092 time to evaluate : 6.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 46 THR Chi-restraints excluded: chain AB residue 50 PHE Chi-restraints excluded: chain AB residue 186 ILE Chi-restraints excluded: chain AB residue 199 VAL Chi-restraints excluded: chain AC residue 18 TRP Chi-restraints excluded: chain AC residue 34 ASP Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AC residue 82 GLU Chi-restraints excluded: chain AC residue 191 THR Chi-restraints excluded: chain AD residue 12 SER Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 55 LEU Chi-restraints excluded: chain AD residue 81 ARG Chi-restraints excluded: chain AD residue 94 LEU Chi-restraints excluded: chain AD residue 138 SER Chi-restraints excluded: chain AD residue 142 VAL Chi-restraints excluded: chain AD residue 152 GLN Chi-restraints excluded: chain AD residue 200 ILE Chi-restraints excluded: chain AE residue 15 LEU Chi-restraints excluded: chain AE residue 30 ILE Chi-restraints excluded: chain AE residue 48 PHE Chi-restraints excluded: chain AE residue 90 THR Chi-restraints excluded: chain AE residue 103 THR Chi-restraints excluded: chain AE residue 131 THR Chi-restraints excluded: chain AE residue 148 ASN Chi-restraints excluded: chain AF residue 3 HIS Chi-restraints excluded: chain AF residue 5 GLU Chi-restraints excluded: chain AF residue 10 VAL Chi-restraints excluded: chain AF residue 16 GLU Chi-restraints excluded: chain AF residue 60 VAL Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AF residue 96 VAL Chi-restraints excluded: chain AG residue 35 LYS Chi-restraints excluded: chain AG residue 83 SER Chi-restraints excluded: chain AG residue 89 VAL Chi-restraints excluded: chain AG residue 135 VAL Chi-restraints excluded: chain AG residue 141 VAL Chi-restraints excluded: chain AH residue 12 THR Chi-restraints excluded: chain AH residue 15 ARG Chi-restraints excluded: chain AH residue 30 SER Chi-restraints excluded: chain AH residue 40 LEU Chi-restraints excluded: chain AH residue 51 VAL Chi-restraints excluded: chain AH residue 83 LEU Chi-restraints excluded: chain AH residue 111 MET Chi-restraints excluded: chain AH residue 112 THR Chi-restraints excluded: chain AH residue 121 LEU Chi-restraints excluded: chain AI residue 29 VAL Chi-restraints excluded: chain AI residue 111 VAL Chi-restraints excluded: chain AI residue 116 VAL Chi-restraints excluded: chain AI residue 120 LYS Chi-restraints excluded: chain AJ residue 10 LEU Chi-restraints excluded: chain AK residue 26 SER Chi-restraints excluded: chain AK residue 35 THR Chi-restraints excluded: chain AK residue 84 VAL Chi-restraints excluded: chain AK residue 98 ARG Chi-restraints excluded: chain AK residue 113 VAL Chi-restraints excluded: chain AL residue 3 THR Chi-restraints excluded: chain AL residue 55 VAL Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 28 THR Chi-restraints excluded: chain AM residue 63 PHE Chi-restraints excluded: chain AM residue 65 VAL Chi-restraints excluded: chain AM residue 66 GLU Chi-restraints excluded: chain AO residue 11 ILE Chi-restraints excluded: chain AO residue 24 SER Chi-restraints excluded: chain AO residue 36 ILE Chi-restraints excluded: chain AO residue 61 SER Chi-restraints excluded: chain AO residue 66 LEU Chi-restraints excluded: chain AP residue 19 VAL Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AQ residue 8 LEU Chi-restraints excluded: chain AQ residue 17 MET Chi-restraints excluded: chain AQ residue 22 VAL Chi-restraints excluded: chain AQ residue 41 THR Chi-restraints excluded: chain AQ residue 42 THR Chi-restraints excluded: chain AQ residue 58 VAL Chi-restraints excluded: chain AQ residue 65 ARG Chi-restraints excluded: chain AQ residue 79 VAL Chi-restraints excluded: chain AR residue 51 TYR Chi-restraints excluded: chain AR residue 65 LEU Chi-restraints excluded: chain AS residue 79 THR Chi-restraints excluded: chain AT residue 58 VAL Chi-restraints excluded: chain AU residue 14 VAL Chi-restraints excluded: chain AU residue 40 LYS Chi-restraints excluded: chain BC residue 14 ARG Chi-restraints excluded: chain BC residue 35 GLU Chi-restraints excluded: chain BC residue 104 ILE Chi-restraints excluded: chain BC residue 116 ILE Chi-restraints excluded: chain BC residue 130 LEU Chi-restraints excluded: chain BC residue 187 ASP Chi-restraints excluded: chain BC residue 195 VAL Chi-restraints excluded: chain BC residue 220 VAL Chi-restraints excluded: chain BC residue 228 VAL Chi-restraints excluded: chain BC residue 232 HIS Chi-restraints excluded: chain BC residue 259 SER Chi-restraints excluded: chain BD residue 29 VAL Chi-restraints excluded: chain BD residue 50 VAL Chi-restraints excluded: chain BD residue 92 VAL Chi-restraints excluded: chain BD residue 109 VAL Chi-restraints excluded: chain BD residue 113 SER Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 155 VAL Chi-restraints excluded: chain BD residue 171 THR Chi-restraints excluded: chain BE residue 12 LEU Chi-restraints excluded: chain BE residue 40 ARG Chi-restraints excluded: chain BE residue 43 THR Chi-restraints excluded: chain BE residue 55 SER Chi-restraints excluded: chain BE residue 69 ARG Chi-restraints excluded: chain BE residue 113 VAL Chi-restraints excluded: chain BE residue 115 GLN Chi-restraints excluded: chain BE residue 126 VAL Chi-restraints excluded: chain BE residue 133 LEU Chi-restraints excluded: chain BE residue 149 ILE Chi-restraints excluded: chain BE residue 165 HIS Chi-restraints excluded: chain BE residue 187 VAL Chi-restraints excluded: chain BF residue 25 VAL Chi-restraints excluded: chain BF residue 40 VAL Chi-restraints excluded: chain BF residue 56 ASP Chi-restraints excluded: chain BF residue 61 SER Chi-restraints excluded: chain BF residue 66 LEU Chi-restraints excluded: chain BF residue 81 GLN Chi-restraints excluded: chain BF residue 113 ASP Chi-restraints excluded: chain BF residue 121 SER Chi-restraints excluded: chain BF residue 132 VAL Chi-restraints excluded: chain BG residue 26 ILE Chi-restraints excluded: chain BG residue 51 THR Chi-restraints excluded: chain BG residue 92 VAL Chi-restraints excluded: chain BG residue 102 VAL Chi-restraints excluded: chain BG residue 106 SER Chi-restraints excluded: chain BG residue 133 LEU Chi-restraints excluded: chain BI residue 36 MET Chi-restraints excluded: chain BI residue 49 ILE Chi-restraints excluded: chain BJ residue 24 THR Chi-restraints excluded: chain BJ residue 30 THR Chi-restraints excluded: chain BJ residue 41 LYS Chi-restraints excluded: chain BJ residue 62 VAL Chi-restraints excluded: chain BJ residue 64 VAL Chi-restraints excluded: chain BJ residue 70 THR Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BJ residue 80 HIS Chi-restraints excluded: chain BJ residue 84 ILE Chi-restraints excluded: chain BJ residue 122 LEU Chi-restraints excluded: chain BJ residue 139 VAL Chi-restraints excluded: chain BK residue 3 GLN Chi-restraints excluded: chain BK residue 10 VAL Chi-restraints excluded: chain BK residue 29 HIS Chi-restraints excluded: chain BK residue 38 ILE Chi-restraints excluded: chain BK residue 39 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 76 VAL Chi-restraints excluded: chain BK residue 84 CYS Chi-restraints excluded: chain BK residue 103 VAL Chi-restraints excluded: chain BL residue 25 SER Chi-restraints excluded: chain BL residue 42 SER Chi-restraints excluded: chain BL residue 61 LEU Chi-restraints excluded: chain BL residue 101 ILE Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BL residue 123 ARG Chi-restraints excluded: chain BL residue 125 LEU Chi-restraints excluded: chain BM residue 42 THR Chi-restraints excluded: chain BM residue 54 THR Chi-restraints excluded: chain BM residue 62 LYS Chi-restraints excluded: chain BM residue 88 ASN Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BM residue 105 MET Chi-restraints excluded: chain BM residue 126 ILE Chi-restraints excluded: chain BM residue 134 THR Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 29 VAL Chi-restraints excluded: chain BN residue 42 LYS Chi-restraints excluded: chain BN residue 52 ILE Chi-restraints excluded: chain BN residue 76 VAL Chi-restraints excluded: chain BN residue 116 VAL Chi-restraints excluded: chain BO residue 43 ASN Chi-restraints excluded: chain BO residue 48 LEU Chi-restraints excluded: chain BO residue 53 THR Chi-restraints excluded: chain BO residue 91 SER Chi-restraints excluded: chain BO residue 103 VAL Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BP residue 57 SER Chi-restraints excluded: chain BP residue 62 ARG Chi-restraints excluded: chain BQ residue 9 ILE Chi-restraints excluded: chain BQ residue 20 GLN Chi-restraints excluded: chain BQ residue 29 SER Chi-restraints excluded: chain BQ residue 77 SER Chi-restraints excluded: chain BQ residue 80 ILE Chi-restraints excluded: chain BQ residue 110 VAL Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 64 VAL Chi-restraints excluded: chain BS residue 12 SER Chi-restraints excluded: chain BS residue 39 THR Chi-restraints excluded: chain BS residue 47 VAL Chi-restraints excluded: chain BS residue 76 VAL Chi-restraints excluded: chain BS residue 101 SER Chi-restraints excluded: chain BT residue 1 MET Chi-restraints excluded: chain BT residue 11 LEU Chi-restraints excluded: chain BT residue 22 THR Chi-restraints excluded: chain BT residue 57 VAL Chi-restraints excluded: chain BU residue 15 THR Chi-restraints excluded: chain BU residue 25 VAL Chi-restraints excluded: chain BU residue 36 VAL Chi-restraints excluded: chain BU residue 49 VAL Chi-restraints excluded: chain BU residue 58 ILE Chi-restraints excluded: chain BU residue 59 VAL Chi-restraints excluded: chain BV residue 53 LYS Chi-restraints excluded: chain BV residue 60 VAL Chi-restraints excluded: chain BV residue 63 ILE Chi-restraints excluded: chain BV residue 64 VAL Chi-restraints excluded: chain BV residue 86 LEU Chi-restraints excluded: chain BW residue 15 ASP Chi-restraints excluded: chain BW residue 17 GLU Chi-restraints excluded: chain BW residue 38 VAL Chi-restraints excluded: chain BW residue 50 ASN Chi-restraints excluded: chain BW residue 62 LYS Chi-restraints excluded: chain BW residue 70 GLU Chi-restraints excluded: chain BX residue 19 SER Chi-restraints excluded: chain BX residue 35 SER Chi-restraints excluded: chain BX residue 48 THR Chi-restraints excluded: chain BX residue 60 ASP Chi-restraints excluded: chain BY residue 14 LEU Chi-restraints excluded: chain BY residue 36 GLN Chi-restraints excluded: chain BY residue 45 GLN Chi-restraints excluded: chain BY residue 49 ASP Chi-restraints excluded: chain BZ residue 8 THR Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B0 residue 26 THR Chi-restraints excluded: chain B0 residue 44 THR Chi-restraints excluded: chain B1 residue 23 THR Chi-restraints excluded: chain B1 residue 48 ILE Chi-restraints excluded: chain B3 residue 28 ASN Chi-restraints excluded: chain B3 residue 49 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 601 optimal weight: 10.0000 chunk 387 optimal weight: 30.0000 chunk 580 optimal weight: 20.0000 chunk 292 optimal weight: 8.9990 chunk 190 optimal weight: 7.9990 chunk 188 optimal weight: 8.9990 chunk 617 optimal weight: 7.9990 chunk 661 optimal weight: 10.0000 chunk 480 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 763 optimal weight: 20.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 18 HIS ** AC 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AG 28 ASN ** AG 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 142 HIS ** AH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AO 35 GLN AO 40 GLN ** AT 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 68 HIS AT 70 ASN AT 84 ASN ** BC 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 239 ASN BC 251 GLN BD 94 GLN BE 156 ASN ** BF 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BI 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 107 ASN ** BP 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 15 GLN ** BU 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BV 78 GLN BW 76 ASN ** BX 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BY 15 ASN BZ 9 GLN B0 6 ASN B5 -2 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.7107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 157882 Z= 0.419 Angle : 0.898 29.301 236520 Z= 0.447 Chirality : 0.049 2.119 30235 Planarity : 0.008 0.159 12439 Dihedral : 23.842 179.572 79768 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.58 % Favored : 89.70 % Rotamer: Outliers : 6.64 % Allowed : 24.44 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.53 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.10), residues: 5522 helix: -0.95 (0.12), residues: 1684 sheet: -2.26 (0.15), residues: 912 loop : -1.94 (0.11), residues: 2926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRPAB 23 HIS 0.016 0.002 HISAB 18 PHE 0.046 0.004 PHEAU 37 TYR 0.055 0.003 TYRB1 49 ARG 0.013 0.001 ARGAB 21 *********************** 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 1482 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1177 time to evaluate : 6.039 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 43 LEU cc_start: 0.6528 (pp) cc_final: 0.6258 (tp) REVERT: AB 78 GLU cc_start: 0.3885 (tp30) cc_final: 0.3460 (tp30) REVERT: AB 142 GLU cc_start: 0.5916 (pp20) cc_final: 0.5618 (pp20) REVERT: AB 145 GLU cc_start: 0.5978 (tp30) cc_final: 0.5775 (tp30) REVERT: AB 146 ASN cc_start: 0.5976 (p0) cc_final: 0.5611 (p0) REVERT: AD 136 GLN cc_start: 0.7491 (tp-100) cc_final: 0.7203 (mm-40) REVERT: AE 60 ILE cc_start: 0.8133 (pp) cc_final: 0.7771 (mp) REVERT: AF 5 GLU cc_start: 0.5565 (OUTLIER) cc_final: 0.4961 (mt-10) REVERT: AF 16 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5711 (pm20) REVERT: AF 17 GLN cc_start: 0.5929 (tp40) cc_final: 0.5651 (tp-100) REVERT: AI 38 TYR cc_start: 0.6356 (t80) cc_final: 0.5843 (t80) REVERT: AI 57 MET cc_start: 0.2035 (ppp) cc_final: 0.1737 (ppp) REVERT: AK 98 ARG cc_start: 0.6406 (OUTLIER) cc_final: 0.6143 (tpt170) REVERT: AL 36 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.4523 (ptm160) REVERT: AM 17 ILE cc_start: 0.7323 (mp) cc_final: 0.7067 (mm) REVERT: AM 81 MET cc_start: 0.7112 (tmm) cc_final: 0.6702 (tmm) REVERT: AN 75 ARG cc_start: 0.7478 (mmt90) cc_final: 0.7063 (mtp85) REVERT: AN 96 LEU cc_start: 0.7733 (tp) cc_final: 0.7404 (tt) REVERT: AP 17 TYR cc_start: 0.6482 (m-80) cc_final: 0.6200 (m-10) REVERT: AP 25 ARG cc_start: 0.7358 (ptt-90) cc_final: 0.6880 (ptt-90) REVERT: AQ 57 ASP cc_start: 0.4460 (m-30) cc_final: 0.4040 (p0) REVERT: BC 14 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7057 (mtp85) REVERT: BC 59 LYS cc_start: 0.8107 (ttmt) cc_final: 0.7879 (tttp) REVERT: BC 79 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6736 (tm-30) REVERT: BD 103 ASP cc_start: 0.7289 (t0) cc_final: 0.7059 (t70) REVERT: BD 126 ASN cc_start: 0.8153 (m110) cc_final: 0.7951 (t0) REVERT: BE 40 ARG cc_start: 0.6702 (OUTLIER) cc_final: 0.6089 (ttm-80) REVERT: BE 60 TRP cc_start: 0.8039 (p90) cc_final: 0.7706 (p90) REVERT: BE 69 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7902 (ptp-170) REVERT: BE 141 MET cc_start: 0.4667 (ptp) cc_final: 0.4461 (ptp) REVERT: BE 154 ASP cc_start: 0.2295 (t0) cc_final: 0.1894 (m-30) REVERT: BE 156 ASN cc_start: 0.6145 (OUTLIER) cc_final: 0.4906 (t0) REVERT: BF 17 MET cc_start: 0.5459 (mmm) cc_final: 0.4997 (tpt) REVERT: BG 133 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6451 (pp) REVERT: BJ 39 LYS cc_start: 0.6918 (mmmt) cc_final: 0.6412 (ttmm) REVERT: BJ 106 LYS cc_start: 0.7273 (ttmm) cc_final: 0.7048 (tttt) REVERT: BK 75 SER cc_start: 0.8472 (t) cc_final: 0.7840 (m) REVERT: BM 17 ASN cc_start: 0.8198 (t0) cc_final: 0.7936 (t0) REVERT: BM 41 LEU cc_start: 0.8022 (tp) cc_final: 0.7817 (tp) REVERT: BM 136 MET cc_start: 0.2598 (ttp) cc_final: 0.1727 (mmm) REVERT: BN 9 GLN cc_start: 0.7005 (tt0) cc_final: 0.6503 (tt0) REVERT: BN 42 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7750 (mttp) REVERT: BN 58 ASP cc_start: 0.4567 (t0) cc_final: 0.3789 (p0) REVERT: BN 107 ASN cc_start: 0.8569 (t0) cc_final: 0.7772 (m-40) REVERT: BO 28 VAL cc_start: 0.7824 (p) cc_final: 0.7536 (m) REVERT: BO 95 SER cc_start: 0.8332 (m) cc_final: 0.8129 (p) REVERT: BQ 20 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: BQ 109 LEU cc_start: 0.7958 (mm) cc_final: 0.7708 (tp) REVERT: BR 10 LYS cc_start: 0.5123 (OUTLIER) cc_final: 0.4161 (mtmm) REVERT: BR 97 LYS cc_start: 0.7818 (ttpp) cc_final: 0.7377 (mtpp) REVERT: BS 84 ARG cc_start: 0.7264 (mpt180) cc_final: 0.6928 (mmt180) REVERT: BT 1 MET cc_start: 0.5057 (OUTLIER) cc_final: 0.3289 (pmm) REVERT: BU 74 ASN cc_start: 0.5084 (t0) cc_final: 0.4151 (p0) REVERT: BW 36 ILE cc_start: 0.8661 (tp) cc_final: 0.8361 (tt) REVERT: BW 62 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7553 (mmtm) REVERT: BY 60 LYS cc_start: 0.5948 (ttmm) cc_final: 0.5609 (ttpt) REVERT: B4 34 LYS cc_start: 0.8476 (tppt) cc_final: 0.8121 (mmmt) outliers start: 305 outliers final: 234 residues processed: 1349 average time/residue: 1.3627 time to fit residues: 3187.9089 Evaluate side-chains 1343 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1095 time to evaluate : 5.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 46 THR Chi-restraints excluded: chain AB residue 50 PHE Chi-restraints excluded: chain AB residue 93 ASN Chi-restraints excluded: chain AC residue 18 TRP Chi-restraints excluded: chain AC residue 34 ASP Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AC residue 52 VAL Chi-restraints excluded: chain AC residue 69 HIS Chi-restraints excluded: chain AC residue 82 GLU Chi-restraints excluded: chain AC residue 162 ILE Chi-restraints excluded: chain AC residue 191 THR Chi-restraints excluded: chain AD residue 12 SER Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 55 LEU Chi-restraints excluded: chain AD residue 81 ARG Chi-restraints excluded: chain AD residue 94 LEU Chi-restraints excluded: chain AD residue 138 SER Chi-restraints excluded: chain AD residue 142 VAL Chi-restraints excluded: chain AD residue 152 GLN Chi-restraints excluded: chain AD residue 200 ILE Chi-restraints excluded: chain AE residue 48 PHE Chi-restraints excluded: chain AE residue 103 THR Chi-restraints excluded: chain AE residue 131 THR Chi-restraints excluded: chain AF residue 3 HIS Chi-restraints excluded: chain AF residue 5 GLU Chi-restraints excluded: chain AF residue 10 VAL Chi-restraints excluded: chain AF residue 16 GLU Chi-restraints excluded: chain AF residue 60 VAL Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AF residue 96 VAL Chi-restraints excluded: chain AG residue 35 LYS Chi-restraints excluded: chain AG residue 83 SER Chi-restraints excluded: chain AG residue 89 VAL Chi-restraints excluded: chain AG residue 135 VAL Chi-restraints excluded: chain AG residue 141 VAL Chi-restraints excluded: chain AG residue 142 HIS Chi-restraints excluded: chain AH residue 12 THR Chi-restraints excluded: chain AH residue 15 ARG Chi-restraints excluded: chain AH residue 30 SER Chi-restraints excluded: chain AH residue 40 LEU Chi-restraints excluded: chain AH residue 51 VAL Chi-restraints excluded: chain AH residue 63 LEU Chi-restraints excluded: chain AH residue 83 LEU Chi-restraints excluded: chain AH residue 112 THR Chi-restraints excluded: chain AH residue 121 LEU Chi-restraints excluded: chain AI residue 29 VAL Chi-restraints excluded: chain AI residue 111 VAL Chi-restraints excluded: chain AI residue 116 VAL Chi-restraints excluded: chain AI residue 120 LYS Chi-restraints excluded: chain AI residue 127 PHE Chi-restraints excluded: chain AJ residue 10 LEU Chi-restraints excluded: chain AK residue 26 SER Chi-restraints excluded: chain AK residue 35 THR Chi-restraints excluded: chain AK residue 84 VAL Chi-restraints excluded: chain AK residue 97 ILE Chi-restraints excluded: chain AK residue 98 ARG Chi-restraints excluded: chain AK residue 100 LEU Chi-restraints excluded: chain AL residue 3 THR Chi-restraints excluded: chain AL residue 36 ARG Chi-restraints excluded: chain AL residue 52 VAL Chi-restraints excluded: chain AL residue 55 VAL Chi-restraints excluded: chain AL residue 123 LYS Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 28 THR Chi-restraints excluded: chain AM residue 63 PHE Chi-restraints excluded: chain AM residue 65 VAL Chi-restraints excluded: chain AM residue 66 GLU Chi-restraints excluded: chain AO residue 11 ILE Chi-restraints excluded: chain AO residue 24 SER Chi-restraints excluded: chain AO residue 36 ILE Chi-restraints excluded: chain AO residue 61 SER Chi-restraints excluded: chain AO residue 66 LEU Chi-restraints excluded: chain AP residue 19 VAL Chi-restraints excluded: chain AP residue 26 ASN Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AQ residue 8 LEU Chi-restraints excluded: chain AQ residue 9 GLN Chi-restraints excluded: chain AQ residue 17 MET Chi-restraints excluded: chain AQ residue 22 VAL Chi-restraints excluded: chain AQ residue 41 THR Chi-restraints excluded: chain AQ residue 42 THR Chi-restraints excluded: chain AQ residue 58 VAL Chi-restraints excluded: chain AQ residue 67 LEU Chi-restraints excluded: chain AQ residue 79 VAL Chi-restraints excluded: chain AQ residue 81 LYS Chi-restraints excluded: chain AR residue 51 TYR Chi-restraints excluded: chain AR residue 65 LEU Chi-restraints excluded: chain AT residue 58 VAL Chi-restraints excluded: chain AT residue 70 ASN Chi-restraints excluded: chain AU residue 14 VAL Chi-restraints excluded: chain BC residue 14 ARG Chi-restraints excluded: chain BC residue 20 VAL Chi-restraints excluded: chain BC residue 35 GLU Chi-restraints excluded: chain BC residue 104 ILE Chi-restraints excluded: chain BC residue 116 ILE Chi-restraints excluded: chain BC residue 130 LEU Chi-restraints excluded: chain BC residue 187 ASP Chi-restraints excluded: chain BC residue 195 VAL Chi-restraints excluded: chain BC residue 220 VAL Chi-restraints excluded: chain BC residue 228 VAL Chi-restraints excluded: chain BC residue 232 HIS Chi-restraints excluded: chain BC residue 259 SER Chi-restraints excluded: chain BD residue 29 VAL Chi-restraints excluded: chain BD residue 50 VAL Chi-restraints excluded: chain BD residue 92 VAL Chi-restraints excluded: chain BD residue 113 SER Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 155 VAL Chi-restraints excluded: chain BD residue 171 THR Chi-restraints excluded: chain BE residue 12 LEU Chi-restraints excluded: chain BE residue 40 ARG Chi-restraints excluded: chain BE residue 43 THR Chi-restraints excluded: chain BE residue 55 SER Chi-restraints excluded: chain BE residue 69 ARG Chi-restraints excluded: chain BE residue 113 VAL Chi-restraints excluded: chain BE residue 126 VAL Chi-restraints excluded: chain BE residue 133 LEU Chi-restraints excluded: chain BE residue 149 ILE Chi-restraints excluded: chain BE residue 156 ASN Chi-restraints excluded: chain BE residue 165 HIS Chi-restraints excluded: chain BE residue 187 VAL Chi-restraints excluded: chain BF residue 25 VAL Chi-restraints excluded: chain BF residue 40 VAL Chi-restraints excluded: chain BF residue 56 ASP Chi-restraints excluded: chain BF residue 81 GLN Chi-restraints excluded: chain BF residue 83 TYR Chi-restraints excluded: chain BF residue 113 ASP Chi-restraints excluded: chain BF residue 121 SER Chi-restraints excluded: chain BF residue 132 VAL Chi-restraints excluded: chain BF residue 153 ASP Chi-restraints excluded: chain BG residue 26 ILE Chi-restraints excluded: chain BG residue 71 LEU Chi-restraints excluded: chain BG residue 92 VAL Chi-restraints excluded: chain BG residue 102 VAL Chi-restraints excluded: chain BG residue 106 SER Chi-restraints excluded: chain BG residue 133 LEU Chi-restraints excluded: chain BG residue 172 LYS Chi-restraints excluded: chain BI residue 9 VAL Chi-restraints excluded: chain BJ residue 24 THR Chi-restraints excluded: chain BJ residue 30 THR Chi-restraints excluded: chain BJ residue 41 LYS Chi-restraints excluded: chain BJ residue 48 VAL Chi-restraints excluded: chain BJ residue 62 VAL Chi-restraints excluded: chain BJ residue 64 VAL Chi-restraints excluded: chain BJ residue 70 THR Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BJ residue 80 HIS Chi-restraints excluded: chain BJ residue 88 THR Chi-restraints excluded: chain BJ residue 122 LEU Chi-restraints excluded: chain BJ residue 139 VAL Chi-restraints excluded: chain BJ residue 142 ILE Chi-restraints excluded: chain BK residue 29 HIS Chi-restraints excluded: chain BK residue 38 ILE Chi-restraints excluded: chain BK residue 39 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 76 VAL Chi-restraints excluded: chain BK residue 84 CYS Chi-restraints excluded: chain BK residue 103 VAL Chi-restraints excluded: chain BL residue 25 SER Chi-restraints excluded: chain BL residue 42 SER Chi-restraints excluded: chain BL residue 61 LEU Chi-restraints excluded: chain BL residue 77 ILE Chi-restraints excluded: chain BL residue 101 ILE Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BL residue 123 ARG Chi-restraints excluded: chain BL residue 129 LYS Chi-restraints excluded: chain BM residue 42 THR Chi-restraints excluded: chain BM residue 54 THR Chi-restraints excluded: chain BM residue 62 LYS Chi-restraints excluded: chain BM residue 88 ASN Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BM residue 101 VAL Chi-restraints excluded: chain BM residue 105 MET Chi-restraints excluded: chain BM residue 106 ASP Chi-restraints excluded: chain BM residue 126 ILE Chi-restraints excluded: chain BM residue 134 THR Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 34 ILE Chi-restraints excluded: chain BN residue 42 LYS Chi-restraints excluded: chain BN residue 52 ILE Chi-restraints excluded: chain BN residue 76 VAL Chi-restraints excluded: chain BN residue 116 VAL Chi-restraints excluded: chain BO residue 3 LYS Chi-restraints excluded: chain BO residue 43 ASN Chi-restraints excluded: chain BO residue 48 LEU Chi-restraints excluded: chain BO residue 53 THR Chi-restraints excluded: chain BO residue 64 TYR Chi-restraints excluded: chain BO residue 100 HIS Chi-restraints excluded: chain BO residue 103 VAL Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BP residue 57 SER Chi-restraints excluded: chain BQ residue 9 ILE Chi-restraints excluded: chain BQ residue 20 GLN Chi-restraints excluded: chain BQ residue 29 SER Chi-restraints excluded: chain BQ residue 74 ILE Chi-restraints excluded: chain BQ residue 77 SER Chi-restraints excluded: chain BQ residue 80 ILE Chi-restraints excluded: chain BQ residue 98 ILE Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 10 LYS Chi-restraints excluded: chain BR residue 64 VAL Chi-restraints excluded: chain BS residue 1 MET Chi-restraints excluded: chain BS residue 12 SER Chi-restraints excluded: chain BS residue 34 ASP Chi-restraints excluded: chain BS residue 39 THR Chi-restraints excluded: chain BS residue 47 VAL Chi-restraints excluded: chain BS residue 76 VAL Chi-restraints excluded: chain BS residue 101 SER Chi-restraints excluded: chain BT residue 1 MET Chi-restraints excluded: chain BT residue 11 LEU Chi-restraints excluded: chain BT residue 22 THR Chi-restraints excluded: chain BT residue 32 LEU Chi-restraints excluded: chain BT residue 54 GLU Chi-restraints excluded: chain BT residue 57 VAL Chi-restraints excluded: chain BU residue 15 THR Chi-restraints excluded: chain BU residue 25 VAL Chi-restraints excluded: chain BU residue 49 VAL Chi-restraints excluded: chain BU residue 58 ILE Chi-restraints excluded: chain BU residue 85 PHE Chi-restraints excluded: chain BV residue 53 LYS Chi-restraints excluded: chain BV residue 60 VAL Chi-restraints excluded: chain BV residue 86 LEU Chi-restraints excluded: chain BW residue 15 ASP Chi-restraints excluded: chain BW residue 38 VAL Chi-restraints excluded: chain BW residue 50 ASN Chi-restraints excluded: chain BW residue 62 LYS Chi-restraints excluded: chain BX residue 19 SER Chi-restraints excluded: chain BX residue 48 THR Chi-restraints excluded: chain BY residue 14 LEU Chi-restraints excluded: chain BY residue 19 LEU Chi-restraints excluded: chain BY residue 22 LEU Chi-restraints excluded: chain BY residue 36 GLN Chi-restraints excluded: chain BY residue 49 ASP Chi-restraints excluded: chain BY residue 57 LEU Chi-restraints excluded: chain BZ residue 8 THR Chi-restraints excluded: chain BZ residue 57 VAL Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B0 residue 26 THR Chi-restraints excluded: chain B1 residue 11 LEU Chi-restraints excluded: chain B1 residue 23 THR Chi-restraints excluded: chain B1 residue 48 ILE Chi-restraints excluded: chain B3 residue 28 ASN Chi-restraints excluded: chain B3 residue 50 VAL Chi-restraints excluded: chain B4 residue 20 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 883 optimal weight: 0.4980 chunk 930 optimal weight: 6.9990 chunk 849 optimal weight: 4.9990 chunk 905 optimal weight: 2.9990 chunk 544 optimal weight: 20.0000 chunk 394 optimal weight: 10.0000 chunk 710 optimal weight: 10.0000 chunk 277 optimal weight: 0.0070 chunk 818 optimal weight: 4.9990 chunk 856 optimal weight: 6.9990 chunk 902 optimal weight: 6.9990 overall best weight: 2.7004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 18 HIS ** AC 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 41 HIS AD 116 GLN AE 122 ASN AG 28 ASN ** AG 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 142 HIS ** AH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 58 ASN AO 35 GLN ** AP 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 70 ASN BC 90 ASN ** BC 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 239 ASN BC 251 GLN ** BG 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 33 GLN BI 43 ASN BI 105 GLN BK 3 GLN ** BO 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 72 ASN BS 15 GLN BW 76 ASN BX 36 HIS BZ 9 GLN ** B1 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.7031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.120 157882 Z= 0.179 Angle : 0.673 26.911 236520 Z= 0.344 Chirality : 0.040 2.132 30235 Planarity : 0.006 0.154 12439 Dihedral : 23.597 179.760 79768 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.71 % Allowed : 7.32 % Favored : 91.98 % Rotamer: Outliers : 4.44 % Allowed : 27.19 % Favored : 68.37 % 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: -2.00 (0.11), residues: 5522 helix: -0.42 (0.12), residues: 1674 sheet: -1.89 (0.16), residues: 844 loop : -1.68 (0.11), residues: 3004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRPAB 23 HIS 0.017 0.001 HISAG 142 PHE 0.035 0.002 PHEBU 73 TYR 0.029 0.002 TYRBF 128 ARG 0.010 0.001 ARGAG 143 *********************** 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 1373 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1169 time to evaluate : 5.975 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 21 ARG cc_start: 0.5225 (tpm170) cc_final: 0.3363 (mtp180) REVERT: AB 43 LEU cc_start: 0.6503 (pp) cc_final: 0.6262 (tp) REVERT: AB 105 LYS cc_start: 0.6486 (OUTLIER) cc_final: 0.5726 (pttt) REVERT: AD 136 GLN cc_start: 0.7146 (tp-100) cc_final: 0.6887 (mm-40) REVERT: AE 60 ILE cc_start: 0.8003 (pp) cc_final: 0.7663 (mp) REVERT: AF 5 GLU cc_start: 0.5181 (OUTLIER) cc_final: 0.4630 (mt-10) REVERT: AH 121 LEU cc_start: 0.7219 (pt) cc_final: 0.6716 (tt) REVERT: AI 38 TYR cc_start: 0.6218 (t80) cc_final: 0.5754 (t80) REVERT: AI 57 MET cc_start: 0.1873 (ppp) cc_final: 0.1532 (ppp) REVERT: AK 125 LYS cc_start: 0.5960 (tmtt) cc_final: 0.5513 (mmtt) REVERT: AL 36 ARG cc_start: 0.5878 (OUTLIER) cc_final: 0.4154 (ptm160) REVERT: AM 81 MET cc_start: 0.7101 (tmm) cc_final: 0.6624 (tmm) REVERT: AP 17 TYR cc_start: 0.6373 (m-80) cc_final: 0.6129 (m-10) REVERT: AQ 57 ASP cc_start: 0.4535 (m-30) cc_final: 0.4172 (p0) REVERT: AR 57 ARG cc_start: 0.7305 (mtt-85) cc_final: 0.7084 (mtt-85) REVERT: AU 8 GLU cc_start: 0.6643 (tm-30) cc_final: 0.6394 (tm-30) REVERT: AU 34 ARG cc_start: 0.4354 (ttt-90) cc_final: 0.4123 (ptm160) REVERT: BC 146 MET cc_start: 0.6108 (mtt) cc_final: 0.5711 (mtt) REVERT: BC 195 VAL cc_start: 0.7248 (OUTLIER) cc_final: 0.6962 (t) REVERT: BC 201 MET cc_start: 0.6456 (ttp) cc_final: 0.6212 (ttm) REVERT: BD 11 MET cc_start: 0.7215 (mmm) cc_final: 0.6958 (mmp) REVERT: BE 69 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7352 (ptp-170) REVERT: BE 141 MET cc_start: 0.4520 (ptp) cc_final: 0.4277 (ptp) REVERT: BF 17 MET cc_start: 0.5506 (mmm) cc_final: 0.4743 (tpt) REVERT: BF 27 GLN cc_start: 0.5998 (tm-30) cc_final: 0.5565 (tt0) REVERT: BG 133 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6497 (pp) REVERT: BG 149 ARG cc_start: 0.6780 (mmm-85) cc_final: 0.6156 (mmm160) REVERT: BG 151 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.6208 (m-80) REVERT: BI 49 ILE cc_start: -0.1197 (OUTLIER) cc_final: -0.2466 (tp) REVERT: BI 117 MET cc_start: 0.2598 (mmt) cc_final: -0.0263 (tpt) REVERT: BJ 39 LYS cc_start: 0.6941 (mmmt) cc_final: 0.6398 (ttmm) REVERT: BJ 106 LYS cc_start: 0.7360 (ttmm) cc_final: 0.7131 (tttt) REVERT: BM 17 ASN cc_start: 0.8288 (t0) cc_final: 0.8010 (t0) REVERT: BM 129 THR cc_start: 0.7083 (p) cc_final: 0.6776 (t) REVERT: BM 136 MET cc_start: 0.2648 (ttp) cc_final: 0.1739 (mmm) REVERT: BN 42 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7592 (mttp) REVERT: BN 58 ASP cc_start: 0.4498 (t0) cc_final: 0.3844 (p0) REVERT: BN 107 ASN cc_start: 0.8463 (t0) cc_final: 0.7997 (t0) REVERT: BO 28 VAL cc_start: 0.7731 (p) cc_final: 0.7421 (m) REVERT: BO 95 SER cc_start: 0.8372 (m) cc_final: 0.7971 (p) REVERT: BQ 20 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7551 (mp10) REVERT: BR 97 LYS cc_start: 0.7703 (ttpp) cc_final: 0.7309 (mtpp) REVERT: BS 48 LYS cc_start: 0.8307 (tttp) cc_final: 0.8106 (tttp) REVERT: BS 76 VAL cc_start: 0.8950 (t) cc_final: 0.8459 (p) REVERT: BS 84 ARG cc_start: 0.7267 (mpt180) cc_final: 0.7055 (mmt180) REVERT: BS 95 ARG cc_start: 0.7517 (mtm110) cc_final: 0.7234 (ttm110) REVERT: BT 1 MET cc_start: 0.5538 (OUTLIER) cc_final: 0.3397 (pmm) REVERT: BU 7 ARG cc_start: 0.4613 (tpp-160) cc_final: 0.3936 (mmm160) REVERT: BU 74 ASN cc_start: 0.5236 (t0) cc_final: 0.4603 (p0) REVERT: BW 36 ILE cc_start: 0.8533 (tp) cc_final: 0.8239 (tt) REVERT: BY 60 LYS cc_start: 0.5545 (ttmm) cc_final: 0.5232 (ttpt) REVERT: B1 48 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7457 (mm) REVERT: B4 2 LYS cc_start: 0.7710 (mtmm) cc_final: 0.7456 (mtmt) outliers start: 204 outliers final: 154 residues processed: 1288 average time/residue: 1.2614 time to fit residues: 2816.1240 Evaluate side-chains 1278 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1112 time to evaluate : 5.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 50 PHE Chi-restraints excluded: chain AB residue 93 ASN Chi-restraints excluded: chain AB residue 105 LYS Chi-restraints excluded: chain AC residue 18 TRP Chi-restraints excluded: chain AC residue 34 ASP Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AC residue 82 GLU Chi-restraints excluded: chain AC residue 191 THR Chi-restraints excluded: chain AC residue 195 VAL Chi-restraints excluded: chain AD residue 12 SER Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 55 LEU Chi-restraints excluded: chain AD residue 81 ARG Chi-restraints excluded: chain AD residue 94 LEU Chi-restraints excluded: chain AD residue 124 MET Chi-restraints excluded: chain AD residue 138 SER Chi-restraints excluded: chain AD residue 142 VAL Chi-restraints excluded: chain AD residue 152 GLN Chi-restraints excluded: chain AD residue 200 ILE Chi-restraints excluded: chain AE residue 30 ILE Chi-restraints excluded: chain AE residue 103 THR Chi-restraints excluded: chain AE residue 115 LEU Chi-restraints excluded: chain AE residue 131 THR Chi-restraints excluded: chain AF residue 3 HIS Chi-restraints excluded: chain AF residue 5 GLU Chi-restraints excluded: chain AF residue 10 VAL Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AF residue 96 VAL Chi-restraints excluded: chain AG residue 35 LYS Chi-restraints excluded: chain AG residue 38 THR Chi-restraints excluded: chain AG residue 83 SER Chi-restraints excluded: chain AG residue 89 VAL Chi-restraints excluded: chain AG residue 135 VAL Chi-restraints excluded: chain AG residue 142 HIS Chi-restraints excluded: chain AH residue 12 THR Chi-restraints excluded: chain AH residue 30 SER Chi-restraints excluded: chain AH residue 40 LEU Chi-restraints excluded: chain AH residue 51 VAL Chi-restraints excluded: chain AH residue 83 LEU Chi-restraints excluded: chain AH residue 112 THR Chi-restraints excluded: chain AI residue 29 VAL Chi-restraints excluded: chain AI residue 111 VAL Chi-restraints excluded: chain AJ residue 10 LEU Chi-restraints excluded: chain AK residue 26 SER Chi-restraints excluded: chain AK residue 35 THR Chi-restraints excluded: chain AK residue 84 VAL Chi-restraints excluded: chain AL residue 3 THR Chi-restraints excluded: chain AL residue 36 ARG Chi-restraints excluded: chain AL residue 52 VAL Chi-restraints excluded: chain AL residue 55 VAL Chi-restraints excluded: chain AL residue 123 LYS Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 65 VAL Chi-restraints excluded: chain AM residue 66 GLU Chi-restraints excluded: chain AM residue 102 THR Chi-restraints excluded: chain AO residue 24 SER Chi-restraints excluded: chain AO residue 36 ILE Chi-restraints excluded: chain AO residue 61 SER Chi-restraints excluded: chain AO residue 66 LEU Chi-restraints excluded: chain AP residue 19 VAL Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AQ residue 17 MET Chi-restraints excluded: chain AQ residue 22 VAL Chi-restraints excluded: chain AQ residue 41 THR Chi-restraints excluded: chain AQ residue 42 THR Chi-restraints excluded: chain AQ residue 58 VAL Chi-restraints excluded: chain AQ residue 79 VAL Chi-restraints excluded: chain AR residue 51 TYR Chi-restraints excluded: chain AR residue 65 LEU Chi-restraints excluded: chain AT residue 70 ASN Chi-restraints excluded: chain BC residue 104 ILE Chi-restraints excluded: chain BC residue 121 ASP Chi-restraints excluded: chain BC residue 130 LEU Chi-restraints excluded: chain BC residue 187 ASP Chi-restraints excluded: chain BC residue 195 VAL Chi-restraints excluded: chain BC residue 228 VAL Chi-restraints excluded: chain BC residue 259 SER Chi-restraints excluded: chain BD residue 29 VAL Chi-restraints excluded: chain BD residue 92 VAL Chi-restraints excluded: chain BD residue 109 VAL Chi-restraints excluded: chain BD residue 113 SER Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 171 THR Chi-restraints excluded: chain BE residue 12 LEU Chi-restraints excluded: chain BE residue 43 THR Chi-restraints excluded: chain BE residue 55 SER Chi-restraints excluded: chain BE residue 69 ARG Chi-restraints excluded: chain BE residue 113 VAL Chi-restraints excluded: chain BE residue 146 VAL Chi-restraints excluded: chain BE residue 165 HIS Chi-restraints excluded: chain BE residue 187 VAL Chi-restraints excluded: chain BF residue 40 VAL Chi-restraints excluded: chain BF residue 81 GLN Chi-restraints excluded: chain BF residue 83 TYR Chi-restraints excluded: chain BF residue 113 ASP Chi-restraints excluded: chain BF residue 121 SER Chi-restraints excluded: chain BF residue 132 VAL Chi-restraints excluded: chain BG residue 80 THR Chi-restraints excluded: chain BG residue 107 LEU Chi-restraints excluded: chain BG residue 133 LEU Chi-restraints excluded: chain BG residue 151 TYR Chi-restraints excluded: chain BH residue 19 VAL Chi-restraints excluded: chain BI residue 9 VAL Chi-restraints excluded: chain BI residue 49 ILE Chi-restraints excluded: chain BJ residue 64 VAL Chi-restraints excluded: chain BJ residue 70 THR Chi-restraints excluded: chain BJ residue 73 VAL Chi-restraints excluded: chain BK residue 10 VAL Chi-restraints excluded: chain BK residue 38 ILE Chi-restraints excluded: chain BK residue 39 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 BL residue 25 SER Chi-restraints excluded: chain BL residue 42 SER Chi-restraints excluded: chain BL residue 77 ILE Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BM residue 42 THR Chi-restraints excluded: chain BM residue 88 ASN Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BM residue 105 MET Chi-restraints excluded: chain BM residue 106 ASP Chi-restraints excluded: chain BM residue 126 ILE Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 29 VAL Chi-restraints excluded: chain BN residue 42 LYS Chi-restraints excluded: chain BN residue 76 VAL Chi-restraints excluded: chain BN residue 116 VAL Chi-restraints excluded: chain BO residue 43 ASN Chi-restraints excluded: chain BO residue 48 LEU Chi-restraints excluded: chain BP residue 17 VAL Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BP residue 57 SER Chi-restraints excluded: chain BQ residue 20 GLN Chi-restraints excluded: chain BQ residue 80 ILE Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 19 THR Chi-restraints excluded: chain BS residue 12 SER Chi-restraints excluded: chain BS residue 31 GLN Chi-restraints excluded: chain BS residue 101 SER Chi-restraints excluded: chain BS residue 106 VAL Chi-restraints excluded: chain BT residue 1 MET Chi-restraints excluded: chain BT residue 11 LEU Chi-restraints excluded: chain BT residue 57 VAL Chi-restraints excluded: chain BU residue 15 THR Chi-restraints excluded: chain BU residue 25 VAL Chi-restraints excluded: chain BU residue 49 VAL Chi-restraints excluded: chain BU residue 58 ILE Chi-restraints excluded: chain BV residue 64 VAL Chi-restraints excluded: chain BW residue 15 ASP Chi-restraints excluded: chain BW residue 38 VAL Chi-restraints excluded: chain BX residue 19 SER Chi-restraints excluded: chain BY residue 22 LEU Chi-restraints excluded: chain BY residue 36 GLN Chi-restraints excluded: chain BY residue 45 GLN Chi-restraints excluded: chain BY residue 49 ASP Chi-restraints excluded: chain BY residue 57 LEU Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B0 residue 26 THR Chi-restraints excluded: chain B0 residue 44 THR Chi-restraints excluded: chain B1 residue 23 THR Chi-restraints excluded: chain B1 residue 47 VAL Chi-restraints excluded: chain B1 residue 48 ILE Chi-restraints excluded: chain B4 residue 20 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 594 optimal weight: 10.0000 chunk 957 optimal weight: 10.0000 chunk 584 optimal weight: 20.0000 chunk 454 optimal weight: 10.0000 chunk 665 optimal weight: 10.0000 chunk 1004 optimal weight: 2.9990 chunk 924 optimal weight: 9.9990 chunk 799 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 617 optimal weight: 10.0000 chunk 490 optimal weight: 10.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 18 HIS ** AC 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 28 ASN AG 68 ASN ** AG 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 126 GLN AT 3 ASN ** AT 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 68 HIS ** BC 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 251 GLN ** BG 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 33 GLN ** BP 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 72 ASN ** BR 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BZ 9 GLN B0 6 ASN B5 -2 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.7270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 157882 Z= 0.370 Angle : 0.828 28.944 236520 Z= 0.412 Chirality : 0.046 2.127 30235 Planarity : 0.007 0.157 12439 Dihedral : 23.694 179.575 79768 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.69 % Favored : 89.62 % Rotamer: Outliers : 4.42 % Allowed : 27.47 % Favored : 68.11 % 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: -2.31 (0.11), residues: 5522 helix: -0.71 (0.12), residues: 1680 sheet: -2.03 (0.16), residues: 868 loop : -1.87 (0.11), residues: 2974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRPAB 23 HIS 0.014 0.002 HISAG 142 PHE 0.035 0.003 PHEAC 203 TYR 0.042 0.003 TYRB1 49 ARG 0.020 0.001 ARGAG 143 ********************** 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 1310 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1107 time to evaluate : 6.087 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: AB 43 LEU cc_start: 0.6543 (pp) cc_final: 0.6289 (tp) REVERT: AB 105 LYS cc_start: 0.6457 (OUTLIER) cc_final: 0.5696 (pttt) REVERT: AD 71 GLN cc_start: 0.7601 (tm-30) cc_final: 0.6706 (tm-30) REVERT: AD 75 TYR cc_start: 0.5585 (m-80) cc_final: 0.5171 (m-80) REVERT: AD 136 GLN cc_start: 0.7396 (tp-100) cc_final: 0.7175 (mm-40) REVERT: AE 60 ILE cc_start: 0.8081 (pp) cc_final: 0.7735 (mp) REVERT: AF 1 MET cc_start: 0.4090 (tpt) cc_final: 0.3274 (tpt) REVERT: AF 5 GLU cc_start: 0.5410 (OUTLIER) cc_final: 0.4831 (mt-10) REVERT: AF 8 PHE cc_start: 0.7972 (p90) cc_final: 0.7676 (p90) REVERT: AF 16 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.5899 (pm20) REVERT: AI 38 TYR cc_start: 0.6315 (t80) cc_final: 0.5738 (t80) REVERT: AI 57 MET cc_start: 0.1963 (ppp) cc_final: 0.1601 (ppp) REVERT: AJ 47 GLU cc_start: 0.5124 (OUTLIER) cc_final: 0.4393 (mm-30) REVERT: AL 36 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.4583 (ptm160) REVERT: AM 81 MET cc_start: 0.7166 (tmm) cc_final: 0.6526 (tmm) REVERT: AP 17 TYR cc_start: 0.6401 (m-80) cc_final: 0.6173 (m-10) REVERT: AQ 57 ASP cc_start: 0.4604 (m-30) cc_final: 0.4105 (p0) REVERT: AQ 65 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6292 (ptt90) REVERT: AT 28 MET cc_start: 0.7208 (tmm) cc_final: 0.6494 (ttp) REVERT: BC 145 GLU cc_start: 0.7612 (tp30) cc_final: 0.7386 (tp30) REVERT: BE 40 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.6010 (ttm-80) REVERT: BE 69 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7656 (ptp-170) REVERT: BF 17 MET cc_start: 0.5656 (mmm) cc_final: 0.4728 (tpt) REVERT: BF 27 GLN cc_start: 0.6317 (tm-30) cc_final: 0.5928 (tt0) REVERT: BG 133 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6446 (pp) REVERT: BG 149 ARG cc_start: 0.6947 (mmm-85) cc_final: 0.6413 (mmm160) REVERT: BI 117 MET cc_start: 0.2994 (mmt) cc_final: -0.0116 (tpt) REVERT: BJ 39 LYS cc_start: 0.6872 (mmmt) cc_final: 0.6354 (ttmm) REVERT: BJ 99 ARG cc_start: 0.7186 (mmp80) cc_final: 0.6979 (mmp80) REVERT: BJ 106 LYS cc_start: 0.7325 (ttmm) cc_final: 0.7108 (tttt) REVERT: BK 66 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8464 (mttp) REVERT: BM 17 ASN cc_start: 0.8279 (t0) cc_final: 0.7952 (t0) REVERT: BM 129 THR cc_start: 0.7187 (p) cc_final: 0.6718 (t) REVERT: BM 136 MET cc_start: 0.2449 (ttp) cc_final: 0.1475 (mmm) REVERT: BN 42 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7769 (mttp) REVERT: BN 58 ASP cc_start: 0.4646 (t0) cc_final: 0.3849 (p0) REVERT: BN 107 ASN cc_start: 0.8406 (t0) cc_final: 0.8032 (t0) REVERT: BO 28 VAL cc_start: 0.7758 (p) cc_final: 0.7519 (m) REVERT: BO 95 SER cc_start: 0.8388 (m) cc_final: 0.8093 (p) REVERT: BQ 20 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7651 (mp10) REVERT: BQ 109 LEU cc_start: 0.8072 (mm) cc_final: 0.7798 (tp) REVERT: BR 10 LYS cc_start: 0.5423 (OUTLIER) cc_final: 0.4538 (mtmm) REVERT: BR 40 MET cc_start: 0.6546 (tpt) cc_final: 0.6193 (tpt) REVERT: BR 97 LYS cc_start: 0.7797 (ttpp) cc_final: 0.7352 (mtpp) REVERT: BS 76 VAL cc_start: 0.8901 (t) cc_final: 0.8343 (p) REVERT: BS 84 ARG cc_start: 0.7298 (mpt180) cc_final: 0.7076 (mmt180) REVERT: BS 98 LYS cc_start: 0.7728 (mtpp) cc_final: 0.7239 (mttt) REVERT: BT 1 MET cc_start: 0.5045 (OUTLIER) cc_final: 0.3764 (pmm) REVERT: BT 52 GLU cc_start: 0.6464 (pm20) cc_final: 0.6093 (pm20) REVERT: BT 91 GLN cc_start: 0.4823 (pm20) cc_final: 0.4136 (tm-30) REVERT: BU 74 ASN cc_start: 0.5477 (t0) cc_final: 0.4569 (p0) REVERT: BW 36 ILE cc_start: 0.8640 (tp) cc_final: 0.8340 (tt) REVERT: BW 62 LYS cc_start: 0.8149 (mttt) cc_final: 0.7948 (mttm) REVERT: BY 60 LYS cc_start: 0.5902 (ttmm) cc_final: 0.5579 (ttpt) outliers start: 203 outliers final: 173 residues processed: 1234 average time/residue: 1.2917 time to fit residues: 2765.9067 Evaluate side-chains 1262 residues out of total 4596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1075 time to evaluate : 5.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AB residue 50 PHE Chi-restraints excluded: chain AB residue 93 ASN Chi-restraints excluded: chain AB residue 105 LYS Chi-restraints excluded: chain AC residue 18 TRP Chi-restraints excluded: chain AC residue 34 ASP Chi-restraints excluded: chain AC residue 43 LEU Chi-restraints excluded: chain AC residue 82 GLU Chi-restraints excluded: chain AC residue 191 THR Chi-restraints excluded: chain AC residue 195 VAL Chi-restraints excluded: chain AD residue 12 SER Chi-restraints excluded: chain AD residue 17 THR Chi-restraints excluded: chain AD residue 25 VAL Chi-restraints excluded: chain AD residue 55 LEU Chi-restraints excluded: chain AD residue 81 ARG Chi-restraints excluded: chain AD residue 94 LEU Chi-restraints excluded: chain AD residue 138 SER Chi-restraints excluded: chain AD residue 142 VAL Chi-restraints excluded: chain AD residue 152 GLN Chi-restraints excluded: chain AD residue 200 ILE Chi-restraints excluded: chain AE residue 15 LEU Chi-restraints excluded: chain AE residue 30 ILE Chi-restraints excluded: chain AE residue 103 THR Chi-restraints excluded: chain AE residue 131 THR Chi-restraints excluded: chain AF residue 3 HIS Chi-restraints excluded: chain AF residue 5 GLU Chi-restraints excluded: chain AF residue 10 VAL Chi-restraints excluded: chain AF residue 16 GLU Chi-restraints excluded: chain AF residue 89 VAL Chi-restraints excluded: chain AF residue 96 VAL Chi-restraints excluded: chain AG residue 35 LYS Chi-restraints excluded: chain AG residue 38 THR Chi-restraints excluded: chain AG residue 83 SER Chi-restraints excluded: chain AG residue 89 VAL Chi-restraints excluded: chain AG residue 135 VAL Chi-restraints excluded: chain AH residue 12 THR Chi-restraints excluded: chain AH residue 30 SER Chi-restraints excluded: chain AH residue 40 LEU Chi-restraints excluded: chain AH residue 51 VAL Chi-restraints excluded: chain AH residue 63 LEU Chi-restraints excluded: chain AH residue 83 LEU Chi-restraints excluded: chain AH residue 112 THR Chi-restraints excluded: chain AH residue 121 LEU Chi-restraints excluded: chain AI residue 29 VAL Chi-restraints excluded: chain AJ residue 10 LEU Chi-restraints excluded: chain AJ residue 47 GLU Chi-restraints excluded: chain AK residue 26 SER Chi-restraints excluded: chain AK residue 35 THR Chi-restraints excluded: chain AK residue 79 ILE Chi-restraints excluded: chain AK residue 84 VAL Chi-restraints excluded: chain AL residue 3 THR Chi-restraints excluded: chain AL residue 36 ARG Chi-restraints excluded: chain AL residue 52 VAL Chi-restraints excluded: chain AL residue 55 VAL Chi-restraints excluded: chain AL residue 123 LYS Chi-restraints excluded: chain AM residue 16 VAL Chi-restraints excluded: chain AM residue 25 VAL Chi-restraints excluded: chain AM residue 63 PHE Chi-restraints excluded: chain AM residue 65 VAL Chi-restraints excluded: chain AM residue 102 THR Chi-restraints excluded: chain AN residue 48 LEU Chi-restraints excluded: chain AO residue 24 SER Chi-restraints excluded: chain AO residue 36 ILE Chi-restraints excluded: chain AO residue 61 SER Chi-restraints excluded: chain AO residue 66 LEU Chi-restraints excluded: chain AP residue 19 VAL Chi-restraints excluded: chain AP residue 50 THR Chi-restraints excluded: chain AP residue 57 ILE Chi-restraints excluded: chain AQ residue 9 GLN Chi-restraints excluded: chain AQ residue 17 MET Chi-restraints excluded: chain AQ residue 22 VAL Chi-restraints excluded: chain AQ residue 41 THR Chi-restraints excluded: chain AQ residue 42 THR Chi-restraints excluded: chain AQ residue 58 VAL Chi-restraints excluded: chain AQ residue 65 ARG Chi-restraints excluded: chain AQ residue 79 VAL Chi-restraints excluded: chain AR residue 51 TYR Chi-restraints excluded: chain AR residue 65 LEU Chi-restraints excluded: chain AT residue 82 GLN Chi-restraints excluded: chain BC residue 104 ILE Chi-restraints excluded: chain BC residue 116 ILE Chi-restraints excluded: chain BC residue 121 ASP Chi-restraints excluded: chain BC residue 130 LEU Chi-restraints excluded: chain BC residue 187 ASP Chi-restraints excluded: chain BC residue 195 VAL Chi-restraints excluded: chain BC residue 228 VAL Chi-restraints excluded: chain BC residue 232 HIS Chi-restraints excluded: chain BC residue 259 SER Chi-restraints excluded: chain BD residue 29 VAL Chi-restraints excluded: chain BD residue 50 VAL Chi-restraints excluded: chain BD residue 92 VAL Chi-restraints excluded: chain BD residue 113 SER Chi-restraints excluded: chain BD residue 151 THR Chi-restraints excluded: chain BD residue 171 THR Chi-restraints excluded: chain BE residue 12 LEU Chi-restraints excluded: chain BE residue 40 ARG Chi-restraints excluded: chain BE residue 43 THR Chi-restraints excluded: chain BE residue 55 SER Chi-restraints excluded: chain BE residue 69 ARG Chi-restraints excluded: chain BE residue 113 VAL Chi-restraints excluded: chain BE residue 165 HIS Chi-restraints excluded: chain BE residue 187 VAL Chi-restraints excluded: chain BF residue 40 VAL Chi-restraints excluded: chain BF residue 81 GLN Chi-restraints excluded: chain BF residue 83 TYR Chi-restraints excluded: chain BF residue 113 ASP Chi-restraints excluded: chain BF residue 121 SER Chi-restraints excluded: chain BF residue 132 VAL Chi-restraints excluded: chain BG residue 80 THR Chi-restraints excluded: chain BG residue 107 LEU Chi-restraints excluded: chain BG residue 111 HIS Chi-restraints excluded: chain BG residue 133 LEU Chi-restraints excluded: chain BI residue 9 VAL Chi-restraints excluded: chain BI residue 49 ILE Chi-restraints excluded: chain BJ residue 10 THR Chi-restraints excluded: chain BJ residue 48 VAL Chi-restraints excluded: chain BJ residue 64 VAL Chi-restraints excluded: chain BJ residue 70 THR Chi-restraints excluded: chain BJ residue 91 GLU Chi-restraints excluded: chain BJ residue 139 VAL Chi-restraints excluded: chain BK residue 10 VAL Chi-restraints excluded: chain BK residue 29 HIS Chi-restraints excluded: chain BK residue 38 ILE Chi-restraints excluded: chain BK residue 39 ILE Chi-restraints excluded: chain BK residue 51 LYS 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 66 LYS Chi-restraints excluded: chain BK residue 76 VAL Chi-restraints excluded: chain BL residue 25 SER Chi-restraints excluded: chain BL residue 42 SER Chi-restraints excluded: chain BL residue 61 LEU Chi-restraints excluded: chain BL residue 77 ILE Chi-restraints excluded: chain BL residue 111 ILE Chi-restraints excluded: chain BM residue 42 THR Chi-restraints excluded: chain BM residue 88 ASN Chi-restraints excluded: chain BM residue 93 VAL Chi-restraints excluded: chain BM residue 105 MET Chi-restraints excluded: chain BM residue 126 ILE Chi-restraints excluded: chain BM residue 134 THR Chi-restraints excluded: chain BN residue 13 ASN Chi-restraints excluded: chain BN residue 29 VAL Chi-restraints excluded: chain BN residue 42 LYS Chi-restraints excluded: chain BN residue 52 ILE Chi-restraints excluded: chain BN residue 76 VAL Chi-restraints excluded: chain BN residue 116 VAL Chi-restraints excluded: chain BO residue 43 ASN Chi-restraints excluded: chain BO residue 48 LEU Chi-restraints excluded: chain BP residue 17 VAL Chi-restraints excluded: chain BP residue 46 VAL Chi-restraints excluded: chain BP residue 57 SER Chi-restraints excluded: chain BP residue 62 ARG Chi-restraints excluded: chain BQ residue 20 GLN Chi-restraints excluded: chain BQ residue 80 ILE Chi-restraints excluded: chain BQ residue 117 LEU Chi-restraints excluded: chain BR residue 10 LYS Chi-restraints excluded: chain BR residue 19 THR Chi-restraints excluded: chain BR residue 64 VAL Chi-restraints excluded: chain BS residue 12 SER Chi-restraints excluded: chain BS residue 31 GLN Chi-restraints excluded: chain BS residue 39 THR Chi-restraints excluded: chain BS residue 101 SER Chi-restraints excluded: chain BT residue 1 MET Chi-restraints excluded: chain BT residue 11 LEU Chi-restraints excluded: chain BT residue 57 VAL Chi-restraints excluded: chain BU residue 15 THR Chi-restraints excluded: chain BU residue 25 VAL Chi-restraints excluded: chain BU residue 49 VAL Chi-restraints excluded: chain BU residue 58 ILE Chi-restraints excluded: chain BV residue 7 GLU Chi-restraints excluded: chain BV residue 85 LYS Chi-restraints excluded: chain BW residue 15 ASP Chi-restraints excluded: chain BW residue 38 VAL Chi-restraints excluded: chain BX residue 19 SER Chi-restraints excluded: chain BX residue 48 THR Chi-restraints excluded: chain BY residue 36 GLN Chi-restraints excluded: chain BY residue 45 GLN Chi-restraints excluded: chain BY residue 49 ASP Chi-restraints excluded: chain BY residue 57 LEU Chi-restraints excluded: chain B0 residue 9 THR Chi-restraints excluded: chain B0 residue 26 THR Chi-restraints excluded: chain B0 residue 44 THR Chi-restraints excluded: chain B1 residue 23 THR Chi-restraints excluded: chain B1 residue 47 VAL Chi-restraints excluded: chain B1 residue 48 ILE Chi-restraints excluded: chain B3 residue 34 THR Chi-restraints excluded: chain B4 residue 20 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 635 optimal weight: 10.0000 chunk 851 optimal weight: 20.0000 chunk 244 optimal weight: 0.4980 chunk 737 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 222 optimal weight: 6.9990 chunk 800 optimal weight: 9.9990 chunk 335 optimal weight: 2.9990 chunk 822 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 overall best weight: 6.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AB 18 HIS ** AC 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 28 ASN ** AG 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AG 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AH 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AM 52 GLN ** AS 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AT 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AT 70 ASN ** BC 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BC 251 GLN ** BG 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 33 GLN BN 11 ASN ** BR 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BY 15 ASN BZ 9 GLN B0 6 ASN B5 -2 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.137117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.113079 restraints weight = 331013.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.113724 restraints weight = 195452.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.115461 restraints weight = 122422.447| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.7374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 157882 Z= 0.298 Angle : 0.764 28.096 236520 Z= 0.384 Chirality : 0.044 2.121 30235 Planarity : 0.007 0.156 12439 Dihedral : 23.691 179.614 79768 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.67 % Allowed : 9.38 % Favored : 89.95 % Rotamer: Outliers : 4.85 % Allowed : 27.45 % Favored : 67.70 % 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: -2.27 (0.11), residues: 5522 helix: -0.65 (0.12), residues: 1674 sheet: -1.92 (0.16), residues: 861 loop : -1.89 (0.11), residues: 2987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRPAB 23 HIS 0.014 0.002 HISAJ 70 PHE 0.031 0.003 PHEAC 203 TYR 0.033 0.002 TYRB1 49 ARG 0.010 0.001 ARGAG 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41080.34 seconds wall clock time: 716 minutes 52.63 seconds (43012.63 seconds total)