Starting phenix.real_space_refine on Mon Mar 25 11:18:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcs_8238/03_2024/5kcs_8238_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcs_8238/03_2024/5kcs_8238.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcs_8238/03_2024/5kcs_8238_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcs_8238/03_2024/5kcs_8238_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcs_8238/03_2024/5kcs_8238_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcs_8238/03_2024/5kcs_8238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcs_8238/03_2024/5kcs_8238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcs_8238/03_2024/5kcs_8238_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcs_8238/03_2024/5kcs_8238_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4641 5.49 5 S 155 5.16 5 Cl 2 4.86 5 C 74993 2.51 5 N 27898 2.21 5 O 41256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1E ARG 13": "NH1" <-> "NH2" Residue "1E ARG 33": "NH1" <-> "NH2" Residue "1E TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E ARG 59": "NH1" <-> "NH2" Residue "1E ARG 77": "NH1" <-> "NH2" Residue "1E ARG 83": "NH1" <-> "NH2" Residue "1E ARG 169": "NH1" <-> "NH2" Residue "1E ARG 184": "NH1" <-> "NH2" Residue "1F ARG 21": "NH1" <-> "NH2" Residue "1F ARG 44": "NH1" <-> "NH2" Residue "1F ARG 49": "NH1" <-> "NH2" Residue "1F ARG 61": "NH1" <-> "NH2" Residue "1F ARG 88": "NH1" <-> "NH2" Residue "1F ARG 102": "NH1" <-> "NH2" Residue "1F ARG 162": "NH1" <-> "NH2" Residue "1F ARG 170": "NH1" <-> "NH2" Residue "1G ARG 70": "NH1" <-> "NH2" Residue "1G ARG 79": "NH1" <-> "NH2" Residue "1G ARG 91": "NH1" <-> "NH2" Residue "1G ARG 101": "NH1" <-> "NH2" Residue "1G ARG 109": "NH1" <-> "NH2" Residue "1G ARG 111": "NH1" <-> "NH2" Residue "1G ARG 114": "NH1" <-> "NH2" Residue "1G ARG 132": "NH1" <-> "NH2" Residue "1H ARG 2": "NH1" <-> "NH2" Residue "1H ARG 152": "NH1" <-> "NH2" Residue "1H ARG 162": "NH1" <-> "NH2" Residue "1H ARG 169": "NH1" <-> "NH2" Residue "1J TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1K TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1K PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1K PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1N ARG 13": "NH1" <-> "NH2" Residue "1N ARG 37": "NH1" <-> "NH2" Residue "1N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1N ARG 96": "NH1" <-> "NH2" Residue "1N ARG 120": "NH1" <-> "NH2" Residue "1O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1P ARG 21": "NH1" <-> "NH2" Residue "1P ARG 33": "NH1" <-> "NH2" Residue "1P ARG 41": "NH1" <-> "NH2" Residue "1P ARG 47": "NH1" <-> "NH2" Residue "1P TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1P ARG 60": "NH1" <-> "NH2" Residue "1P PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1P ARG 78": "NH1" <-> "NH2" Residue "1P ARG 126": "NH1" <-> "NH2" Residue "1Q ARG 10": "NH1" <-> "NH2" Residue "1Q ARG 18": "NH1" <-> "NH2" Residue "1Q ARG 40": "NH1" <-> "NH2" Residue "1Q ARG 44": "NH1" <-> "NH2" Residue "1Q ARG 50": "NH1" <-> "NH2" Residue "1Q ARG 59": "NH1" <-> "NH2" Residue "1Q ARG 114": "NH1" <-> "NH2" Residue "1R ARG 8": "NH1" <-> "NH2" Residue "1R ARG 12": "NH1" <-> "NH2" Residue "1R ARG 17": "NH1" <-> "NH2" Residue "1R ARG 22": "NH1" <-> "NH2" Residue "1R ARG 46": "NH1" <-> "NH2" Residue "1R ARG 63": "NH1" <-> "NH2" Residue "1R ARG 64": "NH1" <-> "NH2" Residue "1R ARG 69": "NH1" <-> "NH2" Residue "1R ARG 71": "NH1" <-> "NH2" Residue "1R PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1R ARG 96": "NH1" <-> "NH2" Residue "1R ARG 118": "NH1" <-> "NH2" Residue "1S ARG 10": "NH1" <-> "NH2" Residue "1S ARG 16": "NH1" <-> "NH2" Residue "1S ARG 25": "NH1" <-> "NH2" Residue "1S ARG 81": "NH1" <-> "NH2" Residue "1S ARG 94": "NH1" <-> "NH2" Residue "1S ARG 102": "NH1" <-> "NH2" Residue "1S ARG 111": "NH1" <-> "NH2" Residue "1S PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1T ARG 20": "NH1" <-> "NH2" Residue "1T ARG 38": "NH1" <-> "NH2" Residue "1T PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1T ARG 61": "NH1" <-> "NH2" Residue "1T ARG 88": "NH1" <-> "NH2" Residue "1T ARG 100": "NH1" <-> "NH2" Residue "1T ARG 108": "NH1" <-> "NH2" Residue "1U ARG 2": "NH1" <-> "NH2" Residue "1U ARG 5": "NH1" <-> "NH2" Residue "1U ARG 12": "NH1" <-> "NH2" Residue "1U ARG 32": "NH1" <-> "NH2" Residue "1U ARG 47": "NH1" <-> "NH2" Residue "1U ARG 69": "NH1" <-> "NH2" Residue "1V TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1V PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1V ARG 21": "NH1" <-> "NH2" Residue "1V ARG 68": "NH1" <-> "NH2" Residue "1V ARG 78": "NH1" <-> "NH2" Residue "1V ARG 79": "NH1" <-> "NH2" Residue "1V ARG 84": "NH1" <-> "NH2" Residue "1W PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1W ARG 84": "NH1" <-> "NH2" Residue "1W ARG 88": "NH1" <-> "NH2" Residue "1W ARG 95": "NH1" <-> "NH2" Residue "1W ARG 110": "NH1" <-> "NH2" Residue "1X ARG 73": "NH1" <-> "NH2" Residue "1Y ARG 5": "NH1" <-> "NH2" Residue "1Y ARG 6": "NH1" <-> "NH2" Residue "1Y ARG 81": "NH1" <-> "NH2" Residue "1Y ARG 85": "NH1" <-> "NH2" Residue "1Y ARG 93": "NH1" <-> "NH2" Residue "1Y PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1Z PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1Z TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1Z TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "10 PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "10 PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "11 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "12 ARG 29": "NH1" <-> "NH2" Residue "12 ARG 47": "NH1" <-> "NH2" Residue "12 ARG 52": "NH1" <-> "NH2" Residue "13 ARG 10": "NH1" <-> "NH2" Residue "13 ARG 29": "NH1" <-> "NH2" Residue "13 ARG 44": "NH1" <-> "NH2" Residue "13 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "14 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "14 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "14 ARG 49": "NH1" <-> "NH2" Residue "14 ARG 56": "NH1" <-> "NH2" Residue "15 ARG 9": "NH1" <-> "NH2" Residue "15 ARG 15": "NH1" <-> "NH2" Residue "15 ARG 39": "NH1" <-> "NH2" Residue "15 ARG 51": "NH1" <-> "NH2" Residue "16 ARG 43": "NH1" <-> "NH2" Residue "17 ARG 3": "NH1" <-> "NH2" Residue "17 ARG 12": "NH1" <-> "NH2" Residue "17 ARG 14": "NH1" <-> "NH2" Residue "17 ARG 19": "NH1" <-> "NH2" Residue "17 ARG 21": "NH1" <-> "NH2" Residue "17 ARG 33": "NH1" <-> "NH2" Residue "17 ARG 41": "NH1" <-> "NH2" Residue "18 ARG 12": "NH1" <-> "NH2" Residue "18 ARG 29": "NH1" <-> "NH2" Residue "18 ARG 39": "NH1" <-> "NH2" Residue "18 ARG 41": "NH1" <-> "NH2" Residue "18 TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "19 ARG 12": "NH1" <-> "NH2" Residue "19 ARG 24": "NH1" <-> "NH2" Residue "1b PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1b TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1b PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1b ARG 107": "NH1" <-> "NH2" Residue "1b PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1b PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1b ARG 224": "NH1" <-> "NH2" Residue "1c ARG 106": "NH1" <-> "NH2" Residue "1c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1c ARG 130": "NH1" <-> "NH2" Residue "1d TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1e PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1e ARG 156": "NH1" <-> "NH2" Residue "1f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1g PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1h PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1i PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1i ARG 123": "NH1" <-> "NH2" Residue "1l ARG 55": "NH1" <-> "NH2" Residue "1l TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1n ASP 33": "OD1" <-> "OD2" Residue "1p TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1p ARG 28": "NH1" <-> "NH2" Residue "1p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1r TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1u PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1w TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 148945 Number of models: 1 Model: "" Number of chains: 59 Chain: "1A" Number of atoms: 62276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62276 Classifications: {'RNA': 2900} Modifications used: {'p5*END': 1, 'rna2p': 6, 'rna2p_pur': 203, 'rna2p_pyr': 88, 'rna3p': 18, 'rna3p_pur': 1463, 'rna3p_pyr': 1122} Link IDs: {'rna2p': 297, 'rna3p': 2602} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "1B" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2570 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 54} Link IDs: {'rna2p': 5, 'rna3p': 114} Chain: "1D" 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: "1E" 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: "1F" 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: "1G" 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: "1H" 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: "1L" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 276 Classifications: {'peptide': 69} Incomplete info: {'backbone_only': 63} Link IDs: {'PCIS': 1, 'TRANS': 67} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 319 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 68 Chain: "1I" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "1J" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "1K" 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: "1N" 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: "1O" 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: "1P" 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: "1Q" 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: "1R" 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: "1S" 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: "1T" 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: "1U" 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: "1V" 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: "1W" 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: "1X" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "1Y" 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: "1Z" 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: "10" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "11" 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: "12" 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: "13" 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: "14" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "15" 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: "16" 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: "17" 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: "18" 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: "19" 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: "1a" Number of atoms: 33029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33029 Classifications: {'RNA': 1539} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 87, 'rna2p_pyr': 42, 'rna3p': 10, 'rna3p_pur': 781, 'rna3p_pyr': 618} Link IDs: {'rna2p': 130, 'rna3p': 1408} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 8 Chain: "1b" 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: "1c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198} Chain: "1d" 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: "1e" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1141 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "1f" 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: "1g" 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: "1h" 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: "1i" 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: "1j" 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: "1k" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "1l" 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: "1m" 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: "1n" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 794 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "1o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "1p" 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: "1q" 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: "1r" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 504 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "1s" 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: "1t" 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: "1u" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 495 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "1v" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 192 Classifications: {'RNA': 9} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 7} Chain: "1w" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 2590 Classifications: {'peptide': 639} Incomplete info: {'backbone_only': 596} Link IDs: {'CIS': 16, 'PCIS': 1, 'PTRANS': 27, 'TRANS': 594} Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 2600 Unresolved non-hydrogen angles: 3760 Unresolved non-hydrogen dihedrals: 1640 Unresolved non-hydrogen chiralities: 801 Planarities with less than four sites: {'GLN:plan1': 27, 'HIS:plan': 11, 'TYR:plan': 30, 'ASN:plan1': 31, 'TRP:plan': 3, 'ASP:plan': 27, 'PHE:plan': 20, 'GLU:plan': 52, 'ARG:plan': 28} Unresolved non-hydrogen planarities: 1164 Chain: "1x" Number of atoms: 1567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1567 Classifications: {'RNA': 73} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p': 4, 'rna3p_pur': 34, 'rna3p_pyr': 28} Link IDs: {'rna2p': 6, 'rna3p': 66} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "1A" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 111 Unusual residues: {'EVN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 56.55, per 1000 atoms: 0.38 Number of scatterers: 148945 At special positions: 0 Unit cell: (265.92, 278.108, 242.652, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 155 16.00 P 4641 15.00 O 41256 8.00 N 27898 7.00 C 74993 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS14 18 " - pdb=" SG CYS14 40 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 62.17 Conformation dependent library (CDL) restraints added in 7.3 seconds 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10942 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: 205 helices and 71 sheets defined 38.6% alpha, 15.2% beta 1176 base pairs and 2664 stacking pairs defined. Time for finding SS restraints: 76.65 Creating SS restraints... Processing helix chain '1D' and resid 11 through 16 removed outlier: 4.899A pdb=" N VAL1D 15 " --> pdb=" O GLY1D 11 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL1D 16 " --> pdb=" O ARG1D 12 " (cutoff:3.500A) No H-bonds generated for 'chain '1D' and resid 11 through 16' Processing helix chain '1D' and resid 130 through 135 removed outlier: 4.152A pdb=" N ILE1D 134 " --> pdb=" O PRO1D 130 " (cutoff:3.500A) Proline residue: 1D 135 - end of helix No H-bonds generated for 'chain '1D' and resid 130 through 135' Processing helix chain '1D' and resid 206 through 214 removed outlier: 4.655A pdb=" N ALA1D 210 " --> pdb=" O LYS1D 206 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG1D 211 " --> pdb=" O ALA1D 207 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP1D 212 " --> pdb=" O GLY1D 208 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG1D 213 " --> pdb=" O ALA1D 209 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY1D 214 " --> pdb=" O ALA1D 210 " (cutoff:3.500A) No H-bonds generated for 'chain '1D' and resid 206 through 214' Processing helix chain '1D' and resid 220 through 225 removed outlier: 3.595A pdb=" N MET1D 224 " --> pdb=" O ARG1D 220 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN1D 225 " --> pdb=" O GLY1D 221 " (cutoff:3.500A) No H-bonds generated for 'chain '1D' and resid 220 through 225' Processing helix chain '1D' and resid 259 through 267 removed outlier: 5.511A pdb=" N ASP1D 263 " --> pdb=" O ASN1D 259 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS1D 264 " --> pdb=" O LYS1D 260 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N PHE1D 265 " --> pdb=" O ARG1D 261 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE1D 266 " --> pdb=" O THR1D 262 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N VAL1D 267 " --> pdb=" O ASP1D 263 " (cutoff:3.500A) No H-bonds generated for 'chain '1D' and resid 259 through 267' Processing helix chain '1D' and resid 196 through 201 removed outlier: 3.608A pdb=" N HIS1D 199 " --> pdb=" O ASN1D 196 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET1D 200 " --> pdb=" O ALA1D 197 " (cutoff:3.500A) Processing helix chain '1E' and resid 61 through 72 removed outlier: 3.728A pdb=" N ALA1E 69 " --> pdb=" O ALA1E 65 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS1E 70 " --> pdb=" O GLY1E 66 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA1E 71 " --> pdb=" O HIS1E 67 " (cutoff:3.500A) Processing helix chain '1E' and resid 98 through 105 removed outlier: 4.042A pdb=" N ALA1E 102 " --> pdb=" O VAL1E 98 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP1E 103 " --> pdb=" O GLU1E 99 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL1E 104 " --> pdb=" O LEU1E 100 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS1E 105 " --> pdb=" O PHE1E 101 " (cutoff:3.500A) No H-bonds generated for 'chain '1E' and resid 98 through 105' Processing helix chain '1E' and resid 120 through 125 Processing helix chain '1F' and resid 15 through 20 Processing helix chain '1F' and resid 24 through 40 removed outlier: 3.775A pdb=" N GLN1F 30 " --> pdb=" O ALA1F 26 " (cutoff:3.500A) Processing helix chain '1F' and resid 48 through 53 removed outlier: 5.974A pdb=" N THR1F 53 " --> pdb=" O ARG1F 49 " (cutoff:3.500A) Processing helix chain '1F' and resid 97 through 116 removed outlier: 3.670A pdb=" N SER1F 110 " --> pdb=" O LYS1F 106 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG1F 114 " --> pdb=" O SER1F 110 " (cutoff:3.500A) Processing helix chain '1F' and resid 130 through 142 removed outlier: 4.303A pdb=" N LEU1F 134 " --> pdb=" O LYS1F 130 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET1F 141 " --> pdb=" O LYS1F 137 " (cutoff:3.500A) Processing helix chain '1F' and resid 154 through 163 removed outlier: 3.561A pdb=" N LEU1F 159 " --> pdb=" O GLU1F 155 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA1F 160 " --> pdb=" O ASN1F 156 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASN1F 163 " --> pdb=" O LEU1F 159 " (cutoff:3.500A) Processing helix chain '1F' and resid 176 through 183 removed outlier: 3.637A pdb=" N LEU1F 180 " --> pdb=" O ASP1F 176 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE1F 181 " --> pdb=" O PRO1F 177 " (cutoff:3.500A) Processing helix chain '1F' and resid 189 through 201 removed outlier: 3.542A pdb=" N LYS1F 194 " --> pdb=" O ALA1F 190 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN1F 195 " --> pdb=" O ASP1F 191 " (cutoff:3.500A) Processing helix chain '1G' and resid 1 through 19 removed outlier: 4.304A pdb=" N ASP1G 5 " --> pdb=" O ALA1G 1 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR1G 6 " --> pdb=" O LYS1G 2 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS1G 8 " --> pdb=" O HIS1G 4 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP1G 9 " --> pdb=" O ASP1G 5 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL1G 11 " --> pdb=" O TYR1G 7 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL1G 12 " --> pdb=" O LYS1G 8 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS1G 14 " --> pdb=" O GLU1G 10 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR1G 17 " --> pdb=" O LYS1G 13 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU1G 18 " --> pdb=" O LYS1G 14 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE1G 19 " --> pdb=" O LEU1G 15 " (cutoff:3.500A) Processing helix chain '1G' and resid 41 through 46 removed outlier: 3.639A pdb=" N ASP1G 45 " --> pdb=" O GLU1G 41 " (cutoff:3.500A) Processing helix chain '1G' and resid 47 through 60 removed outlier: 3.557A pdb=" N ASN1G 51 " --> pdb=" O LYS1G 47 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA1G 58 " --> pdb=" O ALA1G 54 " (cutoff:3.500A) Processing helix chain '1G' and resid 92 through 110 removed outlier: 4.390A pdb=" N TRP1G 96 " --> pdb=" O GLY1G 92 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU1G 97 " --> pdb=" O GLU1G 93 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR1G 104 " --> pdb=" O GLU1G 100 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE1G 105 " --> pdb=" O ARG1G 101 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL1G 107 " --> pdb=" O ILE1G 103 " (cutoff:3.500A) Proline residue: 1G 108 - end of helix Processing helix chain '1G' and resid 141 through 146 removed outlier: 6.248A pdb=" N VAL1G 145 " --> pdb=" O ASP1G 141 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP1G 146 " --> pdb=" O TYR1G 142 " (cutoff:3.500A) No H-bonds generated for 'chain '1G' and resid 141 through 146' Processing helix chain '1G' and resid 161 through 173 removed outlier: 4.351A pdb=" N ALA1G 167 " --> pdb=" O GLU1G 163 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU1G 168 " --> pdb=" O GLU1G 164 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU1G 169 " --> pdb=" O GLY1G 165 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA1G 170 " --> pdb=" O ARG1G 166 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA1G 171 " --> pdb=" O ALA1G 167 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE1G 172 " --> pdb=" O LEU1G 168 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP1G 173 " --> pdb=" O LEU1G 169 " (cutoff:3.500A) Processing helix chain '1G' and resid 133 through 138 removed outlier: 3.702A pdb=" N ILE1G 136 " --> pdb=" O GLU1G 133 " (cutoff:3.500A) Proline residue: 1G 138 - end of helix Processing helix chain '1H' and resid 1 through 6 removed outlier: 3.551A pdb=" N LYS1H 5 " --> pdb=" O SER1H 1 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA1H 6 " --> pdb=" O ARG1H 2 " (cutoff:3.500A) No H-bonds generated for 'chain '1H' and resid 1 through 6' Processing helix chain '1H' and resid 59 through 80 removed outlier: 3.834A pdb=" N ALA1H 69 " --> pdb=" O GLY1H 65 " (cutoff:3.500A) Processing helix chain '1H' and resid 136 through 152 removed outlier: 3.517A pdb=" N ALA1H 149 " --> pdb=" O ALA1H 145 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR1H 150 " --> pdb=" O ASP1H 146 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG1H 151 " --> pdb=" O LEU1H 147 " (cutoff:3.500A) Processing helix chain '1L' and resid 64 through 77 removed outlier: 3.820A pdb=" N LYS1L 70 " --> pdb=" O VAL1L 66 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR1L 76 " --> pdb=" O VAL1L 72 " (cutoff:3.500A) Processing helix chain '1L' and resid 79 through 90 removed outlier: 3.637A pdb=" N VAL1L 87 " --> pdb=" O ALA1L 83 " (cutoff:3.500A) Processing helix chain '1L' and resid 99 through 114 removed outlier: 3.838A pdb=" N ALA1L 105 " --> pdb=" O ASP1L 101 " (cutoff:3.500A) Processing helix chain '1I' and resid 22 through 29 removed outlier: 3.580A pdb=" N ALA1I 26 " --> pdb=" O LYS1I 22 " (cutoff:3.500A) Processing helix chain '1I' and resid 40 through 50 removed outlier: 4.388A pdb=" N ILE1I 44 " --> pdb=" O THR1I 40 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE1I 47 " --> pdb=" O ASN1I 43 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA1I 49 " --> pdb=" O GLU1I 45 " (cutoff:3.500A) Processing helix chain '1I' and resid 53 through 73 removed outlier: 5.990A pdb=" N LYS1I 57 " --> pdb=" O GLU1I 53 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU1I 60 " --> pdb=" O ALA1I 56 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU1I 70 " --> pdb=" O ASN1I 66 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS1I 71 " --> pdb=" O ALA1I 67 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASN1I 73 " --> pdb=" O ALA1I 69 " (cutoff:3.500A) Processing helix chain '1I' and resid 95 through 107 removed outlier: 3.587A pdb=" N ILE1I 99 " --> pdb=" O GLY1I 95 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA1I 106 " --> pdb=" O ALA1I 102 " (cutoff:3.500A) Processing helix chain '1I' and resid 111 through 116 removed outlier: 3.990A pdb=" N VAL1I 115 " --> pdb=" O ALA1I 111 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ARG1I 116 " --> pdb=" O LYS1I 112 " (cutoff:3.500A) No H-bonds generated for 'chain '1I' and resid 111 through 116' Processing helix chain '1J' and resid 3 through 21 removed outlier: 3.700A pdb=" N GLN1J 9 " --> pdb=" O LEU1J 5 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU1J 14 " --> pdb=" O ALA1J 10 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS1J 20 " --> pdb=" O SER1J 16 " (cutoff:3.500A) Processing helix chain '1J' and resid 33 through 48 removed outlier: 3.788A pdb=" N THR1J 39 " --> pdb=" O VAL1J 35 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU1J 40 " --> pdb=" O ASP1J 36 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU1J 41 " --> pdb=" O LYS1J 37 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG1J 42 " --> pdb=" O MET1J 38 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA1J 44 " --> pdb=" O GLU1J 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY1J 45 " --> pdb=" O LEU1J 41 " (cutoff:3.500A) Processing helix chain '1J' and resid 62 through 71 removed outlier: 3.992A pdb=" N GLY1J 66 " --> pdb=" O ARG1J 62 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR1J 67 " --> pdb=" O ALA1J 63 " (cutoff:3.500A) Proline residue: 1J 68 - end of helix removed outlier: 3.783A pdb=" N CYS1J 71 " --> pdb=" O THR1J 67 " (cutoff:3.500A) No H-bonds generated for 'chain '1J' and resid 62 through 71' Processing helix chain '1J' and resid 72 through 79 removed outlier: 4.812A pdb=" N PHE1J 76 " --> pdb=" O LEU1J 72 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL1J 77 " --> pdb=" O LYS1J 73 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY1J 78 " --> pdb=" O ASP1J 74 " (cutoff:3.500A) Proline residue: 1J 79 - end of helix No H-bonds generated for 'chain '1J' and resid 72 through 79' Processing helix chain '1J' and resid 94 through 106 removed outlier: 3.792A pdb=" N GLU1J 98 " --> pdb=" O ARG1J 94 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE1J 99 " --> pdb=" O LEU1J 95 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA1J 100 " --> pdb=" O PHE1J 96 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE1J 106 " --> pdb=" O ALA1J 102 " (cutoff:3.500A) Processing helix chain '1J' and resid 109 through 114 removed outlier: 6.527A pdb=" N ALA1J 112 " --> pdb=" O LYS1J 109 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU1J 114 " --> pdb=" O ALA1J 111 " (cutoff:3.500A) Processing helix chain '1K' and resid 23 through 29 removed outlier: 5.080A pdb=" N LEU1K 27 " --> pdb=" O VAL1K 23 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY1K 28 " --> pdb=" O GLY1K 24 " (cutoff:3.500A) Processing helix chain '1K' and resid 33 through 47 removed outlier: 4.338A pdb=" N PHE1K 37 " --> pdb=" O ASN1K 33 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N CYS1K 38 " --> pdb=" O ILE1K 34 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA1K 40 " --> pdb=" O GLU1K 36 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N PHE1K 41 " --> pdb=" O PHE1K 37 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA1K 43 " --> pdb=" O LYS1K 39 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS1K 44 " --> pdb=" O ALA1K 40 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR1K 45 " --> pdb=" O PHE1K 41 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER1K 47 " --> pdb=" O ALA1K 43 " (cutoff:3.500A) Processing helix chain '1K' and resid 74 through 83 removed outlier: 4.744A pdb=" N LYS1K 80 " --> pdb=" O ALA1K 76 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LYS1K 81 " --> pdb=" O VAL1K 77 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA1K 82 " --> pdb=" O LEU1K 78 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ALA1K 83 " --> pdb=" O LEU1K 79 " (cutoff:3.500A) Processing helix chain '1K' and resid 101 through 114 removed outlier: 4.074A pdb=" N GLU1K 107 " --> pdb=" O ALA1K 103 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN1K 110 " --> pdb=" O GLN1K 106 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N THR1K 111 " --> pdb=" O GLU1K 107 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS1K 112 " --> pdb=" O ILE1K 108 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ALA1K 114 " --> pdb=" O GLN1K 110 " (cutoff:3.500A) Processing helix chain '1K' and resid 120 through 136 removed outlier: 3.918A pdb=" N ARG1K 126 " --> pdb=" O GLU1K 122 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER1K 127 " --> pdb=" O ALA1K 123 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE1K 128 " --> pdb=" O MET1K 124 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR1K 131 " --> pdb=" O SER1K 127 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA1K 132 " --> pdb=" O ILE1K 128 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG1K 133 " --> pdb=" O GLU1K 129 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER1K 134 " --> pdb=" O GLY1K 130 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET1K 135 " --> pdb=" O THR1K 131 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY1K 136 " --> pdb=" O ALA1K 132 " (cutoff:3.500A) Processing helix chain '1N' and resid 24 through 38 removed outlier: 3.679A pdb=" N GLU1N 31 " --> pdb=" O ARG1N 27 " (cutoff:3.500A) Processing helix chain '1N' and resid 67 through 72 Processing helix chain '1N' and resid 88 through 96 removed outlier: 3.526A pdb=" N ALA1N 94 " --> pdb=" O GLU1N 90 " (cutoff:3.500A) Processing helix chain '1N' and resid 97 through 110 removed outlier: 4.098A pdb=" N ILE1N 101 " --> pdb=" O PRO1N 97 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N MET1N 108 " --> pdb=" O ALA1N 104 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU1N 109 " --> pdb=" O VAL1N 105 " (cutoff:3.500A) Proline residue: 1N 110 - end of helix Processing helix chain '1N' and resid 112 through 122 removed outlier: 4.224A pdb=" N LYS1N 121 " --> pdb=" O ALA1N 117 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU1N 122 " --> pdb=" O MET1N 118 " (cutoff:3.500A) Processing helix chain '1O' and resid 109 through 120 removed outlier: 5.496A pdb=" N MET1O 113 " --> pdb=" O SER1O 109 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS1O 114 " --> pdb=" O GLU1O 110 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE1O 115 " --> pdb=" O LYS1O 111 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU1O 118 " --> pdb=" O LYS1O 114 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA1O 119 " --> pdb=" O ILE1O 115 " (cutoff:3.500A) Proline residue: 1O 120 - end of helix Processing helix chain '1P' and resid 56 through 62 removed outlier: 3.508A pdb=" N LEU1P 61 " --> pdb=" O LEU1P 57 " (cutoff:3.500A) Proline residue: 1P 62 - end of helix Processing helix chain '1P' and resid 68 through 75 removed outlier: 3.581A pdb=" N ALA1P 72 " --> pdb=" O SER1P 68 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE1P 73 " --> pdb=" O ARG1P 69 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR1P 74 " --> pdb=" O LYS1P 70 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA1P 75 " --> pdb=" O ALA1P 71 " (cutoff:3.500A) No H-bonds generated for 'chain '1P' and resid 68 through 75' Processing helix chain '1P' and resid 78 through 83 removed outlier: 3.703A pdb=" N LEU1P 82 " --> pdb=" O ARG1P 78 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA1P 83 " --> pdb=" O LEU1P 79 " (cutoff:3.500A) No H-bonds generated for 'chain '1P' and resid 78 through 83' Processing helix chain '1P' and resid 91 through 99 removed outlier: 4.411A pdb=" N LEU1P 95 " --> pdb=" O ASP1P 91 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS1P 96 " --> pdb=" O LEU1P 92 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA1P 97 " --> pdb=" O ASN1P 93 " (cutoff:3.500A) Processing helix chain '1P' and resid 128 through 139 removed outlier: 4.928A pdb=" N ARG1P 132 " --> pdb=" O THR1P 128 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA1P 133 " --> pdb=" O LYS1P 129 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA1P 137 " --> pdb=" O ALA1P 133 " (cutoff:3.500A) Processing helix chain '1Q' and resid 42 through 58 removed outlier: 4.159A pdb=" N ALA1Q 56 " --> pdb=" O ALA1Q 52 " (cutoff:3.500A) Processing helix chain '1Q' and resid 109 through 125 removed outlier: 4.292A pdb=" N LYS1Q 123 " --> pdb=" O LEU1Q 119 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU1Q 124 " --> pdb=" O ALA1Q 120 " (cutoff:3.500A) Proline residue: 1Q 125 - end of helix Processing helix chain '1R' and resid 13 through 31 removed outlier: 3.917A pdb=" N GLY1R 26 " --> pdb=" O ARG1R 22 " (cutoff:3.500A) Processing helix chain '1R' and resid 39 through 57 removed outlier: 3.624A pdb=" N ARG1R 45 " --> pdb=" O ALA1R 41 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG1R 46 " --> pdb=" O LYS1R 42 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL1R 47 " --> pdb=" O GLU1R 43 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU1R 49 " --> pdb=" O ARG1R 45 " (cutoff:3.500A) Proline residue: 1R 50 - end of helix removed outlier: 4.841A pdb=" N THR1R 57 " --> pdb=" O THR1R 53 " (cutoff:3.500A) Processing helix chain '1R' and resid 59 through 71 removed outlier: 4.901A pdb=" N ARG1R 63 " --> pdb=" O SER1R 59 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG1R 69 " --> pdb=" O LEU1R 65 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR1R 70 " --> pdb=" O ALA1R 66 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG1R 71 " --> pdb=" O PHE1R 67 " (cutoff:3.500A) Processing helix chain '1R' and resid 72 through 87 removed outlier: 3.603A pdb=" N LYS1R 78 " --> pdb=" O GLU1R 74 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE1R 80 " --> pdb=" O VAL1R 76 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN1R 81 " --> pdb=" O ALA1R 77 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU1R 83 " --> pdb=" O LEU1R 79 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY1R 84 " --> pdb=" O PHE1R 80 " (cutoff:3.500A) Proline residue: 1R 85 - end of helix Processing helix chain '1S' and resid 2 through 22 removed outlier: 3.990A pdb=" N ARG1S 7 " --> pdb=" O LYS1S 3 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE1S 8 " --> pdb=" O LYS1S 4 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG1S 13 " --> pdb=" O ARG1S 9 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ALA1S 14 " --> pdb=" O ARG1S 10 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN1S 19 " --> pdb=" O ARG1S 15 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU1S 21 " --> pdb=" O LYS1S 17 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY1S 22 " --> pdb=" O LEU1S 18 " (cutoff:3.500A) Processing helix chain '1S' and resid 55 through 63 removed outlier: 5.004A pdb=" N GLN1S 61 " --> pdb=" O ALA1S 57 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS1S 63 " --> pdb=" O ALA1S 59 " (cutoff:3.500A) Processing helix chain '1S' and resid 67 through 86 Processing helix chain '1S' and resid 101 through 114 removed outlier: 3.519A pdb=" N ARG1S 111 " --> pdb=" O ALA1S 107 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY1S 114 " --> pdb=" O ALA1S 110 " (cutoff:3.500A) Processing helix chain '1T' and resid 1 through 12 removed outlier: 3.532A pdb=" N LEU1T 7 " --> pdb=" O ILE1T 3 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN1T 11 " --> pdb=" O LEU1T 7 " (cutoff:3.500A) Processing helix chain '1T' and resid 96 through 103 removed outlier: 4.318A pdb=" N ARG1T 100 " --> pdb=" O LEU1T 96 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU1T 101 " --> pdb=" O TYR1T 97 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG1T 102 " --> pdb=" O TYR1T 98 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N THR1T 103 " --> pdb=" O LEU1T 99 " (cutoff:3.500A) No H-bonds generated for 'chain '1T' and resid 96 through 103' Processing helix chain '1U' and resid 5 through 21 removed outlier: 3.656A pdb=" N ALA1U 9 " --> pdb=" O ARG1U 5 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG1U 10 " --> pdb=" O GLY1U 6 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA1U 11 " --> pdb=" O VAL1U 7 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG1U 12 " --> pdb=" O ILE1U 8 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN1U 19 " --> pdb=" O LYS1U 15 " (cutoff:3.500A) Processing helix chain '1U' and resid 25 through 30 removed outlier: 4.211A pdb=" N ARG1U 29 " --> pdb=" O GLY1U 25 " (cutoff:3.500A) Processing helix chain '1U' and resid 38 through 60 removed outlier: 3.824A pdb=" N ARG1U 49 " --> pdb=" O ALA1U 45 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG1U 50 " --> pdb=" O TYR1U 46 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS1U 53 " --> pdb=" O ARG1U 49 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG1U 54 " --> pdb=" O ARG1U 50 " (cutoff:3.500A) Processing helix chain '1U' and resid 62 through 71 Processing helix chain '1U' and resid 74 through 86 Processing helix chain '1U' and resid 90 through 101 removed outlier: 3.752A pdb=" N ASP1U 96 " --> pdb=" O LYS1U 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA1U 98 " --> pdb=" O LEU1U 94 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE1U 100 " --> pdb=" O ASP1U 96 " (cutoff:3.500A) Processing helix chain '1U' and resid 102 through 117 removed outlier: 3.506A pdb=" N GLU1U 110 " --> pdb=" O THR1U 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS1U 111 " --> pdb=" O ALA1U 107 " (cutoff:3.500A) Processing helix chain '1W' and resid 13 through 25 removed outlier: 3.514A pdb=" N ARG1W 18 " --> pdb=" O ALA1W 14 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU1W 19 " --> pdb=" O GLN1W 15 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL1W 20 " --> pdb=" O LYS1W 16 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU1W 23 " --> pdb=" O LEU1W 19 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE1W 24 " --> pdb=" O VAL1W 20 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG1W 25 " --> pdb=" O ALA1W 21 " (cutoff:3.500A) Processing helix chain '1W' and resid 28 through 39 removed outlier: 3.610A pdb=" N ASP1W 34 " --> pdb=" O SER1W 30 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR1W 38 " --> pdb=" O ASP1W 34 " (cutoff:3.500A) Processing helix chain '1W' and resid 41 through 61 removed outlier: 3.596A pdb=" N VAL1W 50 " --> pdb=" O LEU1W 46 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA1W 58 " --> pdb=" O ALA1W 54 " (cutoff:3.500A) Processing helix chain '1X' and resid 1 through 11 removed outlier: 4.552A pdb=" N GLU1X 5 " --> pdb=" O MET1X 1 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU1X 7 " --> pdb=" O ARG1X 3 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU1X 8 " --> pdb=" O GLU1X 4 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS1X 9 " --> pdb=" O GLU1X 5 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU1X 11 " --> pdb=" O LEU1X 7 " (cutoff:3.500A) Processing helix chain '1X' and resid 17 through 26 Processing helix chain '1X' and resid 39 through 50 removed outlier: 3.522A pdb=" N ALA1X 45 " --> pdb=" O ALA1X 41 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA1X 46 " --> pdb=" O GLU1X 42 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL1X 47 " --> pdb=" O ILE1X 43 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS1X 49 " --> pdb=" O ALA1X 45 " (cutoff:3.500A) Processing helix chain '1Y' and resid 65 through 70 removed outlier: 3.858A pdb=" N VAL1Y 69 " --> pdb=" O GLN1Y 65 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA1Y 70 " --> pdb=" O VAL1Y 66 " (cutoff:3.500A) No H-bonds generated for 'chain '1Y' and resid 65 through 70' Processing helix chain '1Z' and resid 13 through 24 removed outlier: 3.582A pdb=" N ARG1Z 19 " --> pdb=" O GLY1Z 15 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA1Z 23 " --> pdb=" O ARG1Z 19 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASN1Z 24 " --> pdb=" O LEU1Z 20 " (cutoff:3.500A) Processing helix chain '1Z' and resid 43 through 53 removed outlier: 4.083A pdb=" N VAL1Z 47 " --> pdb=" O ASP1Z 43 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN1Z 49 " --> pdb=" O ASP1Z 45 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET1Z 50 " --> pdb=" O LYS1Z 46 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA1Z 52 " --> pdb=" O MET1Z 48 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS1Z 53 " --> pdb=" O ASN1Z 49 " (cutoff:3.500A) Processing helix chain '1Z' and resid 54 through 59 removed outlier: 3.884A pdb=" N SER1Z 58 " --> pdb=" O ALA1Z 54 " (cutoff:3.500A) Processing helix chain '11' and resid 51 through 61 removed outlier: 3.616A pdb=" N VAL11 57 " --> pdb=" O LYS11 53 " (cutoff:3.500A) Processing helix chain '11' and resid 62 through 74 Processing helix chain '12' and resid 1 through 7 removed outlier: 3.770A pdb=" N LEU12 6 " --> pdb=" O LYS12 2 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG12 7 " --> pdb=" O ALA12 3 " (cutoff:3.500A) Processing helix chain '12' and resid 9 through 23 Processing helix chain '12' and resid 25 through 35 removed outlier: 3.826A pdb=" N ARG12 29 " --> pdb=" O GLN12 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA12 33 " --> pdb=" O ARG12 29 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER12 34 " --> pdb=" O MET12 30 " (cutoff:3.500A) Processing helix chain '12' and resid 39 through 63 removed outlier: 4.612A pdb=" N LEU12 43 " --> pdb=" O GLN12 39 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS12 44 " --> pdb=" O SER12 40 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG12 47 " --> pdb=" O LEU12 43 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS12 60 " --> pdb=" O LEU12 56 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY12 62 " --> pdb=" O ASN12 58 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ALA12 63 " --> pdb=" O GLU12 59 " (cutoff:3.500A) Processing helix chain '13' and resid 16 through 27 Processing helix chain '13' and resid 40 through 51 removed outlier: 3.690A pdb=" N VAL13 50 " --> pdb=" O MET13 46 " (cutoff:3.500A) Processing helix chain '14' and resid 43 through 54 removed outlier: 4.352A pdb=" N GLN14 48 " --> pdb=" O PHE14 44 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA14 52 " --> pdb=" O GLN14 48 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR14 53 " --> pdb=" O ARG14 49 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLY14 54 " --> pdb=" O ASP14 50 " (cutoff:3.500A) Processing helix chain '14' and resid 55 through 65 removed outlier: 4.856A pdb=" N ARG14 59 " --> pdb=" O GLY14 55 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG14 63 " --> pdb=" O ARG14 59 " (cutoff:3.500A) Processing helix chain '15' and resid 8 through 20 removed outlier: 3.698A pdb=" N ARG15 16 " --> pdb=" O ARG15 12 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER15 17 " --> pdb=" O GLY15 13 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N HIS15 18 " --> pdb=" O MET15 14 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP15 19 " --> pdb=" O ARG15 15 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA15 20 " --> pdb=" O ARG15 16 " (cutoff:3.500A) Processing helix chain '16' and resid 25 through 30 Proline residue: 16 30 - end of helix Processing helix chain '17' and resid 8 through 16 removed outlier: 3.642A pdb=" N SER17 15 " --> pdb=" O LYS17 11 " (cutoff:3.500A) Processing helix chain '17' and resid 17 through 25 removed outlier: 3.749A pdb=" N ARG17 21 " --> pdb=" O GLY17 17 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR17 24 " --> pdb=" O ALA17 20 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LYS17 25 " --> pdb=" O ARG17 21 " (cutoff:3.500A) Processing helix chain '17' and resid 26 through 38 removed outlier: 3.706A pdb=" N VAL17 30 " --> pdb=" O ASN17 26 " (cutoff:3.500A) Processing helix chain '18' and resid 6 through 13 removed outlier: 3.521A pdb=" N ALA18 10 " --> pdb=" O VAL18 6 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS18 11 " --> pdb=" O ARG18 7 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG18 12 " --> pdb=" O GLY18 8 " (cutoff:3.500A) Processing helix chain '18' and resid 31 through 36 removed outlier: 4.758A pdb=" N LYS18 35 " --> pdb=" O ILE18 31 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ALA18 36 " --> pdb=" O LEU18 32 " (cutoff:3.500A) No H-bonds generated for 'chain '18' and resid 31 through 36' Processing helix chain '18' and resid 37 through 45 removed outlier: 4.195A pdb=" N HIS18 42 " --> pdb=" O LYS18 38 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG18 44 " --> pdb=" O LYS18 40 " (cutoff:3.500A) Proline residue: 18 45 - end of helix Processing helix chain '18' and resid 50 through 62 removed outlier: 4.279A pdb=" N GLY18 55 " --> pdb=" O LYS18 51 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N LEU18 56 " --> pdb=" O GLY18 52 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL18 57 " --> pdb=" O ASP18 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE18 58 " --> pdb=" O LEU18 54 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA18 59 " --> pdb=" O GLY18 55 " (cutoff:3.500A) Proline residue: 18 62 - end of helix Processing helix chain '18' and resid 25 through 30 removed outlier: 4.391A pdb=" N LEU18 28 " --> pdb=" O HIS18 25 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ARG18 29 " --> pdb=" O ALA18 26 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS18 30 " --> pdb=" O ASN18 27 " (cutoff:3.500A) No H-bonds generated for 'chain '18' and resid 25 through 30' Processing helix chain '19' and resid 30 through 35 removed outlier: 4.037A pdb=" N LYS19 34 " --> pdb=" O GLU19 30 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLN19 35 " --> pdb=" O PRO19 31 " (cutoff:3.500A) No H-bonds generated for 'chain '19' and resid 30 through 35' Processing helix chain '1b' and resid 43 through 63 Proline residue: 1b 47 - end of helix removed outlier: 3.526A pdb=" N ASN1b 50 " --> pdb=" O VAL1b 46 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER1b 61 " --> pdb=" O ASN1b 57 " (cutoff:3.500A) Processing helix chain '1b' and resid 73 through 87 removed outlier: 3.889A pdb=" N GLU1b 77 " --> pdb=" O ARG1b 73 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA1b 78 " --> pdb=" O ALA1b 74 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL1b 79 " --> pdb=" O ALA1b 75 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER1b 85 " --> pdb=" O ASP1b 81 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS1b 86 " --> pdb=" O ALA1b 82 " (cutoff:3.500A) Processing helix chain '1b' and resid 102 through 123 removed outlier: 4.078A pdb=" N GLN1b 108 " --> pdb=" O LYS1b 104 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN1b 119 " --> pdb=" O ASP1b 115 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN1b 121 " --> pdb=" O GLU1b 117 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP1b 122 " --> pdb=" O THR1b 118 " (cutoff:3.500A) Processing helix chain '1b' and resid 129 through 147 removed outlier: 3.501A pdb=" N ASN1b 145 " --> pdb=" O GLU1b 141 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER1b 146 " --> pdb=" O LYS1b 142 " (cutoff:3.500A) Processing helix chain '1b' and resid 164 through 169 removed outlier: 3.947A pdb=" N GLU1b 168 " --> pdb=" O ASP1b 164 " (cutoff:3.500A) Processing helix chain '1b' and resid 170 through 179 removed outlier: 3.645A pdb=" N ALA1b 175 " --> pdb=" O ALA1b 171 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN1b 177 " --> pdb=" O LYS1b 173 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU1b 178 " --> pdb=" O GLU1b 174 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLY1b 179 " --> pdb=" O ALA1b 175 " (cutoff:3.500A) Processing helix chain '1b' and resid 205 through 225 removed outlier: 3.636A pdb=" N VAL1b 209 " --> pdb=" O ALA1b 205 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU1b 211 " --> pdb=" O ARG1b 207 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA1b 218 " --> pdb=" O GLY1b 214 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY1b 223 " --> pdb=" O THR1b 219 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG1b 224 " --> pdb=" O VAL1b 220 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER1b 225 " --> pdb=" O ARG1b 221 " (cutoff:3.500A) Processing helix chain '1c' and resid 5 through 12 removed outlier: 3.588A pdb=" N ILE1c 9 " --> pdb=" O HIS1c 5 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG1c 10 " --> pdb=" O PRO1c 6 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU1c 11 " --> pdb=" O ASN1c 7 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLY1c 12 " --> pdb=" O GLY1c 8 " (cutoff:3.500A) No H-bonds generated for 'chain '1c' and resid 5 through 12' Processing helix chain '1c' and resid 26 through 47 removed outlier: 4.620A pdb=" N ASP1c 30 " --> pdb=" O LYS1c 26 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP1c 33 " --> pdb=" O ALA1c 29 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG1c 39 " --> pdb=" O ASP1c 35 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN1c 40 " --> pdb=" O PHE1c 36 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR1c 41 " --> pdb=" O LYS1c 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU1c 42 " --> pdb=" O VAL1c 38 " (cutoff:3.500A) Processing helix chain '1c' and resid 71 through 77 removed outlier: 3.664A pdb=" N VAL1c 75 " --> pdb=" O ARG1c 71 " (cutoff:3.500A) Processing helix chain '1c' and resid 80 through 94 removed outlier: 4.153A pdb=" N GLU1c 84 " --> pdb=" O GLY1c 80 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS1c 85 " --> pdb=" O GLU1c 81 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS1c 88 " --> pdb=" O GLU1c 84 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL1c 90 " --> pdb=" O LEU1c 86 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA1c 91 " --> pdb=" O ARG1c 87 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE1c 93 " --> pdb=" O VAL1c 89 " (cutoff:3.500A) Processing helix chain '1c' and resid 107 through 112 removed outlier: 4.241A pdb=" N ASP1c 111 " --> pdb=" O LYS1c 107 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ALA1c 112 " --> pdb=" O PRO1c 108 " (cutoff:3.500A) No H-bonds generated for 'chain '1c' and resid 107 through 112' Processing helix chain '1c' and resid 113 through 126 removed outlier: 3.598A pdb=" N LEU1c 123 " --> pdb=" O ILE1c 119 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU1c 124 " --> pdb=" O THR1c 120 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG1c 125 " --> pdb=" O SER1c 121 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG1c 126 " --> pdb=" O GLN1c 122 " (cutoff:3.500A) Processing helix chain '1c' and resid 128 through 144 removed outlier: 3.668A pdb=" N ARG1c 135 " --> pdb=" O ARG1c 131 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA1c 136 " --> pdb=" O ALA1c 132 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL1c 137 " --> pdb=" O MET1c 133 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA1c 140 " --> pdb=" O ALA1c 136 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU1c 143 " --> pdb=" O ASN1c 139 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY1c 144 " --> pdb=" O ALA1c 140 " (cutoff:3.500A) Processing helix chain '1d' and resid 6 through 15 removed outlier: 3.523A pdb=" N LEU1d 10 " --> pdb=" O PRO1d 6 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER1d 11 " --> pdb=" O LYS1d 7 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG1d 12 " --> pdb=" O LEU1d 8 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG1d 13 " --> pdb=" O LYS1d 9 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU1d 14 " --> pdb=" O LEU1d 10 " (cutoff:3.500A) Processing helix chain '1d' and resid 48 through 65 removed outlier: 3.968A pdb=" N GLN1d 53 " --> pdb=" O ASP1d 49 " (cutoff:3.500A) Processing helix chain '1d' and resid 67 through 82 removed outlier: 3.513A pdb=" N ASN1d 73 " --> pdb=" O ARG1d 69 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG1d 80 " --> pdb=" O LYS1d 76 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU1d 81 " --> pdb=" O GLU1d 77 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS1d 82 " --> pdb=" O ALA1d 78 " (cutoff:3.500A) Processing helix chain '1d' and resid 84 through 96 removed outlier: 3.580A pdb=" N ASN1d 88 " --> pdb=" O ASN1d 84 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU1d 90 " --> pdb=" O GLY1d 86 " (cutoff:3.500A) Processing helix chain '1d' and resid 97 through 105 removed outlier: 3.708A pdb=" N GLY1d 105 " --> pdb=" O VAL1d 101 " (cutoff:3.500A) Processing helix chain '1d' and resid 109 through 120 removed outlier: 4.508A pdb=" N LYS1d 120 " --> pdb=" O LEU1d 116 " (cutoff:3.500A) Processing helix chain '1d' and resid 151 through 165 removed outlier: 5.317A pdb=" N LYS1d 155 " --> pdb=" O GLN1d 151 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA1d 156 " --> pdb=" O SER1d 152 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU1d 158 " --> pdb=" O VAL1d 154 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU1d 159 " --> pdb=" O LYS1d 155 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU1d 160 " --> pdb=" O ALA1d 156 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA1d 161 " --> pdb=" O ALA1d 157 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU1d 162 " --> pdb=" O LEU1d 158 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN1d 163 " --> pdb=" O GLU1d 159 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLU1d 165 " --> pdb=" O ALA1d 161 " (cutoff:3.500A) Processing helix chain '1d' and resid 186 through 191 removed outlier: 5.143A pdb=" N SER1d 191 " --> pdb=" O ARG1d 187 " (cutoff:3.500A) Processing helix chain '1d' and resid 195 through 205 removed outlier: 4.091A pdb=" N ILE1d 199 " --> pdb=" O ASN1d 195 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL1d 200 " --> pdb=" O GLU1d 196 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU1d 201 " --> pdb=" O HIS1d 197 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS1d 205 " --> pdb=" O GLU1d 201 " (cutoff:3.500A) Processing helix chain '1e' and resid 54 through 70 removed outlier: 3.586A pdb=" N MET1e 63 " --> pdb=" O ILE1e 59 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU1e 64 " --> pdb=" O GLN1e 60 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG1e 67 " --> pdb=" O MET1e 63 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG1e 68 " --> pdb=" O GLU1e 64 " (cutoff:3.500A) Processing helix chain '1e' and resid 108 through 118 removed outlier: 6.032A pdb=" N ALA1e 112 " --> pdb=" O GLY1e 108 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL1e 113 " --> pdb=" O ALA1e 109 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU1e 114 " --> pdb=" O MET1e 110 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA1e 117 " --> pdb=" O VAL1e 113 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY1e 118 " --> pdb=" O LEU1e 114 " (cutoff:3.500A) Processing helix chain '1e' and resid 131 through 147 removed outlier: 3.916A pdb=" N ARG1e 137 " --> pdb=" O ILE1e 133 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN1e 147 " --> pdb=" O LEU1e 143 " (cutoff:3.500A) Processing helix chain '1e' and resid 148 through 156 removed outlier: 3.997A pdb=" N ALA1e 154 " --> pdb=" O GLU1e 150 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS1e 155 " --> pdb=" O MET1e 151 " (cutoff:3.500A) Processing helix chain '1e' and resid 159 through 165 removed outlier: 3.512A pdb=" N LEU1e 164 " --> pdb=" O VAL1e 160 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY1e 165 " --> pdb=" O GLU1e 161 " (cutoff:3.500A) Processing helix chain '1f' and resid 11 through 19 removed outlier: 4.445A pdb=" N GLU1f 16 " --> pdb=" O PRO1f 12 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLN1f 17 " --> pdb=" O ASP1f 13 " (cutoff:3.500A) Proline residue: 1f 19 - end of helix Processing helix chain '1f' and resid 20 through 33 removed outlier: 3.760A pdb=" N ARG1f 24 " --> pdb=" O GLY1f 20 " (cutoff:3.500A) Processing helix chain '1f' and resid 67 through 81 removed outlier: 3.800A pdb=" N GLU1f 73 " --> pdb=" O GLU1f 69 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N PHE1f 78 " --> pdb=" O LEU1f 74 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG1f 79 " --> pdb=" O GLU1f 75 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN1f 81 " --> pdb=" O THR1f 77 " (cutoff:3.500A) Processing helix chain '1g' and resid 19 through 30 removed outlier: 4.197A pdb=" N PHE1g 25 " --> pdb=" O LEU1g 21 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL1g 26 " --> pdb=" O LEU1g 22 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN1g 27 " --> pdb=" O ALA1g 23 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE1g 28 " --> pdb=" O LYS1g 24 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU1g 29 " --> pdb=" O PHE1g 25 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET1g 30 " --> pdb=" O VAL1g 26 " (cutoff:3.500A) Processing helix chain '1g' and resid 34 through 54 removed outlier: 4.052A pdb=" N LEU1g 46 " --> pdb=" O VAL1g 42 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU1g 47 " --> pdb=" O TYR1g 43 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR1g 48 " --> pdb=" O SER1g 44 " (cutoff:3.500A) Processing helix chain '1g' and resid 57 through 69 removed outlier: 4.168A pdb=" N ALA1g 64 " --> pdb=" O ALA1g 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU1g 66 " --> pdb=" O GLU1g 62 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN1g 67 " --> pdb=" O VAL1g 63 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL1g 68 " --> pdb=" O ALA1g 64 " (cutoff:3.500A) Processing helix chain '1g' and resid 92 through 111 removed outlier: 3.757A pdb=" N ASN1g 96 " --> pdb=" O PRO1g 92 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA1g 97 " --> pdb=" O VAL1g 93 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA1g 99 " --> pdb=" O ARG1g 95 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG1g 101 " --> pdb=" O ALA1g 97 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS1g 109 " --> pdb=" O GLU1g 105 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG1g 110 " --> pdb=" O ALA1g 106 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLY1g 111 " --> pdb=" O ALA1g 107 " (cutoff:3.500A) Processing helix chain '1g' and resid 114 through 129 removed outlier: 4.147A pdb=" N GLU1g 128 " --> pdb=" O SER1g 124 " (cutoff:3.500A) Processing helix chain '1g' and resid 131 through 146 removed outlier: 3.505A pdb=" N LYS1g 135 " --> pdb=" O GLY1g 131 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU1g 145 " --> pdb=" O HIS1g 141 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA1g 146 " --> pdb=" O ARG1g 142 " (cutoff:3.500A) Processing helix chain '1h' and resid 4 through 20 removed outlier: 3.617A pdb=" N ILE1h 13 " --> pdb=" O MET1h 9 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY1h 16 " --> pdb=" O ARG1h 12 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA1h 18 " --> pdb=" O ARG1h 14 " (cutoff:3.500A) Processing helix chain '1h' and resid 29 through 43 Processing helix chain '1h' and resid 111 through 119 removed outlier: 3.611A pdb=" N ARG1h 116 " --> pdb=" O ASP1h 112 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN1h 117 " --> pdb=" O ARG1h 113 " (cutoff:3.500A) Processing helix chain '1i' and resid 33 through 38 removed outlier: 3.611A pdb=" N PHE1i 38 " --> pdb=" O LEU1i 34 " (cutoff:3.500A) Processing helix chain '1i' and resid 45 through 55 Proline residue: 1i 50 - end of helix removed outlier: 4.898A pdb=" N LEU1i 53 " --> pdb=" O GLN1i 49 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL1i 54 " --> pdb=" O PRO1i 50 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP1i 55 " --> pdb=" O LEU1i 51 " (cutoff:3.500A) Processing helix chain '1i' and resid 70 through 86 removed outlier: 3.720A pdb=" N GLN1i 74 " --> pdb=" O GLY1i 70 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA1i 75 " --> pdb=" O ILE1i 71 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR1i 83 " --> pdb=" O ARG1i 79 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG1i 84 " --> pdb=" O HIS1i 80 " (cutoff:3.500A) Processing helix chain '1i' and resid 91 through 101 removed outlier: 5.070A pdb=" N GLU1i 96 " --> pdb=" O SER1i 92 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS1i 99 " --> pdb=" O SER1i 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA1i 100 " --> pdb=" O GLU1i 96 " (cutoff:3.500A) Processing helix chain '1j' and resid 14 through 33 removed outlier: 3.786A pdb=" N ILE1j 18 " --> pdb=" O ASP1j 14 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP1j 19 " --> pdb=" O HIS1j 15 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN1j 20 " --> pdb=" O ARG1j 16 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA1j 21 " --> pdb=" O LEU1j 17 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE1j 25 " --> pdb=" O ALA1j 21 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA1j 29 " --> pdb=" O ILE1j 25 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG1j 31 " --> pdb=" O GLU1j 27 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THR1j 32 " --> pdb=" O THR1j 28 " (cutoff:3.500A) Processing helix chain '1j' and resid 80 through 90 removed outlier: 3.925A pdb=" N ASP1j 85 " --> pdb=" O GLU1j 81 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA1j 86 " --> pdb=" O LYS1j 82 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N MET1j 88 " --> pdb=" O VAL1j 84 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ARG1j 89 " --> pdb=" O ASP1j 85 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU1j 90 " --> pdb=" O ALA1j 86 " (cutoff:3.500A) Processing helix chain '1k' and resid 45 through 50 removed outlier: 4.824A pdb=" N GLY1k 50 " --> pdb=" O ALA1k 46 " (cutoff:3.500A) Processing helix chain '1k' and resid 53 through 58 removed outlier: 4.121A pdb=" N SER1k 57 " --> pdb=" O GLY1k 53 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR1k 58 " --> pdb=" O SER1k 54 " (cutoff:3.500A) No H-bonds generated for 'chain '1k' and resid 53 through 58' Processing helix chain '1k' and resid 59 through 73 removed outlier: 4.804A pdb=" N ALA1k 72 " --> pdb=" O ARG1k 68 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VAL1k 73 " --> pdb=" O CYS1k 69 " (cutoff:3.500A) Processing helix chain '1k' and resid 92 through 103 removed outlier: 3.747A pdb=" N ILE1k 96 " --> pdb=" O ARG1k 92 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ARG1k 97 " --> pdb=" O GLU1k 93 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA1k 98 " --> pdb=" O SER1k 94 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU1k 99 " --> pdb=" O THR1k 95 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN1k 100 " --> pdb=" O ILE1k 96 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY1k 103 " --> pdb=" O LEU1k 99 " (cutoff:3.500A) Processing helix chain '1l' and resid 2 through 10 removed outlier: 3.897A pdb=" N LEU1l 6 " --> pdb=" O THR1l 2 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL1l 7 " --> pdb=" O VAL1l 3 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG1l 8 " --> pdb=" O ASN1l 4 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS1l 9 " --> pdb=" O GLN1l 5 " (cutoff:3.500A) Proline residue: 1l 10 - end of helix No H-bonds generated for 'chain '1l' and resid 2 through 10' Processing helix chain '1l' and resid 112 through 117 removed outlier: 5.268A pdb=" N TYR1l 116 " --> pdb=" O ALA1l 112 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY1l 117 " --> pdb=" O ARG1l 113 " (cutoff:3.500A) No H-bonds generated for 'chain '1l' and resid 112 through 117' Processing helix chain '1m' and resid 13 through 22 removed outlier: 3.658A pdb=" N LEU1m 18 " --> pdb=" O ALA1m 14 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR1m 19 " --> pdb=" O VAL1m 15 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER1m 20 " --> pdb=" O ILE1m 16 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE1m 21 " --> pdb=" O ALA1m 17 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TYR1m 22 " --> pdb=" O LEU1m 18 " (cutoff:3.500A) Processing helix chain '1m' and resid 25 through 37 Processing helix chain '1m' and resid 43 through 48 removed outlier: 5.024A pdb=" N SER1m 48 " --> pdb=" O ILE1m 44 " (cutoff:3.500A) Processing helix chain '1m' and resid 49 through 63 removed outlier: 4.141A pdb=" N ASP1m 53 " --> pdb=" O GLU1m 49 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N THR1m 54 " --> pdb=" O GLY1m 50 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU1m 55 " --> pdb=" O GLN1m 51 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP1m 57 " --> pdb=" O ASP1m 53 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU1m 58 " --> pdb=" O THR1m 54 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS1m 61 " --> pdb=" O ASP1m 57 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE1m 62 " --> pdb=" O GLU1m 58 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL1m 63 " --> pdb=" O VAL1m 59 " (cutoff:3.500A) Processing helix chain '1m' and resid 65 through 83 removed outlier: 3.548A pdb=" N ARG1m 69 " --> pdb=" O GLU1m 65 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG1m 78 " --> pdb=" O MET1m 74 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP1m 81 " --> pdb=" O LYS1m 77 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY1m 83 " --> pdb=" O LEU1m 79 " (cutoff:3.500A) Processing helix chain '1m' and resid 84 through 93 removed outlier: 4.176A pdb=" N HIS1m 90 " --> pdb=" O ARG1m 86 " (cutoff:3.500A) Processing helix chain '1m' and resid 105 through 110 Processing helix chain '1n' and resid 3 through 21 removed outlier: 3.696A pdb=" N ARG1n 13 " --> pdb=" O ARG1n 9 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL1n 14 " --> pdb=" O GLU1n 10 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP1n 18 " --> pdb=" O VAL1n 14 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS1n 19 " --> pdb=" O ALA1n 15 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR1n 20 " --> pdb=" O LEU1n 16 " (cutoff:3.500A) Processing helix chain '1n' and resid 25 through 30 Processing helix chain '1n' and resid 38 through 51 removed outlier: 3.608A pdb=" N TRP1n 42 " --> pdb=" O ASP1n 38 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN1n 43 " --> pdb=" O GLU1n 39 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLN1n 49 " --> pdb=" O VAL1n 45 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR1n 50 " --> pdb=" O LEU1n 46 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU1n 51 " --> pdb=" O LYS1n 47 " (cutoff:3.500A) Processing helix chain '1n' and resid 56 through 61 removed outlier: 3.870A pdb=" N GLN1n 60 " --> pdb=" O SER1n 56 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ARG1n 61 " --> pdb=" O PRO1n 57 " (cutoff:3.500A) No H-bonds generated for 'chain '1n' and resid 56 through 61' Processing helix chain '1n' and resid 80 through 91 removed outlier: 3.646A pdb=" N ARG1n 90 " --> pdb=" O GLU1n 86 " (cutoff:3.500A) Processing helix chain '1o' and resid 3 through 15 removed outlier: 3.531A pdb=" N ILE1o 10 " --> pdb=" O ALA1o 6 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU1o 13 " --> pdb=" O LYS1o 9 " (cutoff:3.500A) Processing helix chain '1o' and resid 23 through 43 removed outlier: 3.816A pdb=" N ALA1o 29 " --> pdb=" O GLU1o 25 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU1o 31 " --> pdb=" O GLN1o 27 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY1o 40 " --> pdb=" O ASN1o 36 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N HIS1o 41 " --> pdb=" O HIS1o 37 " (cutoff:3.500A) Processing helix chain '1o' and resid 48 through 73 removed outlier: 3.629A pdb=" N ARG1o 52 " --> pdb=" O ASP1o 48 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY1o 54 " --> pdb=" O HIS1o 50 " (cutoff:3.500A) Processing helix chain '1o' and resid 74 through 85 removed outlier: 3.867A pdb=" N GLN1o 79 " --> pdb=" O ALA1o 75 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG1o 83 " --> pdb=" O GLN1o 79 " (cutoff:3.500A) Processing helix chain '1p' and resid 53 through 64 removed outlier: 3.629A pdb=" N ILE1p 57 " --> pdb=" O ASP1p 53 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS1p 59 " --> pdb=" O ASP1p 55 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY1p 62 " --> pdb=" O ALA1p 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY1p 64 " --> pdb=" O TRP1p 60 " (cutoff:3.500A) Processing helix chain '1p' and resid 68 through 79 removed outlier: 3.543A pdb=" N ASN1p 79 " --> pdb=" O ILE1p 75 " (cutoff:3.500A) Processing helix chain '1r' and resid 11 through 16 removed outlier: 5.990A pdb=" N GLU1r 15 " --> pdb=" O ARG1r 11 " (cutoff:3.500A) Processing helix chain '1r' and resid 24 through 33 removed outlier: 3.924A pdb=" N ASN1r 30 " --> pdb=" O ALA1r 26 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR1r 31 " --> pdb=" O THR1r 27 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE1r 32 " --> pdb=" O LEU1r 28 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N THR1r 33 " --> pdb=" O LYS1r 29 " (cutoff:3.500A) Processing helix chain '1r' and resid 40 through 45 removed outlier: 3.710A pdb=" N THR1r 44 " --> pdb=" O PRO1r 40 " (cutoff:3.500A) Processing helix chain '1r' and resid 47 through 65 removed outlier: 4.140A pdb=" N GLN1r 53 " --> pdb=" O LYS1r 49 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA1r 61 " --> pdb=" O ALA1r 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU1r 64 " --> pdb=" O ARG1r 60 " (cutoff:3.500A) Processing helix chain '1s' and resid 11 through 25 removed outlier: 3.799A pdb=" N LYS1s 17 " --> pdb=" O HIS1s 13 " (cutoff:3.500A) Processing helix chain '1s' and resid 69 through 75 removed outlier: 4.611A pdb=" N PHE1s 73 " --> pdb=" O LYS1s 69 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA1s 74 " --> pdb=" O LEU1s 70 " (cutoff:3.500A) Proline residue: 1s 75 - end of helix No H-bonds generated for 'chain '1s' and resid 69 through 75' Processing helix chain '1t' and resid 7 through 41 removed outlier: 3.630A pdb=" N ILE1t 11 " --> pdb=" O LYS1t 7 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS1t 18 " --> pdb=" O GLU1t 14 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N HIS1t 19 " --> pdb=" O LYS1t 15 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG1t 23 " --> pdb=" O HIS1t 19 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL1t 34 " --> pdb=" O PHE1t 30 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY1t 41 " --> pdb=" O ALA1t 37 " (cutoff:3.500A) Processing helix chain '1t' and resid 43 through 64 Proline residue: 1t 55 - end of helix removed outlier: 3.723A pdb=" N ALA1t 61 " --> pdb=" O VAL1t 57 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA1t 62 " --> pdb=" O ASP1t 58 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS1t 63 " --> pdb=" O ARG1t 59 " (cutoff:3.500A) Processing helix chain '1t' and resid 67 through 86 removed outlier: 6.492A pdb=" N ALA1t 71 " --> pdb=" O HIS1t 67 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ALA1t 72 " --> pdb=" O LYS1t 68 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU1t 78 " --> pdb=" O HIS1t 74 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR1t 79 " --> pdb=" O LYS1t 75 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS1t 84 " --> pdb=" O ALA1t 80 " (cutoff:3.500A) Processing helix chain '1u' and resid 16 through 23 removed outlier: 4.229A pdb=" N ARG1u 20 " --> pdb=" O ARG1u 16 " (cutoff:3.500A) Processing helix chain '1u' and resid 24 through 34 removed outlier: 4.484A pdb=" N LEU1u 28 " --> pdb=" O LYS1u 24 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA1u 29 " --> pdb=" O ALA1u 25 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU1u 30 " --> pdb=" O GLY1u 26 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL1u 31 " --> pdb=" O VAL1u 27 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG1u 32 " --> pdb=" O LEU1u 28 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARG1u 33 " --> pdb=" O ALA1u 29 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ARG1u 34 " --> pdb=" O GLU1u 30 " (cutoff:3.500A) No H-bonds generated for 'chain '1u' and resid 24 through 34' Processing helix chain '1u' and resid 37 through 61 removed outlier: 4.381A pdb=" N THR1u 41 " --> pdb=" O TYR1u 37 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR1u 42 " --> pdb=" O GLU1u 38 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS1u 45 " --> pdb=" O THR1u 41 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG1u 54 " --> pdb=" O SER1u 50 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU1u 59 " --> pdb=" O HIS1u 55 " (cutoff:3.500A) Processing helix chain '1w' and resid 15 through 28 removed outlier: 3.587A pdb=" N GLU1w 21 " --> pdb=" O THR1w 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER1w 22 " --> pdb=" O THR1w 18 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N TYR1w 25 " --> pdb=" O GLU1w 21 " (cutoff:3.500A) Processing helix chain '1w' and resid 48 through 53 removed outlier: 4.227A pdb=" N ARG1w 52 " --> pdb=" O LEU1w 48 " (cutoff:3.500A) Processing helix chain '1w' and resid 81 through 93 removed outlier: 4.549A pdb=" N VAL1w 85 " --> pdb=" O PHE1w 81 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER1w 88 " --> pdb=" O GLU1w 84 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU1w 89 " --> pdb=" O VAL1w 85 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER1w 90 " --> pdb=" O TYR1w 86 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VAL1w 91 " --> pdb=" O ARG1w 87 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU1w 92 " --> pdb=" O SER1w 88 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP1w 93 " --> pdb=" O LEU1w 89 " (cutoff:3.500A) Processing helix chain '1w' and resid 106 through 120 removed outlier: 3.684A pdb=" N LEU1w 112 " --> pdb=" O GLN1w 108 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG1w 117 " --> pdb=" O PHE1w 113 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS1w 118 " --> pdb=" O HIS1w 114 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY1w 120 " --> pdb=" O LEU1w 116 " (cutoff:3.500A) Processing helix chain '1w' and resid 137 through 149 removed outlier: 5.974A pdb=" N TYR1w 141 " --> pdb=" O LEU1w 137 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN1w 142 " --> pdb=" O SER1w 138 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP1w 143 " --> pdb=" O THR1w 139 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE1w 144 " --> pdb=" O VAL1w 140 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS1w 145 " --> pdb=" O TYR1w 141 " (cutoff:3.500A) Processing helix chain '1w' and resid 176 through 183 removed outlier: 3.669A pdb=" N GLY1w 181 " --> pdb=" O THR1w 177 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN1w 182 " --> pdb=" O VAL1w 178 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP1w 183 " --> pdb=" O ILE1w 179 " (cutoff:3.500A) Processing helix chain '1w' and resid 184 through 192 removed outlier: 3.505A pdb=" N MET1w 190 " --> pdb=" O LEU1w 186 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER1w 191 " --> pdb=" O GLU1w 187 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY1w 192 " --> pdb=" O LYS1w 188 " (cutoff:3.500A) Processing helix chain '1w' and resid 198 through 209 removed outlier: 3.686A pdb=" N GLN1w 202 " --> pdb=" O LEU1w 198 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU1w 203 " --> pdb=" O GLU1w 199 " (cutoff:3.500A) Processing helix chain '1w' and resid 226 through 238 removed outlier: 4.361A pdb=" N ILE1w 231 " --> pdb=" O ILE1w 227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL1w 233 " --> pdb=" O ASN1w 229 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE1w 234 " --> pdb=" O LEU1w 230 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR1w 235 " --> pdb=" O ILE1w 231 " (cutoff:3.500A) Processing helix chain '1w' and resid 355 through 372 removed outlier: 5.371A pdb=" N GLU1w 359 " --> pdb=" O PRO1w 355 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET1w 360 " --> pdb=" O GLU1w 356 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU1w 361 " --> pdb=" O GLN1w 357 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP1w 363 " --> pdb=" O GLU1w 359 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER1w 369 " --> pdb=" O LEU1w 365 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP1w 372 " --> pdb=" O ILE1w 368 " (cutoff:3.500A) Processing helix chain '1w' and resid 392 through 406 removed outlier: 3.752A pdb=" N MET1w 396 " --> pdb=" O GLY1w 392 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU1w 397 " --> pdb=" O LYS1w 393 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL1w 398 " --> pdb=" O VAL1w 394 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE1w 399 " --> pdb=" O GLN1w 395 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU1w 403 " --> pdb=" O ILE1w 399 " (cutoff:3.500A) Processing helix chain '1w' and resid 471 through 488 removed outlier: 5.419A pdb=" N ASN1w 475 " --> pdb=" O GLN1w 471 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA1w 476 " --> pdb=" O SER1w 472 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL1w 477 " --> pdb=" O PHE1w 473 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET1w 478 " --> pdb=" O GLN1w 474 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR1w 483 " --> pdb=" O GLU1w 479 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY1w 484 " --> pdb=" O GLY1w 480 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU1w 486 " --> pdb=" O ARG1w 482 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLN1w 487 " --> pdb=" O TYR1w 483 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLY1w 488 " --> pdb=" O GLY1w 484 " (cutoff:3.500A) Processing helix chain '1w' and resid 512 through 532 Proline residue: 1w 521 - end of helix removed outlier: 3.558A pdb=" N LYS1w 529 " --> pdb=" O GLU1w 525 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY1w 532 " --> pdb=" O LEU1w 528 " (cutoff:3.500A) Processing helix chain '1w' and resid 547 through 561 removed outlier: 3.880A pdb=" N SER1w 552 " --> pdb=" O GLN1w 548 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ARG1w 553 " --> pdb=" O GLU1w 549 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR1w 555 " --> pdb=" O LEU1w 551 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN1w 556 " --> pdb=" O SER1w 552 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP1w 557 " --> pdb=" O ARG1w 553 " (cutoff:3.500A) Proline residue: 1w 559 - end of helix Processing helix chain '1w' and resid 582 through 596 removed outlier: 3.887A pdb=" N GLN1w 587 " --> pdb=" O ALA1w 583 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLU1w 588 " --> pdb=" O ARG1w 584 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG1w 590 " --> pdb=" O ILE1w 586 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER1w 591 " --> pdb=" O GLN1w 587 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP1w 592 " --> pdb=" O GLU1w 588 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE1w 595 " --> pdb=" O SER1w 591 " (cutoff:3.500A) Processing helix chain '1w' and resid 630 through 639 removed outlier: 4.034A pdb=" N MET1w 634 " --> pdb=" O LYS1w 630 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE1w 635 " --> pdb=" O VAL1w 631 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN1w 636 " --> pdb=" O ARG1w 632 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS1w 637 " --> pdb=" O TYR1w 633 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE1w 638 " --> pdb=" O MET1w 634 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR1w 639 " --> pdb=" O PHE1w 635 " (cutoff:3.500A) No H-bonds generated for 'chain '1w' and resid 630 through 639' Processing sheet with id= 1, first strand: chain '1D' and resid 32 through 35 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain '1D' and resid 79 through 82 removed outlier: 3.761A pdb=" N ARG1D 79 " --> pdb=" O LEU1D 92 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU1D 92 " --> pdb=" O GLU1D 78 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASP1D 113 " --> pdb=" O VAL1D 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '1D' and resid 170 through 175 removed outlier: 3.637A pdb=" N LEU1D 175 " --> pdb=" O GLU1D 179 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU1D 179 " --> pdb=" O LEU1D 175 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '1D' and resid 89 through 95 removed outlier: 5.561A pdb=" N ASN1D 89 " --> pdb=" O ALA1D 105 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU1D 99 " --> pdb=" O TYR1D 95 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '1E' and resid 3 through 7 removed outlier: 6.846A pdb=" N ASP1E 200 " --> pdb=" O THR1E 112 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR1E 112 " --> pdb=" O ASP1E 200 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL1E 109 " --> pdb=" O VAL1E 172 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL1E 172 " --> pdb=" O VAL1E 109 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY1E 111 " --> pdb=" O VAL1E 170 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER1E 113 " --> pdb=" O GLU1E 168 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU1E 168 " --> pdb=" O SER1E 113 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '1E' and resid 10 through 16 removed outlier: 4.564A pdb=" N GLY1E 10 " --> pdb=" O VAL1E 26 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL1E 20 " --> pdb=" O THR1E 16 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU1E 186 " --> pdb=" O ASP1E 181 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP1E 181 " --> pdb=" O LEU1E 186 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG1E 179 " --> pdb=" O LEU1E 188 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '1E' and resid 47 through 51 removed outlier: 3.601A pdb=" N ILE1E 48 " --> pdb=" O PHE1E 82 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '1F' and resid 1 through 5 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain '1F' and resid 117 through 120 removed outlier: 5.483A pdb=" N ARG1F 117 " --> pdb=" O ASP1F 184 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL1F 187 " --> pdb=" O LEU1F 147 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE1F 149 " --> pdb=" O VAL1F 187 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL1F 146 " --> pdb=" O LYS1F 166 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP1F 168 " --> pdb=" O VAL1F 146 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '1G' and resid 64 through 68 removed outlier: 3.622A pdb=" N LEU1G 90 " --> pdb=" O ILE1G 33 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE1G 33 " --> pdb=" O LEU1G 90 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS1G 32 " --> pdb=" O THR1G 156 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN1G 36 " --> pdb=" O ASP1G 152 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR1G 157 " --> pdb=" O GLY1G 125 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLY1G 125 " --> pdb=" O THR1G 157 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '1H' and resid 15 through 18 removed outlier: 3.651A pdb=" N ASP1H 15 " --> pdb=" O LYS1H 26 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS1H 17 " --> pdb=" O THR1H 24 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR1H 24 " --> pdb=" O LYS1H 17 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU1H 32 " --> pdb=" O ILE1H 25 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '1H' and resid 93 through 97 removed outlier: 3.765A pdb=" N ALA1H 96 " --> pdb=" O ASN1H 103 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '1H' and resid 120 through 124 removed outlier: 5.756A pdb=" N THR1H 128 " --> pdb=" O LEU1H 88 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY1H 134 " --> pdb=" O PHE1H 82 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE1H 82 " --> pdb=" O GLY1H 134 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '1L' and resid 91 through 94 removed outlier: 3.666A pdb=" N ALA1L 92 " --> pdb=" O LEU1L 58 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL1L 56 " --> pdb=" O LEU1L 94 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS1L 59 " --> pdb=" O GLU1L 116 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLU1L 116 " --> pdb=" O LYS1L 59 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '1I' and resid 2 through 6 removed outlier: 5.768A pdb=" N GLN1I 2 " --> pdb=" O ALA1I 39 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ALA1I 39 " --> pdb=" O GLN1I 2 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LYS1I 35 " --> pdb=" O LEU1I 6 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '1I' and resid 76 through 80 removed outlier: 6.924A pdb=" N GLU1I 76 " --> pdb=" O LYS1I 141 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL1I 78 " --> pdb=" O ILE1I 143 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE1I 132 " --> pdb=" O ALA1I 140 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL1I 142 " --> pdb=" O VAL1I 130 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '1J' and resid 23 through 28 removed outlier: 5.153A pdb=" N LEU1J 23 " --> pdb=" O GLU1J 87 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA1J 25 " --> pdb=" O SER1J 85 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER1J 85 " --> pdb=" O ALA1J 25 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL1J 27 " --> pdb=" O ALA1J 83 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '1K' and resid 54 through 58 No H-bonds generated for sheet with id= 18 Processing sheet with id= 19, first strand: chain '1N' and resid 14 through 19 removed outlier: 3.996A pdb=" N LEU1N 57 " --> pdb=" O VAL1N 18 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '1N' and resid 74 through 78 removed outlier: 4.461A pdb=" N ALA1N 87 " --> pdb=" O TYR1N 74 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS1N 76 " --> pdb=" O LYS1N 85 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS1N 85 " --> pdb=" O HIS1N 76 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N GLY1N 83 " --> pdb=" O THR1N 78 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '1O' and resid 6 through 9 removed outlier: 3.995A pdb=" N THR1O 6 " --> pdb=" O CYS1O 21 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '1O' and resid 38 through 41 removed outlier: 4.181A pdb=" N LYS1O 59 " --> pdb=" O LEU1O 87 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '1Q' and resid 62 through 65 removed outlier: 4.385A pdb=" N TYR1Q 103 " --> pdb=" O LEU1Q 33 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU1Q 33 " --> pdb=" O LEU1Q 102 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS1Q 100 " --> pdb=" O ALA1Q 35 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '1Q' and resid 73 through 76 removed outlier: 6.359A pdb=" N ILE1Q 73 " --> pdb=" O GLU1Q 90 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN1Q 88 " --> pdb=" O GLU1Q 75 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '1Q' and resid 30 through 36 removed outlier: 7.979A pdb=" N SER1Q 30 " --> pdb=" O LYS1Q 133 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY1Q 32 " --> pdb=" O VAL1Q 131 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL1Q 131 " --> pdb=" O GLY1Q 32 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS1Q 127 " --> pdb=" O VAL1Q 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '1R' and resid 95 through 100 removed outlier: 3.533A pdb=" N GLU1R 114 " --> pdb=" O ARG1R 96 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N MET1R 110 " --> pdb=" O CYS1R 100 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '1S' and resid 35 through 41 removed outlier: 4.086A pdb=" N ARG1S 25 " --> pdb=" O ILE1S 40 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL1S 28 " --> pdb=" O ASP1S 93 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '1T' and resid 37 through 44 removed outlier: 5.988A pdb=" N THR1T 24 " --> pdb=" O LYS1T 86 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS1T 86 " --> pdb=" O THR1T 24 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS1T 28 " --> pdb=" O SER1T 82 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER1T 82 " --> pdb=" O LYS1T 28 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '1T' and resid 56 through 63 removed outlier: 7.844A pdb=" N SER1T 56 " --> pdb=" O THR1T 75 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '1V' and resid 2 through 6 Processing sheet with id= 31, first strand: chain '1V' and resid 19 through 23 removed outlier: 6.853A pdb=" N ASP1V 95 " --> pdb=" O VAL1V 64 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS1V 60 " --> pdb=" O THR1V 99 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '1V' and resid 69 through 78 removed outlier: 5.211A pdb=" N GLU1V 70 " --> pdb=" O GLN1V 91 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN1V 91 " --> pdb=" O GLU1V 70 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL1V 72 " --> pdb=" O HIS1V 89 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR1V 83 " --> pdb=" O ARG1V 78 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '1W' and resid 2 through 8 removed outlier: 4.882A pdb=" N THR1W 3 " --> pdb=" O VAL1W 107 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL1W 107 " --> pdb=" O THR1W 3 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA1W 5 " --> pdb=" O VAL1W 105 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL1W 105 " --> pdb=" O ALA1W 5 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR1W 100 " --> pdb=" O GLY1W 79 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL1W 106 " --> pdb=" O LYS1W 73 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS1W 73 " --> pdb=" O VAL1W 106 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '1X' and resid 74 through 78 removed outlier: 4.718A pdb=" N LYS1X 66 " --> pdb=" O ARG1X 77 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL1X 57 " --> pdb=" O THR1X 86 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN1X 59 " --> pdb=" O TYR1X 84 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '1Y' and resid 39 through 44 No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain '1Y' and resid 82 through 86 removed outlier: 3.518A pdb=" N PHE1Y 94 " --> pdb=" O GLY1Y 83 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain '1Z' and resid 6 through 9 removed outlier: 3.854A pdb=" N ARG1Z 9 " --> pdb=" O ALA1Z 39 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA1Z 39 " --> pdb=" O ARG1Z 9 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU1Z 42 " --> pdb=" O PHE1Z 26 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE1Z 89 " --> pdb=" O PRO1Z 27 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE1Z 29 " --> pdb=" O ILE1Z 89 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N LYS1Z 71 " --> pdb=" O ALA1Z 94 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '1Z' and resid 2 through 5 removed outlier: 3.943A pdb=" N ILE1Z 4 " --> pdb=" O THR1Z 62 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain '10' and resid 47 through 50 removed outlier: 4.268A pdb=" N THR10 54 " --> pdb=" O GLY10 50 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain '10' and resid 61 through 67 removed outlier: 3.745A pdb=" N LYS10 62 " --> pdb=" O GLU10 79 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU10 79 " --> pdb=" O LYS10 62 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '11' and resid 11 through 18 removed outlier: 4.060A pdb=" N VAL11 12 " --> pdb=" O PHE11 28 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR11 24 " --> pdb=" O ASN11 16 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER11 18 " --> pdb=" O ASN11 22 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASN11 22 " --> pdb=" O SER11 18 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL11 39 " --> pdb=" O ARG11 44 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '13' and resid 32 through 38 removed outlier: 3.968A pdb=" N HIS13 33 " --> pdb=" O GLN13 8 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN13 8 " --> pdb=" O HIS13 33 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS13 5 " --> pdb=" O GLU13 57 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N MET13 53 " --> pdb=" O THR13 9 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '14' and resid 11 through 15 removed outlier: 4.208A pdb=" N MET14 22 " --> pdb=" O ALA14 14 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '15' and resid 27 through 30 removed outlier: 6.122A pdb=" N SER15 28 " --> pdb=" O LYS15 36 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS15 36 " --> pdb=" O SER15 28 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP15 30 " --> pdb=" O GLY15 34 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '16' and resid 19 through 24 Processing sheet with id= 46, first strand: chain '19' and resid 14 through 19 Processing sheet with id= 47, first strand: chain '1b' and resid 88 through 92 removed outlier: 3.930A pdb=" N LEU1b 67 " --> pdb=" O ALA1b 159 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE1b 161 " --> pdb=" O LEU1b 67 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '1c' and resid 18 through 21 removed outlier: 5.747A pdb=" N ASN1c 18 " --> pdb=" O ILE1c 54 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR1c 20 " --> pdb=" O ILE1c 56 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG1c 58 " --> pdb=" O THR1c 20 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG1c 53 " --> pdb=" O HIS1c 68 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU1c 57 " --> pdb=" O ARG1c 64 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL1c 105 " --> pdb=" O THR1c 69 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '1c' and resid 166 through 170 removed outlier: 3.675A pdb=" N GLY1c 147 " --> pdb=" O PHE1c 202 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER1c 186 " --> pdb=" O VAL1c 197 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL1c 199 " --> pdb=" O ASN1c 184 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN1c 184 " --> pdb=" O VAL1c 199 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ASP1c 180 " --> pdb=" O LYS1c 203 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '1d' and resid 140 through 143 removed outlier: 3.578A pdb=" N VAL1d 142 " --> pdb=" O GLY1d 179 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLU1d 178 " --> pdb=" O ASP1d 173 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain '1e' and resid 10 through 15 removed outlier: 4.068A pdb=" N GLN1e 11 " --> pdb=" O GLY1e 39 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY1e 39 " --> pdb=" O GLN1e 11 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS1e 13 " --> pdb=" O VAL1e 37 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL1e 37 " --> pdb=" O LYS1e 13 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU1e 35 " --> pdb=" O ILE1e 15 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE1e 29 " --> pdb=" O LYS1e 22 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS1e 22 " --> pdb=" O ILE1e 29 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU1e 35 " --> pdb=" O ALA1e 16 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA1e 16 " --> pdb=" O LEU1e 35 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain '1e' and resid 83 through 87 removed outlier: 3.978A pdb=" N VAL1e 84 " --> pdb=" O MET1e 95 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N MET1e 95 " --> pdb=" O VAL1e 84 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N VAL1e 93 " --> pdb=" O GLY1e 86 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N TYR1e 127 " --> pdb=" O ARG1e 92 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain '1e' and resid 33 through 39 removed outlier: 4.587A pdb=" N ALA1e 34 " --> pdb=" O GLY1e 50 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY1e 50 " --> pdb=" O ALA1e 34 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL1e 38 " --> pdb=" O GLY1e 46 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY1e 46 " --> pdb=" O VAL1e 38 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain '1f' and resid 3 through 10 removed outlier: 5.978A pdb=" N ILE1f 6 " --> pdb=" O MET1f 62 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE1f 8 " --> pdb=" O VAL1f 60 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain '1g' and resid 72 through 76 Processing sheet with id= 56, first strand: chain '1h' and resid 22 through 27 removed outlier: 6.546A pdb=" N ALA1h 22 " --> pdb=" O LEU1h 62 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU1h 62 " --> pdb=" O ALA1h 22 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU1h 60 " --> pdb=" O VAL1h 24 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain '1h' and resid 73 through 76 removed outlier: 4.045A pdb=" N SER1h 73 " --> pdb=" O ALA1h 129 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN1h 75 " --> pdb=" O TYR1h 127 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS1h 126 " --> pdb=" O VAL1h 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL1h 128 " --> pdb=" O ILE1h 100 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE1h 100 " --> pdb=" O VAL1h 128 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL1h 102 " --> pdb=" O ILE1h 125 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain '1i' and resid 4 through 10 removed outlier: 4.123A pdb=" N GLY1i 9 " --> pdb=" O ALA1i 16 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS1i 67 " --> pdb=" O ALA1i 15 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LYS1i 26 " --> pdb=" O LEU1i 60 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU1i 62 " --> pdb=" O LYS1i 26 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain '1j' and resid 44 through 52 removed outlier: 3.879A pdb=" N GLU1j 47 " --> pdb=" O ILE1j 67 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA1j 12 " --> pdb=" O HIS1j 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL1j 74 " --> pdb=" O ILE1j 8 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE1j 8 " --> pdb=" O VAL1j 74 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG1j 9 " --> pdb=" O GLN1j 99 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain '1k' and resid 29 through 34 removed outlier: 3.556A pdb=" N GLU1k 82 " --> pdb=" O GLY1k 18 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain '1l' and resid 50 through 56 removed outlier: 5.199A pdb=" N LYS1l 50 " --> pdb=" O ILE1l 66 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE1l 66 " --> pdb=" O LYS1l 50 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS1l 52 " --> pdb=" O SER1l 64 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER1l 64 " --> pdb=" O CYS1l 52 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE1l 60 " --> pdb=" O LEU1l 56 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain '1l' and resid 80 through 83 removed outlier: 5.060A pdb=" N LEU1l 80 " --> pdb=" O VAL1l 97 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain '1p' and resid 4 through 10 removed outlier: 5.582A pdb=" N GLN1p 18 " --> pdb=" O ALA1p 7 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '1q' and resid 6 through 10 removed outlier: 3.612A pdb=" N ILE1q 60 " --> pdb=" O LEU1q 7 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY1q 9 " --> pdb=" O VAL1q 58 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '1q' and resid 18 through 29 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain '1s' and resid 47 through 51 Processing sheet with id= 67, first strand: chain '1w' and resid 6 through 10 removed outlier: 4.194A pdb=" N GLY1w 7 " --> pdb=" O GLY1w 94 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE1w 96 " --> pdb=" O GLY1w 7 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU1w 9 " --> pdb=" O ILE1w 96 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE1w 124 " --> pdb=" O ALA1w 95 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '1w' and resid 301 through 304 removed outlier: 3.717A pdb=" N ILE1w 298 " --> pdb=" O GLU1w 301 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N GLU1w 293 " --> pdb=" O GLN1w 317 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '1w' and resid 348 through 352 removed outlier: 5.542A pdb=" N GLU1w 351 " --> pdb=" O ILE1w 411 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE1w 411 " --> pdb=" O GLU1w 351 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '1w' and resid 426 through 432 removed outlier: 7.862A pdb=" N LYS1w 426 " --> pdb=" O PRO1w 451 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA1w 428 " --> pdb=" O VAL1w 449 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL1w 449 " --> pdb=" O ALA1w 428 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR1w 430 " --> pdb=" O LEU1w 447 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU1w 447 " --> pdb=" O TYR1w 430 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE1w 445 " --> pdb=" O ILE1w 432 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLY1w 446 " --> pdb=" O LYS1w 502 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS1w 502 " --> pdb=" O GLY1w 446 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER1w 448 " --> pdb=" O CYS1w 500 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS1w 498 " --> pdb=" O SER1w 450 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU1w 461 " --> pdb=" O ILE1w 499 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE1w 501 " --> pdb=" O GLU1w 461 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '1w' and resid 492 through 495 removed outlier: 4.009A pdb=" N ASN1w 493 " --> pdb=" O TYR1w 420 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU1w 536 " --> pdb=" O MET1w 421 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER1w 541 " --> pdb=" O GLU1w 606 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU1w 606 " --> pdb=" O SER1w 541 " (cutoff:3.500A) 1520 hydrogen bonds defined for protein. 4509 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2870 hydrogen bonds 4422 hydrogen bond angles 0 basepair planarities 1176 basepair parallelities 2664 stacking parallelities Total time for adding SS restraints: 264.15 Time building geometry restraints manager: 67.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 29176 1.34 - 1.46: 67168 1.46 - 1.59: 55641 1.59 - 1.71: 9268 1.71 - 1.84: 279 Bond restraints: 161532 Sorted by residual: bond pdb=" CCQ EVN1A3001 " pdb=" OCR EVN1A3001 " ideal model delta sigma weight residual 1.052 1.475 -0.423 2.00e-02 2.50e+03 4.48e+02 bond pdb=" CBA EVN1A3001 " pdb=" CBB EVN1A3001 " ideal model delta sigma weight residual 1.146 1.555 -0.409 2.00e-02 2.50e+03 4.18e+02 bond pdb=" CBI EVN1A3001 " pdb=" OBH EVN1A3001 " ideal model delta sigma weight residual 1.037 1.412 -0.375 2.00e-02 2.50e+03 3.52e+02 bond pdb=" CBC EVN1A3001 " pdb=" CBD EVN1A3001 " ideal model delta sigma weight residual 1.141 1.503 -0.362 2.00e-02 2.50e+03 3.28e+02 bond pdb=" CBA EVN1A3001 " pdb=" OAS EVN1A3001 " ideal model delta sigma weight residual 1.788 1.432 0.356 2.00e-02 2.50e+03 3.17e+02 ... (remaining 161527 not shown) Histogram of bond angle deviations from ideal: 94.54 - 103.58: 10349 103.58 - 112.62: 105282 112.62 - 121.66: 86704 121.66 - 130.70: 36849 130.70 - 139.74: 1643 Bond angle restraints: 240827 Sorted by residual: angle pdb=" C1' 2MA1A2503 " pdb=" N9 2MA1A2503 " pdb=" C8 2MA1A2503 " ideal model delta sigma weight residual 106.32 125.66 -19.34 3.00e+00 1.11e-01 4.16e+01 angle pdb=" C ASN1w 439 " pdb=" N PRO1w 440 " pdb=" CA PRO1w 440 " ideal model delta sigma weight residual 119.76 126.40 -6.64 1.03e+00 9.43e-01 4.15e+01 angle pdb=" C1' OMG1A2251 " pdb=" N9 OMG1A2251 " pdb=" C8 OMG1A2251 " ideal model delta sigma weight residual 142.82 125.94 16.88 3.00e+00 1.11e-01 3.17e+01 angle pdb=" C1' OMG1A2251 " pdb=" N9 OMG1A2251 " pdb=" C4 OMG1A2251 " ideal model delta sigma weight residual 108.29 125.09 -16.80 3.00e+00 1.11e-01 3.14e+01 angle pdb=" C6 5MU1A 747 " pdb=" C5 5MU1A 747 " pdb=" C5M 5MU1A 747 " ideal model delta sigma weight residual 106.09 122.56 -16.47 3.00e+00 1.11e-01 3.01e+01 ... (remaining 240822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 90841 35.98 - 71.96: 10058 71.96 - 107.95: 1269 107.95 - 143.93: 21 143.93 - 179.91: 26 Dihedral angle restraints: 102215 sinusoidal: 84555 harmonic: 17660 Sorted by residual: dihedral pdb=" C4' C1A2326 " pdb=" C3' C1A2326 " pdb=" C2' C1A2326 " pdb=" C1' C1A2326 " ideal model delta sinusoidal sigma weight residual -35.00 34.17 -69.17 1 8.00e+00 1.56e-02 9.67e+01 dihedral pdb=" C5' C1A2326 " pdb=" C4' C1A2326 " pdb=" C3' C1A2326 " pdb=" O3' C1A2326 " ideal model delta sinusoidal sigma weight residual 147.00 79.45 67.55 1 8.00e+00 1.56e-02 9.27e+01 dihedral pdb=" O4' C1A2326 " pdb=" C4' C1A2326 " pdb=" C3' C1A2326 " pdb=" C2' C1A2326 " ideal model delta sinusoidal sigma weight residual 24.00 -35.64 59.64 1 8.00e+00 1.56e-02 7.42e+01 ... (remaining 102212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.072: 30223 1.072 - 2.143: 2 2.143 - 3.215: 0 3.215 - 4.287: 0 4.287 - 5.358: 1 Chirality restraints: 30226 Sorted by residual: chirality pdb=" CAY EVN1A3001 " pdb=" CAX EVN1A3001 " pdb=" CAZ EVN1A3001 " pdb=" CDV EVN1A3001 " both_signs ideal model delta sigma weight residual False 2.64 -2.71 5.36 2.00e-01 2.50e+01 7.18e+02 chirality pdb=" CBD EVN1A3001 " pdb=" CBC EVN1A3001 " pdb=" OBE EVN1A3001 " pdb=" OBK EVN1A3001 " both_signs ideal model delta sigma weight residual False -1.15 -2.39 1.25 2.00e-01 2.50e+01 3.90e+01 chirality pdb=" CCQ EVN1A3001 " pdb=" CCS EVN1A3001 " pdb=" OCR EVN1A3001 " pdb=" OCW EVN1A3001 " both_signs ideal model delta sigma weight residual False 1.14 2.34 -1.20 2.00e-01 2.50e+01 3.57e+01 ... (remaining 30223 not shown) Planarity restraints: 13517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' H2U1A2449 " -0.809 2.00e-02 2.50e+03 5.74e-01 7.41e+03 pdb=" C4' H2U1A2449 " 0.237 2.00e-02 2.50e+03 pdb=" O4' H2U1A2449 " 0.555 2.00e-02 2.50e+03 pdb=" C3' H2U1A2449 " -0.181 2.00e-02 2.50e+03 pdb=" O3' H2U1A2449 " 0.977 2.00e-02 2.50e+03 pdb=" C2' H2U1A2449 " -0.631 2.00e-02 2.50e+03 pdb=" O2' H2U1A2449 " -0.622 2.00e-02 2.50e+03 pdb=" C1' H2U1A2449 " 0.409 2.00e-02 2.50e+03 pdb=" N1 H2U1A2449 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG1a 527 " 0.043 2.00e-02 2.50e+03 5.73e-01 7.37e+03 pdb=" C4' 7MG1a 527 " 0.430 2.00e-02 2.50e+03 pdb=" O4' 7MG1a 527 " 0.580 2.00e-02 2.50e+03 pdb=" C3' 7MG1a 527 " -0.591 2.00e-02 2.50e+03 pdb=" O3' 7MG1a 527 " -0.588 2.00e-02 2.50e+03 pdb=" C2' 7MG1a 527 " -0.186 2.00e-02 2.50e+03 pdb=" O2' 7MG1a 527 " 0.941 2.00e-02 2.50e+03 pdb=" C1' 7MG1a 527 " 0.240 2.00e-02 2.50e+03 pdb=" N9 7MG1a 527 " -0.868 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU1x 54 " 0.022 2.00e-02 2.50e+03 5.66e-01 7.21e+03 pdb=" C4' 5MU1x 54 " 0.435 2.00e-02 2.50e+03 pdb=" O4' 5MU1x 54 " 0.658 2.00e-02 2.50e+03 pdb=" C3' 5MU1x 54 " -0.590 2.00e-02 2.50e+03 pdb=" O3' 5MU1x 54 " -0.544 2.00e-02 2.50e+03 pdb=" C2' 5MU1x 54 " -0.226 2.00e-02 2.50e+03 pdb=" O2' 5MU1x 54 " 0.879 2.00e-02 2.50e+03 pdb=" C1' 5MU1x 54 " 0.229 2.00e-02 2.50e+03 pdb=" N1 5MU1x 54 " -0.861 2.00e-02 2.50e+03 ... (remaining 13514 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 1097 2.56 - 3.15: 112160 3.15 - 3.73: 281924 3.73 - 4.32: 402701 4.32 - 4.90: 534167 Nonbonded interactions: 1332049 Sorted by model distance: nonbonded pdb=" C2' U1A 827 " pdb=" O2 U1A2068 " model vdw 1.981 3.470 nonbonded pdb=" O2' U1a 707 " pdb=" O GLY1k 38 " model vdw 2.081 2.440 nonbonded pdb=" OP1 U1A1864 " pdb=" O2' G1A2410 " model vdw 2.090 2.440 nonbonded pdb=" OP1 A1a 554 " pdb=" OG SER1l 18 " model vdw 2.091 2.440 nonbonded pdb=" O2' G1A1813 " pdb=" OG1 THR1D 49 " model vdw 2.103 2.440 ... (remaining 1332044 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: 2.940 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: 0.140 Extract box with map and model: 16.170 Check model and map are aligned: 1.580 Set scattering table: 1.000 Process input model: 566.770 Find NCS groups from input model: 3.210 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: 0.030 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 594.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5911 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 : 0.006 0.423 161532 Z= 0.389 Angle : 0.509 19.344 240827 Z= 0.261 Chirality : 0.043 5.358 30226 Planarity : 0.017 0.574 13517 Dihedral : 22.056 179.912 91270 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 2.60 % Allowed : 8.81 % Favored : 88.60 % Rotamer: Outliers : 0.19 % Allowed : 1.57 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % 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: -3.12 (0.09), residues: 6550 helix: -3.59 (0.07), residues: 1791 sheet: -3.94 (0.12), residues: 953 loop : -0.62 (0.10), residues: 3806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP1D 212 HIS 0.006 0.001 HIS1Q 13 PHE 0.012 0.001 PHE1F 85 TYR 0.018 0.001 TYR1Z 57 ARG 0.004 0.000 ARG18 7 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1981 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1972 time to evaluate : 6.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 1D 90 ILE cc_start: 0.8590 (pt) cc_final: 0.7723 (pt) REVERT: 1E 73 VAL cc_start: 0.6643 (m) cc_final: 0.6374 (m) REVERT: 1E 91 THR cc_start: 0.7640 (t) cc_final: 0.7416 (t) REVERT: 1O 3 GLN cc_start: 0.7543 (pt0) cc_final: 0.7237 (pt0) REVERT: 1O 13 ASN cc_start: 0.7788 (p0) cc_final: 0.7199 (p0) REVERT: 1O 58 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7039 (pp) REVERT: 1Q 17 ASN cc_start: 0.8221 (t0) cc_final: 0.7835 (t0) REVERT: 1Q 104 GLU cc_start: 0.5718 (mt-10) cc_final: 0.5300 (mt-10) REVERT: 1R 44 LEU cc_start: 0.8339 (tp) cc_final: 0.7910 (tp) REVERT: 1S 53 THR cc_start: 0.7313 (p) cc_final: 0.6600 (p) REVERT: 1W 88 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.6874 (ttm-80) REVERT: 10 75 PHE cc_start: 0.7855 (m-80) cc_final: 0.7559 (m-80) REVERT: 11 31 ASN cc_start: 0.8254 (t0) cc_final: 0.8022 (t0) REVERT: 12 8 GLU cc_start: 0.4833 (mp0) cc_final: 0.4064 (mt-10) REVERT: 12 40 SER cc_start: 0.8027 (p) cc_final: 0.7463 (t) REVERT: 1c 54 ILE cc_start: 0.6400 (pt) cc_final: 0.6016 (pt) REVERT: 1c 90 VAL cc_start: 0.6606 (t) cc_final: 0.6287 (t) REVERT: 1c 114 LEU cc_start: 0.7355 (mt) cc_final: 0.6764 (mt) REVERT: 1h 15 ASN cc_start: 0.6325 (m-40) cc_final: 0.6051 (m-40) outliers start: 9 outliers final: 2 residues processed: 1978 average time/residue: 1.5747 time to fit residues: 5191.5919 Evaluate side-chains 1299 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1295 time to evaluate : 5.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1O residue 58 LEU Chi-restraints excluded: chain 1W residue 88 ARG Chi-restraints excluded: chain 18 residue 61 LEU Chi-restraints excluded: chain 1n residue 35 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 931 optimal weight: 8.9990 chunk 836 optimal weight: 10.0000 chunk 463 optimal weight: 10.0000 chunk 285 optimal weight: 10.0000 chunk 563 optimal weight: 2.9990 chunk 446 optimal weight: 3.9990 chunk 864 optimal weight: 5.9990 chunk 334 optimal weight: 5.9990 chunk 525 optimal weight: 7.9990 chunk 643 optimal weight: 8.9990 chunk 1001 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1D 45 ASN 1D 85 ASN 1D 225 ASN 1E 36 GLN 1E 150 GLN 1E 164 GLN ** 1E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1F 94 GLN 1G 4 HIS 1H 47 ASN 1H 72 ASN 1H 138 GLN 1J 4 ASN 1J 88 HIS 1N 40 HIS 1N 58 ASN ** 1N 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1N 138 GLN 1O 29 HIS 1Q 3 GLN ** 1R 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1S 98 GLN ** 1U 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1V 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1V 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1V 43 ASN 1V 66 HIS 1W 7 HIS 1W 9 HIS ** 1W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1W 31 GLN ** 1W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1Y 68 ASN 1Z 78 GLN ** 1Z 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 8 ASN 10 42 HIS 12 15 ASN 12 27 ASN 12 38 GLN 12 58 ASN 13 33 HIS 16 18 HIS 16 45 HIS 17 16 HIS 1b 41 ASN 1c 5 HIS 1c 18 ASN ** 1c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1d 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1d 125 ASN 1d 197 HIS ** 1e 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1g 141 HIS 1h 3 GLN 1h 117 GLN ** 1k 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1m 90 HIS ** 1m 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1n 60 GLN 1o 34 GLN 1p 9 HIS 1q 30 HIS 1q 44 HIS 1r 51 GLN 1r 73 HIS 1s 51 HIS 1s 68 HIS ** 1t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 161532 Z= 0.336 Angle : 0.837 22.579 240827 Z= 0.428 Chirality : 0.044 2.534 30226 Planarity : 0.008 0.146 13517 Dihedral : 22.982 179.910 79669 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.95 % Allowed : 7.42 % Favored : 91.63 % Rotamer: Outliers : 4.95 % Allowed : 14.04 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % 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: -2.34 (0.10), residues: 6550 helix: -1.48 (0.10), residues: 1936 sheet: -3.44 (0.12), residues: 1003 loop : -0.89 (0.10), residues: 3611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP1w 442 HIS 0.011 0.002 HIS1e 120 PHE 0.032 0.003 PHE14 60 TYR 0.031 0.003 TYR1N 125 ARG 0.022 0.001 ARG1Q 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1760 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1521 time to evaluate : 6.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1D 83 ASP cc_start: 0.7530 (m-30) cc_final: 0.7047 (m-30) REVERT: 1D 90 ILE cc_start: 0.8848 (pt) cc_final: 0.8252 (pt) REVERT: 1D 110 LYS cc_start: 0.7651 (mtmm) cc_final: 0.7312 (mtmm) REVERT: 1D 177 SER cc_start: 0.8794 (p) cc_final: 0.8528 (t) REVERT: 1D 218 THR cc_start: 0.8526 (m) cc_final: 0.8249 (t) REVERT: 1E 194 PRO cc_start: 0.8714 (Cg_endo) cc_final: 0.8399 (Cg_exo) REVERT: 1E 201 LEU cc_start: 0.7762 (mt) cc_final: 0.7532 (mt) REVERT: 1G 103 ILE cc_start: 0.7462 (pt) cc_final: 0.7261 (pt) REVERT: 1H 33 THR cc_start: 0.7351 (t) cc_final: 0.7140 (t) REVERT: 1H 40 VAL cc_start: 0.6670 (OUTLIER) cc_final: 0.6296 (p) REVERT: 1H 63 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7253 (mm-40) REVERT: 1H 100 ASN cc_start: 0.7637 (t0) cc_final: 0.7347 (t0) REVERT: 1O 13 ASN cc_start: 0.7987 (p0) cc_final: 0.7498 (p0) REVERT: 1P 36 LYS cc_start: 0.8691 (mttt) cc_final: 0.8478 (mtmt) REVERT: 1Q 1 MET cc_start: 0.5351 (ptp) cc_final: 0.4886 (ptm) REVERT: 1Q 104 GLU cc_start: 0.5824 (mt-10) cc_final: 0.5533 (mt-10) REVERT: 1Q 115 GLU cc_start: 0.6521 (mm-30) cc_final: 0.6291 (mm-30) REVERT: 1S 53 THR cc_start: 0.7482 (p) cc_final: 0.6855 (m) REVERT: 1S 93 ASP cc_start: 0.7092 (p0) cc_final: 0.6824 (p0) REVERT: 1U 51 GLN cc_start: 0.6286 (tm-30) cc_final: 0.5624 (tm-30) REVERT: 1W 37 THR cc_start: 0.7482 (p) cc_final: 0.7204 (p) REVERT: 1W 88 ARG cc_start: 0.8011 (mmm-85) cc_final: 0.7737 (ttm-80) REVERT: 1X 37 ASP cc_start: 0.7999 (p0) cc_final: 0.7697 (p0) REVERT: 1X 39 THR cc_start: 0.7917 (p) cc_final: 0.7215 (p) REVERT: 1Y 12 VAL cc_start: 0.7046 (m) cc_final: 0.6786 (m) REVERT: 11 60 LYS cc_start: 0.6912 (ttpt) cc_final: 0.6651 (ttpt) REVERT: 12 40 SER cc_start: 0.7693 (p) cc_final: 0.7269 (t) REVERT: 12 50 VAL cc_start: 0.8303 (t) cc_final: 0.8087 (t) REVERT: 14 43 PHE cc_start: 0.5012 (t80) cc_final: 0.4427 (p90) REVERT: 15 11 LYS cc_start: 0.8983 (tptm) cc_final: 0.8735 (tptm) REVERT: 1b 20 ARG cc_start: 0.5578 (ptt-90) cc_final: 0.5011 (ptt-90) REVERT: 1b 220 VAL cc_start: 0.6537 (m) cc_final: 0.6323 (t) REVERT: 1c 46 LEU cc_start: 0.5467 (mm) cc_final: 0.5156 (mm) REVERT: 1c 90 VAL cc_start: 0.6526 (t) cc_final: 0.6294 (t) REVERT: 1h 62 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7985 (mt) REVERT: 1i 60 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7101 (pt) REVERT: 1j 64 GLN cc_start: 0.7318 (mm-40) cc_final: 0.6947 (mm-40) REVERT: 1l 7 VAL cc_start: 0.7682 (t) cc_final: 0.7256 (t) REVERT: 1m 106 ARG cc_start: 0.7617 (mmm-85) cc_final: 0.7253 (tpp80) REVERT: 1m 108 ARG cc_start: 0.7370 (ttm-80) cc_final: 0.7145 (mmm160) REVERT: 1m 109 LYS cc_start: 0.7171 (tttt) cc_final: 0.6882 (tttm) REVERT: 1s 51 HIS cc_start: 0.6690 (t-90) cc_final: 0.6318 (t-170) REVERT: 1w 507 TYR cc_start: 0.5982 (m-80) cc_final: 0.5774 (m-80) outliers start: 239 outliers final: 137 residues processed: 1631 average time/residue: 1.3600 time to fit residues: 3793.1685 Evaluate side-chains 1430 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1290 time to evaluate : 6.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1D residue 48 ILE Chi-restraints excluded: chain 1D residue 53 ILE Chi-restraints excluded: chain 1D residue 77 VAL Chi-restraints excluded: chain 1D residue 104 LEU Chi-restraints excluded: chain 1D residue 139 THR Chi-restraints excluded: chain 1D residue 161 VAL Chi-restraints excluded: chain 1D residue 183 VAL Chi-restraints excluded: chain 1D residue 194 VAL Chi-restraints excluded: chain 1E residue 5 VAL Chi-restraints excluded: chain 1E residue 51 THR Chi-restraints excluded: chain 1E residue 58 ASN Chi-restraints excluded: chain 1E residue 145 SER Chi-restraints excluded: chain 1E residue 180 VAL Chi-restraints excluded: chain 1E residue 189 VAL Chi-restraints excluded: chain 1F residue 48 THR Chi-restraints excluded: chain 1F residue 105 LEU Chi-restraints excluded: chain 1F residue 108 ILE Chi-restraints excluded: chain 1F residue 109 LEU Chi-restraints excluded: chain 1F residue 112 LEU Chi-restraints excluded: chain 1F residue 131 THR Chi-restraints excluded: chain 1F residue 176 ASP Chi-restraints excluded: chain 1G residue 36 ASN Chi-restraints excluded: chain 1G residue 51 ASN Chi-restraints excluded: chain 1H residue 40 VAL Chi-restraints excluded: chain 1H residue 48 THR Chi-restraints excluded: chain 1H residue 75 VAL Chi-restraints excluded: chain 1H residue 83 THR Chi-restraints excluded: chain 1H residue 132 LEU Chi-restraints excluded: chain 1I residue 37 VAL Chi-restraints excluded: chain 1I residue 134 VAL Chi-restraints excluded: chain 1K residue 57 VAL Chi-restraints excluded: chain 1K residue 120 ASP Chi-restraints excluded: chain 1N residue 30 THR Chi-restraints excluded: chain 1N residue 40 HIS Chi-restraints excluded: chain 1N residue 84 ILE Chi-restraints excluded: chain 1O residue 57 VAL Chi-restraints excluded: chain 1O residue 65 THR Chi-restraints excluded: chain 1O residue 69 VAL Chi-restraints excluded: chain 1O residue 82 ASN Chi-restraints excluded: chain 1P residue 46 VAL Chi-restraints excluded: chain 1P residue 82 LEU Chi-restraints excluded: chain 1Q residue 42 THR Chi-restraints excluded: chain 1Q residue 110 GLU Chi-restraints excluded: chain 1Q residue 117 PHE Chi-restraints excluded: chain 1R residue 13 ASN Chi-restraints excluded: chain 1R residue 24 MET Chi-restraints excluded: chain 1R residue 37 THR Chi-restraints excluded: chain 1R residue 48 VAL Chi-restraints excluded: chain 1S residue 65 THR Chi-restraints excluded: chain 1S residue 106 LEU Chi-restraints excluded: chain 1T residue 31 VAL Chi-restraints excluded: chain 1T residue 47 ILE Chi-restraints excluded: chain 1T residue 77 SER Chi-restraints excluded: chain 1T residue 79 VAL Chi-restraints excluded: chain 1T residue 84 SER Chi-restraints excluded: chain 1T residue 105 LYS Chi-restraints excluded: chain 1U residue 8 ILE Chi-restraints excluded: chain 1V residue 29 THR Chi-restraints excluded: chain 1V residue 75 VAL Chi-restraints excluded: chain 1W residue 74 ILE Chi-restraints excluded: chain 1W residue 96 ILE Chi-restraints excluded: chain 1W residue 108 SER Chi-restraints excluded: chain 1Y residue 33 VAL Chi-restraints excluded: chain 1Y residue 48 VAL Chi-restraints excluded: chain 1Y residue 57 ILE Chi-restraints excluded: chain 1Y residue 58 VAL Chi-restraints excluded: chain 1Y residue 82 VAL Chi-restraints excluded: chain 1Z residue 47 VAL Chi-restraints excluded: chain 1Z residue 60 VAL Chi-restraints excluded: chain 1Z residue 64 VAL Chi-restraints excluded: chain 10 residue 31 SER Chi-restraints excluded: chain 10 residue 54 THR Chi-restraints excluded: chain 11 residue 3 VAL Chi-restraints excluded: chain 11 residue 58 ILE Chi-restraints excluded: chain 12 residue 55 THR Chi-restraints excluded: chain 13 residue 6 ILE Chi-restraints excluded: chain 13 residue 9 THR Chi-restraints excluded: chain 13 residue 34 THR Chi-restraints excluded: chain 14 residue 13 THR Chi-restraints excluded: chain 15 residue 10 SER Chi-restraints excluded: chain 19 residue 4 ARG Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 26 ILE Chi-restraints excluded: chain 1b residue 23 ASN Chi-restraints excluded: chain 1b residue 39 ILE Chi-restraints excluded: chain 1b residue 71 THR Chi-restraints excluded: chain 1b residue 129 THR Chi-restraints excluded: chain 1b residue 186 VAL Chi-restraints excluded: chain 1b residue 188 THR Chi-restraints excluded: chain 1c residue 43 THR Chi-restraints excluded: chain 1c residue 55 VAL Chi-restraints excluded: chain 1c residue 178 ARG Chi-restraints excluded: chain 1d residue 158 LEU Chi-restraints excluded: chain 1d residue 200 VAL Chi-restraints excluded: chain 1d residue 204 SER Chi-restraints excluded: chain 1e residue 12 GLU Chi-restraints excluded: chain 1e residue 17 VAL Chi-restraints excluded: chain 1e residue 80 LEU Chi-restraints excluded: chain 1e residue 113 VAL Chi-restraints excluded: chain 1e residue 144 GLU Chi-restraints excluded: chain 1f residue 10 VAL Chi-restraints excluded: chain 1f residue 38 ARG Chi-restraints excluded: chain 1g residue 22 LEU Chi-restraints excluded: chain 1g residue 93 VAL Chi-restraints excluded: chain 1g residue 115 MET Chi-restraints excluded: chain 1h residue 10 LEU Chi-restraints excluded: chain 1h residue 33 VAL Chi-restraints excluded: chain 1h residue 58 LEU Chi-restraints excluded: chain 1h residue 62 LEU Chi-restraints excluded: chain 1h residue 88 LYS Chi-restraints excluded: chain 1h residue 103 VAL Chi-restraints excluded: chain 1h residue 124 ILE Chi-restraints excluded: chain 1i residue 60 LEU Chi-restraints excluded: chain 1j residue 10 LEU Chi-restraints excluded: chain 1j residue 52 LEU Chi-restraints excluded: chain 1k residue 81 LEU Chi-restraints excluded: chain 1k residue 83 VAL Chi-restraints excluded: chain 1k residue 107 THR Chi-restraints excluded: chain 1k residue 124 LYS Chi-restraints excluded: chain 1l residue 6 LEU Chi-restraints excluded: chain 1l residue 86 VAL Chi-restraints excluded: chain 1m residue 24 VAL Chi-restraints excluded: chain 1m residue 96 VAL Chi-restraints excluded: chain 1m residue 103 THR Chi-restraints excluded: chain 1n residue 56 SER Chi-restraints excluded: chain 1n residue 67 THR Chi-restraints excluded: chain 1o residue 51 SER Chi-restraints excluded: chain 1o residue 59 VAL Chi-restraints excluded: chain 1p residue 19 VAL Chi-restraints excluded: chain 1p residue 36 VAL Chi-restraints excluded: chain 1p residue 40 ASN Chi-restraints excluded: chain 1q residue 7 LEU Chi-restraints excluded: chain 1q residue 49 ASN Chi-restraints excluded: chain 1r residue 39 VAL Chi-restraints excluded: chain 1r residue 44 THR Chi-restraints excluded: chain 1s residue 3 SER Chi-restraints excluded: chain 1s residue 22 VAL Chi-restraints excluded: chain 1s residue 38 THR Chi-restraints excluded: chain 1s residue 42 ASN Chi-restraints excluded: chain 1s residue 57 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 556 optimal weight: 10.0000 chunk 310 optimal weight: 5.9990 chunk 833 optimal weight: 30.0000 chunk 682 optimal weight: 10.0000 chunk 276 optimal weight: 10.0000 chunk 1003 optimal weight: 2.9990 chunk 1084 optimal weight: 7.9990 chunk 893 optimal weight: 5.9990 chunk 995 optimal weight: 2.9990 chunk 342 optimal weight: 10.0000 chunk 805 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1D 116 GLN ** 1E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1F 46 GLN 1F 165 HIS ** 1G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1G 80 GLN 1H 47 ASN 1H 72 ASN ** 1K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1N 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1R 62 ASN ** 1U 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1U 71 ASN ** 1V 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1W 7 HIS ** 1W 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1Y 45 GLN 12 58 ASN 13 19 HIS ** 14 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 17 16 HIS ** 19 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 37 GLN 1b 18 GLN ** 1b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1c 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1c 184 ASN 1d 70 GLN 1d 119 HIS ** 1f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1h 17 GLN ** 1j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1k 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1k 27 ASN ** 1k 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1l 5 GLN ** 1l 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1m 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1r 73 HIS ** 1t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 161532 Z= 0.299 Angle : 0.793 25.588 240827 Z= 0.414 Chirality : 0.041 2.067 30226 Planarity : 0.008 0.129 13517 Dihedral : 23.157 177.625 79659 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.84 % Allowed : 8.12 % Favored : 91.04 % Rotamer: Outliers : 6.81 % Allowed : 16.86 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.10), residues: 6550 helix: -0.81 (0.11), residues: 1937 sheet: -2.92 (0.13), residues: 1075 loop : -1.25 (0.10), residues: 3538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP1b 103 HIS 0.071 0.003 HIS1N 40 PHE 0.034 0.003 PHE1b 68 TYR 0.035 0.003 TYR1o 68 ARG 0.054 0.001 ARG1K 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1899 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 1570 time to evaluate : 6.350 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: 1D 57 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7409 (t-90) REVERT: 1D 83 ASP cc_start: 0.7781 (m-30) cc_final: 0.7518 (m-30) REVERT: 1E 61 THR cc_start: 0.7534 (p) cc_final: 0.7111 (m) REVERT: 1G 84 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7578 (tp) REVERT: 1H 89 VAL cc_start: 0.7348 (t) cc_final: 0.7034 (t) REVERT: 1N 15 TRP cc_start: 0.8708 (m100) cc_final: 0.8246 (m100) REVERT: 1N 43 GLU cc_start: 0.6033 (pm20) cc_final: 0.5698 (pt0) REVERT: 1O 13 ASN cc_start: 0.7694 (p0) cc_final: 0.6876 (p0) REVERT: 1O 106 GLU cc_start: 0.7139 (mp0) cc_final: 0.6898 (mt-10) REVERT: 1P 36 LYS cc_start: 0.9118 (mttt) cc_final: 0.8577 (pttt) REVERT: 1Q 1 MET cc_start: 0.6028 (ptp) cc_final: 0.5772 (ptm) REVERT: 1Q 104 GLU cc_start: 0.6141 (mt-10) cc_final: 0.5792 (mt-10) REVERT: 1U 51 GLN cc_start: 0.6524 (tm-30) cc_final: 0.6246 (tm-30) REVERT: 1V 77 PHE cc_start: 0.8386 (t80) cc_final: 0.7847 (t80) REVERT: 1W 37 THR cc_start: 0.7970 (p) cc_final: 0.7757 (p) REVERT: 1W 88 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7828 (ttm-80) REVERT: 14 43 PHE cc_start: 0.5173 (t80) cc_final: 0.4428 (p90) REVERT: 15 14 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6980 (mtm) REVERT: 17 28 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.8083 (mtt90) REVERT: 19 4 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8508 (ptp-170) REVERT: 19 37 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7593 (tt0) REVERT: 1d 46 ARG cc_start: 0.5935 (tpt90) cc_final: 0.5331 (tpp-160) REVERT: 1d 201 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.5982 (tp30) REVERT: 1e 135 VAL cc_start: 0.8265 (m) cc_final: 0.8046 (t) REVERT: 1f 55 HIS cc_start: 0.7241 (OUTLIER) cc_final: 0.6864 (m170) REVERT: 1f 75 GLU cc_start: 0.6484 (mm-30) cc_final: 0.6164 (mm-30) REVERT: 1g 30 MET cc_start: 0.6110 (mmm) cc_final: 0.5842 (tpt) REVERT: 1g 49 LEU cc_start: 0.8193 (pp) cc_final: 0.7882 (pp) REVERT: 1g 98 LEU cc_start: 0.8408 (tp) cc_final: 0.8062 (tp) REVERT: 1g 102 TRP cc_start: 0.7790 (m-10) cc_final: 0.7548 (m-10) REVERT: 1g 135 LYS cc_start: 0.6869 (mmtm) cc_final: 0.6276 (tptt) REVERT: 1g 142 ARG cc_start: 0.6556 (mmp80) cc_final: 0.6008 (tpp80) REVERT: 1i 47 VAL cc_start: 0.7400 (p) cc_final: 0.7149 (m) REVERT: 1k 105 ARG cc_start: 0.4636 (tpp80) cc_final: 0.4373 (ttm-80) REVERT: 1m 102 LYS cc_start: 0.8368 (tttp) cc_final: 0.7666 (mtpt) REVERT: 1n 13 ARG cc_start: 0.6446 (OUTLIER) cc_final: 0.5946 (mtm110) REVERT: 1u 35 GLU cc_start: 0.7162 (tp30) cc_final: 0.6960 (tp30) outliers start: 329 outliers final: 186 residues processed: 1729 average time/residue: 1.3511 time to fit residues: 4027.7730 Evaluate side-chains 1549 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1356 time to evaluate : 5.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1D residue 53 ILE Chi-restraints excluded: chain 1D residue 57 HIS Chi-restraints excluded: chain 1D residue 77 VAL Chi-restraints excluded: chain 1D residue 139 THR Chi-restraints excluded: chain 1D residue 140 VAL Chi-restraints excluded: chain 1D residue 171 VAL Chi-restraints excluded: chain 1D residue 183 VAL Chi-restraints excluded: chain 1E residue 5 VAL Chi-restraints excluded: chain 1E residue 16 THR Chi-restraints excluded: chain 1E residue 25 THR Chi-restraints excluded: chain 1E residue 34 VAL Chi-restraints excluded: chain 1E residue 51 THR Chi-restraints excluded: chain 1E residue 58 ASN Chi-restraints excluded: chain 1E residue 91 THR Chi-restraints excluded: chain 1E residue 112 THR Chi-restraints excluded: chain 1E residue 122 VAL Chi-restraints excluded: chain 1E residue 145 SER Chi-restraints excluded: chain 1E residue 165 MET Chi-restraints excluded: chain 1E residue 170 VAL Chi-restraints excluded: chain 1E residue 180 VAL Chi-restraints excluded: chain 1E residue 207 VAL Chi-restraints excluded: chain 1E residue 208 LYS Chi-restraints excluded: chain 1F residue 48 THR Chi-restraints excluded: chain 1F residue 53 THR Chi-restraints excluded: chain 1F residue 92 HIS Chi-restraints excluded: chain 1F residue 105 LEU Chi-restraints excluded: chain 1F residue 131 THR Chi-restraints excluded: chain 1F residue 138 LEU Chi-restraints excluded: chain 1F residue 176 ASP Chi-restraints excluded: chain 1F residue 188 MET Chi-restraints excluded: chain 1G residue 56 LEU Chi-restraints excluded: chain 1G residue 84 ILE Chi-restraints excluded: chain 1H residue 36 LEU Chi-restraints excluded: chain 1H residue 37 ASN Chi-restraints excluded: chain 1H residue 42 VAL Chi-restraints excluded: chain 1H residue 48 THR Chi-restraints excluded: chain 1H residue 132 LEU Chi-restraints excluded: chain 1I residue 19 VAL Chi-restraints excluded: chain 1I residue 44 ILE Chi-restraints excluded: chain 1I residue 61 VAL Chi-restraints excluded: chain 1J residue 123 ILE Chi-restraints excluded: chain 1K residue 57 VAL Chi-restraints excluded: chain 1K residue 59 THR Chi-restraints excluded: chain 1K residue 120 ASP Chi-restraints excluded: chain 1N residue 64 VAL Chi-restraints excluded: chain 1N residue 84 ILE Chi-restraints excluded: chain 1O residue 20 MET Chi-restraints excluded: chain 1O residue 21 CYS Chi-restraints excluded: chain 1O residue 24 VAL Chi-restraints excluded: chain 1O residue 29 HIS Chi-restraints excluded: chain 1O residue 57 VAL Chi-restraints excluded: chain 1O residue 61 VAL Chi-restraints excluded: chain 1O residue 65 THR Chi-restraints excluded: chain 1O residue 69 VAL Chi-restraints excluded: chain 1O residue 111 LYS Chi-restraints excluded: chain 1P residue 109 LYS Chi-restraints excluded: chain 1P residue 121 THR Chi-restraints excluded: chain 1Q residue 42 THR Chi-restraints excluded: chain 1Q residue 89 VAL Chi-restraints excluded: chain 1Q residue 105 MET Chi-restraints excluded: chain 1Q residue 108 VAL Chi-restraints excluded: chain 1Q residue 110 GLU Chi-restraints excluded: chain 1R residue 1 MET Chi-restraints excluded: chain 1R residue 13 ASN Chi-restraints excluded: chain 1R residue 23 ASN Chi-restraints excluded: chain 1R residue 24 MET Chi-restraints excluded: chain 1R residue 33 ILE Chi-restraints excluded: chain 1R residue 37 THR Chi-restraints excluded: chain 1S residue 12 THR Chi-restraints excluded: chain 1S residue 35 ILE Chi-restraints excluded: chain 1S residue 65 THR Chi-restraints excluded: chain 1T residue 23 ASP Chi-restraints excluded: chain 1T residue 79 VAL Chi-restraints excluded: chain 1T residue 84 SER Chi-restraints excluded: chain 1T residue 85 VAL Chi-restraints excluded: chain 1U residue 8 ILE Chi-restraints excluded: chain 1V residue 14 VAL Chi-restraints excluded: chain 1V residue 94 THR Chi-restraints excluded: chain 1W residue 22 ASP Chi-restraints excluded: chain 1W residue 74 ILE Chi-restraints excluded: chain 1W residue 96 ILE Chi-restraints excluded: chain 1W residue 105 VAL Chi-restraints excluded: chain 1W residue 108 SER Chi-restraints excluded: chain 1X residue 25 GLU Chi-restraints excluded: chain 1Y residue 11 ILE Chi-restraints excluded: chain 1Y residue 48 VAL Chi-restraints excluded: chain 1Y residue 51 LEU Chi-restraints excluded: chain 1Y residue 57 ILE Chi-restraints excluded: chain 1Y residue 58 VAL Chi-restraints excluded: chain 1Y residue 66 VAL Chi-restraints excluded: chain 1Y residue 82 VAL Chi-restraints excluded: chain 1Z residue 47 VAL Chi-restraints excluded: chain 1Z residue 63 ILE Chi-restraints excluded: chain 1Z residue 64 VAL Chi-restraints excluded: chain 10 residue 42 HIS Chi-restraints excluded: chain 10 residue 49 CYS Chi-restraints excluded: chain 11 residue 3 VAL Chi-restraints excluded: chain 11 residue 12 VAL Chi-restraints excluded: chain 11 residue 15 ASN Chi-restraints excluded: chain 11 residue 39 VAL Chi-restraints excluded: chain 11 residue 58 ILE Chi-restraints excluded: chain 12 residue 19 LEU Chi-restraints excluded: chain 12 residue 42 LEU Chi-restraints excluded: chain 12 residue 55 THR Chi-restraints excluded: chain 13 residue 6 ILE Chi-restraints excluded: chain 13 residue 13 ILE Chi-restraints excluded: chain 13 residue 54 VAL Chi-restraints excluded: chain 15 residue 10 SER Chi-restraints excluded: chain 15 residue 14 MET Chi-restraints excluded: chain 15 residue 24 VAL Chi-restraints excluded: chain 18 residue 6 VAL Chi-restraints excluded: chain 19 residue 4 ARG Chi-restraints excluded: chain 19 residue 26 ILE Chi-restraints excluded: chain 1b residue 71 THR Chi-restraints excluded: chain 1b residue 185 ILE Chi-restraints excluded: chain 1b residue 186 VAL Chi-restraints excluded: chain 1b residue 188 THR Chi-restraints excluded: chain 1c residue 9 ILE Chi-restraints excluded: chain 1c residue 55 VAL Chi-restraints excluded: chain 1c residue 74 ILE Chi-restraints excluded: chain 1c residue 137 VAL Chi-restraints excluded: chain 1c residue 181 ILE Chi-restraints excluded: chain 1c residue 199 VAL Chi-restraints excluded: chain 1d residue 10 LEU Chi-restraints excluded: chain 1d residue 158 LEU Chi-restraints excluded: chain 1d residue 172 VAL Chi-restraints excluded: chain 1d residue 200 VAL Chi-restraints excluded: chain 1d residue 201 GLU Chi-restraints excluded: chain 1e residue 17 VAL Chi-restraints excluded: chain 1e residue 35 LEU Chi-restraints excluded: chain 1e residue 80 LEU Chi-restraints excluded: chain 1e residue 89 THR Chi-restraints excluded: chain 1e residue 113 VAL Chi-restraints excluded: chain 1e residue 115 GLU Chi-restraints excluded: chain 1e residue 119 VAL Chi-restraints excluded: chain 1e residue 121 ASN Chi-restraints excluded: chain 1f residue 10 VAL Chi-restraints excluded: chain 1f residue 55 HIS Chi-restraints excluded: chain 1g residue 22 LEU Chi-restraints excluded: chain 1g residue 72 VAL Chi-restraints excluded: chain 1g residue 93 VAL Chi-restraints excluded: chain 1g residue 115 MET Chi-restraints excluded: chain 1h residue 10 LEU Chi-restraints excluded: chain 1h residue 33 VAL Chi-restraints excluded: chain 1h residue 58 LEU Chi-restraints excluded: chain 1h residue 88 LYS Chi-restraints excluded: chain 1h residue 103 VAL Chi-restraints excluded: chain 1h residue 124 ILE Chi-restraints excluded: chain 1i residue 108 ARG Chi-restraints excluded: chain 1i residue 115 VAL Chi-restraints excluded: chain 1j residue 52 LEU Chi-restraints excluded: chain 1k residue 25 SER Chi-restraints excluded: chain 1k residue 29 THR Chi-restraints excluded: chain 1k residue 81 LEU Chi-restraints excluded: chain 1k residue 107 THR Chi-restraints excluded: chain 1k residue 109 ILE Chi-restraints excluded: chain 1k residue 124 LYS Chi-restraints excluded: chain 1l residue 3 VAL Chi-restraints excluded: chain 1l residue 20 VAL Chi-restraints excluded: chain 1l residue 32 VAL Chi-restraints excluded: chain 1l residue 51 VAL Chi-restraints excluded: chain 1l residue 86 VAL Chi-restraints excluded: chain 1m residue 24 VAL Chi-restraints excluded: chain 1m residue 33 LEU Chi-restraints excluded: chain 1m residue 54 THR Chi-restraints excluded: chain 1m residue 73 SER Chi-restraints excluded: chain 1m residue 96 VAL Chi-restraints excluded: chain 1m residue 103 THR Chi-restraints excluded: chain 1n residue 13 ARG Chi-restraints excluded: chain 1n residue 27 LEU Chi-restraints excluded: chain 1o residue 28 VAL Chi-restraints excluded: chain 1o residue 59 VAL Chi-restraints excluded: chain 1p residue 2 VAL Chi-restraints excluded: chain 1p residue 19 VAL Chi-restraints excluded: chain 1p residue 34 GLU Chi-restraints excluded: chain 1p residue 36 VAL Chi-restraints excluded: chain 1p residue 54 LEU Chi-restraints excluded: chain 1p residue 61 VAL Chi-restraints excluded: chain 1q residue 40 THR Chi-restraints excluded: chain 1q residue 49 ASN Chi-restraints excluded: chain 1q residue 56 ASP Chi-restraints excluded: chain 1q residue 78 VAL Chi-restraints excluded: chain 1r residue 30 ASN Chi-restraints excluded: chain 1r residue 44 THR Chi-restraints excluded: chain 1s residue 3 SER Chi-restraints excluded: chain 1s residue 10 ILE Chi-restraints excluded: chain 1s residue 11 ASP Chi-restraints excluded: chain 1s residue 18 VAL Chi-restraints excluded: chain 1s residue 38 THR Chi-restraints excluded: chain 1s residue 42 ASN Chi-restraints excluded: chain 1t residue 22 SER Chi-restraints excluded: chain 1t residue 60 GLN Chi-restraints excluded: chain 1w residue 510 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 991 optimal weight: 1.9990 chunk 754 optimal weight: 40.0000 chunk 520 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 478 optimal weight: 9.9990 chunk 673 optimal weight: 10.0000 chunk 1007 optimal weight: 0.9990 chunk 1066 optimal weight: 0.0070 chunk 526 optimal weight: 6.9990 chunk 954 optimal weight: 7.9990 chunk 287 optimal weight: 10.0000 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1E 49 GLN 1E 94 GLN 1E 130 GLN ** 1G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1H 47 ASN ** 1H 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1N 40 HIS ** 1N 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1P 104 GLN 1R 31 HIS 1S 98 GLN 1T 2 ASN 1T 6 GLN 1T 11 GLN 1U 19 GLN ** 1U 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1V 66 HIS 1W 57 ASN ** 1X 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1Z 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11 22 ASN ** 19 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1b 41 ASN 1b 176 ASN ** 1c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1e 11 GLN ** 1e 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1h 17 GLN ** 1k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1k 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1l 5 GLN 1l 71 HIS 1m 104 ASN 1p 63 GLN 1r 73 HIS ** 1t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 161532 Z= 0.207 Angle : 0.682 27.058 240827 Z= 0.365 Chirality : 0.038 2.040 30226 Planarity : 0.006 0.126 13517 Dihedral : 23.059 179.963 79659 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.78 % Allowed : 7.04 % Favored : 92.18 % Rotamer: Outliers : 5.86 % Allowed : 21.21 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.10), residues: 6550 helix: -0.33 (0.11), residues: 1944 sheet: -2.63 (0.14), residues: 1031 loop : -1.22 (0.10), residues: 3575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP1c 21 HIS 0.019 0.002 HIS1N 40 PHE 0.026 0.002 PHE1P 64 TYR 0.029 0.002 TYR1n 20 ARG 0.015 0.001 ARG1R 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1740 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1457 time to evaluate : 6.233 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: 1D 57 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7373 (t-90) REVERT: 1E 64 GLU cc_start: 0.6080 (pt0) cc_final: 0.5711 (pt0) REVERT: 1E 161 MET cc_start: 0.7378 (tpp) cc_final: 0.7111 (mtp) REVERT: 1E 201 LEU cc_start: 0.8157 (mt) cc_final: 0.7874 (mt) REVERT: 1F 47 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8167 (ptpt) REVERT: 1G 15 LEU cc_start: 0.7429 (mm) cc_final: 0.7160 (mm) REVERT: 1H 33 THR cc_start: 0.7541 (OUTLIER) cc_final: 0.7249 (t) REVERT: 1H 106 LEU cc_start: 0.5435 (mt) cc_final: 0.5207 (mt) REVERT: 1K 71 LYS cc_start: 0.7750 (ttpp) cc_final: 0.6723 (mppt) REVERT: 1N 15 TRP cc_start: 0.8725 (m100) cc_final: 0.8315 (m100) REVERT: 1O 13 ASN cc_start: 0.7802 (p0) cc_final: 0.6964 (p0) REVERT: 1P 36 LYS cc_start: 0.9101 (mttt) cc_final: 0.8478 (mmtt) REVERT: 1P 78 ARG cc_start: 0.6255 (mtp-110) cc_final: 0.5777 (mtp-110) REVERT: 1Q 1 MET cc_start: 0.6219 (ptp) cc_final: 0.5790 (ptm) REVERT: 1Q 40 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7887 (ptm160) REVERT: 1Q 104 GLU cc_start: 0.6025 (mt-10) cc_final: 0.5752 (mt-10) REVERT: 1R 24 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7233 (ttp) REVERT: 1U 51 GLN cc_start: 0.5924 (tm-30) cc_final: 0.5438 (tm-30) REVERT: 1V 66 HIS cc_start: 0.5670 (OUTLIER) cc_final: 0.5427 (m90) REVERT: 1V 77 PHE cc_start: 0.8319 (t80) cc_final: 0.7781 (t80) REVERT: 1W 88 ARG cc_start: 0.8063 (mmm-85) cc_final: 0.7743 (ttm-80) REVERT: 1W 95 ARG cc_start: 0.7864 (ttp-110) cc_final: 0.7642 (mtp-110) REVERT: 1Y 68 ASN cc_start: 0.6809 (m-40) cc_final: 0.6533 (m110) REVERT: 14 43 PHE cc_start: 0.5014 (t80) cc_final: 0.4185 (p90) REVERT: 17 19 ARG cc_start: 0.8333 (mtp85) cc_final: 0.8047 (mmm-85) REVERT: 18 28 LEU cc_start: 0.8685 (tp) cc_final: 0.8324 (tp) REVERT: 19 4 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8283 (ptp-170) REVERT: 19 37 GLN cc_start: 0.7948 (tp-100) cc_final: 0.7699 (tt0) REVERT: 1b 174 GLU cc_start: 0.6870 (tt0) cc_final: 0.6094 (tt0) REVERT: 1d 46 ARG cc_start: 0.5902 (tpt90) cc_final: 0.5289 (tpp-160) REVERT: 1d 57 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6931 (tttt) REVERT: 1d 201 GLU cc_start: 0.6141 (mm-30) cc_final: 0.5829 (tp30) REVERT: 1e 96 GLN cc_start: 0.6219 (OUTLIER) cc_final: 0.5926 (tp40) REVERT: 1f 47 LEU cc_start: 0.7873 (mm) cc_final: 0.7295 (mt) REVERT: 1g 135 LYS cc_start: 0.6906 (mmtm) cc_final: 0.6442 (tptt) REVERT: 1h 110 MET cc_start: 0.7951 (pmm) cc_final: 0.7477 (pmm) REVERT: 1k 105 ARG cc_start: 0.4766 (tpp80) cc_final: 0.4477 (ttm-80) REVERT: 1k 108 ASN cc_start: 0.7641 (p0) cc_final: 0.7405 (p0) REVERT: 1m 102 LYS cc_start: 0.8235 (tttp) cc_final: 0.7703 (mtpt) REVERT: 1m 109 LYS cc_start: 0.7339 (tttt) cc_final: 0.6976 (tttp) outliers start: 283 outliers final: 182 residues processed: 1597 average time/residue: 1.3177 time to fit residues: 3617.9690 Evaluate side-chains 1537 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1346 time to evaluate : 6.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1D residue 53 ILE Chi-restraints excluded: chain 1D residue 57 HIS Chi-restraints excluded: chain 1D residue 139 THR Chi-restraints excluded: chain 1D residue 171 VAL Chi-restraints excluded: chain 1D residue 183 VAL Chi-restraints excluded: chain 1E residue 14 ILE Chi-restraints excluded: chain 1E residue 22 ILE Chi-restraints excluded: chain 1E residue 25 THR Chi-restraints excluded: chain 1E residue 51 THR Chi-restraints excluded: chain 1E residue 58 ASN Chi-restraints excluded: chain 1E residue 91 THR Chi-restraints excluded: chain 1E residue 109 VAL Chi-restraints excluded: chain 1E residue 113 SER Chi-restraints excluded: chain 1E residue 145 SER Chi-restraints excluded: chain 1E residue 170 VAL Chi-restraints excluded: chain 1E residue 180 VAL Chi-restraints excluded: chain 1E residue 189 VAL Chi-restraints excluded: chain 1E residue 208 LYS Chi-restraints excluded: chain 1F residue 47 LYS Chi-restraints excluded: chain 1F residue 48 THR Chi-restraints excluded: chain 1F residue 70 SER Chi-restraints excluded: chain 1F residue 84 THR Chi-restraints excluded: chain 1F residue 92 HIS Chi-restraints excluded: chain 1F residue 95 LYS Chi-restraints excluded: chain 1F residue 105 LEU Chi-restraints excluded: chain 1F residue 131 THR Chi-restraints excluded: chain 1F residue 176 ASP Chi-restraints excluded: chain 1F residue 188 MET Chi-restraints excluded: chain 1G residue 3 LEU Chi-restraints excluded: chain 1G residue 56 LEU Chi-restraints excluded: chain 1G residue 140 ILE Chi-restraints excluded: chain 1H residue 33 THR Chi-restraints excluded: chain 1H residue 36 LEU Chi-restraints excluded: chain 1H residue 46 ASP Chi-restraints excluded: chain 1H residue 83 THR Chi-restraints excluded: chain 1H residue 132 LEU Chi-restraints excluded: chain 1I residue 3 VAL Chi-restraints excluded: chain 1I residue 19 VAL Chi-restraints excluded: chain 1I residue 37 VAL Chi-restraints excluded: chain 1I residue 44 ILE Chi-restraints excluded: chain 1I residue 134 VAL Chi-restraints excluded: chain 1J residue 123 ILE Chi-restraints excluded: chain 1K residue 59 THR Chi-restraints excluded: chain 1K residue 85 ILE Chi-restraints excluded: chain 1K residue 120 ASP Chi-restraints excluded: chain 1N residue 45 THR Chi-restraints excluded: chain 1N residue 64 VAL Chi-restraints excluded: chain 1N residue 84 ILE Chi-restraints excluded: chain 1O residue 29 HIS Chi-restraints excluded: chain 1O residue 65 THR Chi-restraints excluded: chain 1O residue 69 VAL Chi-restraints excluded: chain 1P residue 82 LEU Chi-restraints excluded: chain 1P residue 109 LYS Chi-restraints excluded: chain 1Q residue 7 THR Chi-restraints excluded: chain 1Q residue 12 MET Chi-restraints excluded: chain 1Q residue 40 ARG Chi-restraints excluded: chain 1Q residue 42 THR Chi-restraints excluded: chain 1Q residue 96 ILE Chi-restraints excluded: chain 1Q residue 105 MET Chi-restraints excluded: chain 1R residue 1 MET Chi-restraints excluded: chain 1R residue 13 ASN Chi-restraints excluded: chain 1R residue 15 SER Chi-restraints excluded: chain 1R residue 18 GLN Chi-restraints excluded: chain 1R residue 24 MET Chi-restraints excluded: chain 1R residue 37 THR Chi-restraints excluded: chain 1R residue 48 VAL Chi-restraints excluded: chain 1S residue 12 THR Chi-restraints excluded: chain 1S residue 39 VAL Chi-restraints excluded: chain 1S residue 47 VAL Chi-restraints excluded: chain 1T residue 7 LEU Chi-restraints excluded: chain 1T residue 43 GLU Chi-restraints excluded: chain 1T residue 47 ILE Chi-restraints excluded: chain 1T residue 79 VAL Chi-restraints excluded: chain 1T residue 84 SER Chi-restraints excluded: chain 1U residue 8 ILE Chi-restraints excluded: chain 1V residue 22 LEU Chi-restraints excluded: chain 1V residue 60 LYS Chi-restraints excluded: chain 1V residue 66 HIS Chi-restraints excluded: chain 1W residue 22 ASP Chi-restraints excluded: chain 1W residue 57 ASN Chi-restraints excluded: chain 1W residue 62 ASP Chi-restraints excluded: chain 1W residue 74 ILE Chi-restraints excluded: chain 1W residue 77 ASP Chi-restraints excluded: chain 1W residue 105 VAL Chi-restraints excluded: chain 1W residue 108 SER Chi-restraints excluded: chain 1Y residue 4 ILE Chi-restraints excluded: chain 1Y residue 33 VAL Chi-restraints excluded: chain 1Y residue 48 VAL Chi-restraints excluded: chain 1Y residue 51 LEU Chi-restraints excluded: chain 1Y residue 57 ILE Chi-restraints excluded: chain 1Y residue 58 VAL Chi-restraints excluded: chain 1Z residue 60 VAL Chi-restraints excluded: chain 1Z residue 63 ILE Chi-restraints excluded: chain 1Z residue 64 VAL Chi-restraints excluded: chain 1Z residue 77 VAL Chi-restraints excluded: chain 1Z residue 90 ASP Chi-restraints excluded: chain 10 residue 12 SER Chi-restraints excluded: chain 10 residue 32 ILE Chi-restraints excluded: chain 10 residue 42 HIS Chi-restraints excluded: chain 10 residue 63 VAL Chi-restraints excluded: chain 11 residue 3 VAL Chi-restraints excluded: chain 11 residue 39 VAL Chi-restraints excluded: chain 12 residue 19 LEU Chi-restraints excluded: chain 12 residue 42 LEU Chi-restraints excluded: chain 12 residue 55 THR Chi-restraints excluded: chain 13 residue 31 ILE Chi-restraints excluded: chain 15 residue 5 ASN Chi-restraints excluded: chain 15 residue 43 THR Chi-restraints excluded: chain 17 residue 9 VAL Chi-restraints excluded: chain 18 residue 6 VAL Chi-restraints excluded: chain 18 residue 53 ASP Chi-restraints excluded: chain 18 residue 61 LEU Chi-restraints excluded: chain 19 residue 4 ARG Chi-restraints excluded: chain 19 residue 26 ILE Chi-restraints excluded: chain 1b residue 71 THR Chi-restraints excluded: chain 1b residue 93 HIS Chi-restraints excluded: chain 1b residue 185 ILE Chi-restraints excluded: chain 1b residue 186 VAL Chi-restraints excluded: chain 1c residue 9 ILE Chi-restraints excluded: chain 1c residue 10 ARG Chi-restraints excluded: chain 1c residue 43 THR Chi-restraints excluded: chain 1c residue 55 VAL Chi-restraints excluded: chain 1c residue 105 VAL Chi-restraints excluded: chain 1c residue 199 VAL Chi-restraints excluded: chain 1d residue 57 LYS Chi-restraints excluded: chain 1d residue 87 GLU Chi-restraints excluded: chain 1d residue 116 LEU Chi-restraints excluded: chain 1d residue 158 LEU Chi-restraints excluded: chain 1d residue 200 VAL Chi-restraints excluded: chain 1e residue 17 VAL Chi-restraints excluded: chain 1e residue 35 LEU Chi-restraints excluded: chain 1e residue 80 LEU Chi-restraints excluded: chain 1e residue 96 GLN Chi-restraints excluded: chain 1e residue 115 GLU Chi-restraints excluded: chain 1e residue 121 ASN Chi-restraints excluded: chain 1f residue 18 VAL Chi-restraints excluded: chain 1g residue 6 ILE Chi-restraints excluded: chain 1g residue 14 ASP Chi-restraints excluded: chain 1g residue 21 LEU Chi-restraints excluded: chain 1g residue 31 VAL Chi-restraints excluded: chain 1g residue 42 VAL Chi-restraints excluded: chain 1g residue 58 LEU Chi-restraints excluded: chain 1g residue 84 TYR Chi-restraints excluded: chain 1g residue 93 VAL Chi-restraints excluded: chain 1g residue 115 MET Chi-restraints excluded: chain 1h residue 10 LEU Chi-restraints excluded: chain 1h residue 13 ILE Chi-restraints excluded: chain 1h residue 33 VAL Chi-restraints excluded: chain 1h residue 47 ASP Chi-restraints excluded: chain 1h residue 58 LEU Chi-restraints excluded: chain 1h residue 88 LYS Chi-restraints excluded: chain 1h residue 103 VAL Chi-restraints excluded: chain 1h residue 120 LEU Chi-restraints excluded: chain 1j residue 52 LEU Chi-restraints excluded: chain 1k residue 25 SER Chi-restraints excluded: chain 1k residue 58 THR Chi-restraints excluded: chain 1k residue 78 ILE Chi-restraints excluded: chain 1k residue 109 ILE Chi-restraints excluded: chain 1l residue 5 GLN Chi-restraints excluded: chain 1l residue 6 LEU Chi-restraints excluded: chain 1l residue 7 VAL Chi-restraints excluded: chain 1l residue 20 VAL Chi-restraints excluded: chain 1l residue 64 SER Chi-restraints excluded: chain 1l residue 86 VAL Chi-restraints excluded: chain 1m residue 24 VAL Chi-restraints excluded: chain 1m residue 33 LEU Chi-restraints excluded: chain 1m residue 73 SER Chi-restraints excluded: chain 1m residue 76 ILE Chi-restraints excluded: chain 1m residue 96 VAL Chi-restraints excluded: chain 1m residue 103 THR Chi-restraints excluded: chain 1n residue 67 THR Chi-restraints excluded: chain 1o residue 59 VAL Chi-restraints excluded: chain 1p residue 2 VAL Chi-restraints excluded: chain 1p residue 19 VAL Chi-restraints excluded: chain 1p residue 34 GLU Chi-restraints excluded: chain 1p residue 36 VAL Chi-restraints excluded: chain 1p residue 50 THR Chi-restraints excluded: chain 1p residue 61 VAL Chi-restraints excluded: chain 1p residue 68 SER Chi-restraints excluded: chain 1q residue 56 ASP Chi-restraints excluded: chain 1r residue 39 VAL Chi-restraints excluded: chain 1r residue 44 THR Chi-restraints excluded: chain 1s residue 3 SER Chi-restraints excluded: chain 1s residue 10 ILE Chi-restraints excluded: chain 1s residue 11 ASP Chi-restraints excluded: chain 1s residue 22 VAL Chi-restraints excluded: chain 1s residue 34 SER Chi-restraints excluded: chain 1s residue 38 THR Chi-restraints excluded: chain 1s residue 59 VAL Chi-restraints excluded: chain 1t residue 11 ILE Chi-restraints excluded: chain 1t residue 19 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 887 optimal weight: 0.6980 chunk 605 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 793 optimal weight: 10.0000 chunk 439 optimal weight: 9.9990 chunk 909 optimal weight: 2.9990 chunk 736 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 544 optimal weight: 0.9980 chunk 956 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1E 49 GLN 1E 94 GLN ** 1F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1H 47 ASN ** 1H 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1N 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1N 128 ASN ** 1P 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1R 31 HIS 1S 98 GLN 1T 2 ASN 1T 11 GLN ** 1V 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1W 9 HIS 1W 61 ASN ** 1X 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 22 ASN ** 13 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1b 176 ASN ** 1c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1d 70 GLN ** 1d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1e 11 GLN 1e 72 ASN 1e 81 GLN ** 1e 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1h 15 ASN 1h 17 GLN 1i 80 HIS 1k 14 GLN 1k 28 ASN ** 1k 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1m 51 GLN ** 1t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.6770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 161532 Z= 0.232 Angle : 0.697 27.238 240827 Z= 0.370 Chirality : 0.038 2.031 30226 Planarity : 0.006 0.126 13517 Dihedral : 23.066 179.408 79659 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.05 % Favored : 91.19 % Rotamer: Outliers : 6.52 % Allowed : 22.20 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.10), residues: 6550 helix: -0.12 (0.12), residues: 1921 sheet: -2.35 (0.14), residues: 1063 loop : -1.28 (0.10), residues: 3566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP1Q 64 HIS 0.055 0.002 HIS1V 66 PHE 0.025 0.002 PHE1Y 72 TYR 0.044 0.002 TYR1d 74 ARG 0.015 0.001 ARG1l 109 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1775 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1460 time to evaluate : 6.462 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: 1D 57 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7342 (t-90) REVERT: 1D 145 MET cc_start: 0.6658 (mmm) cc_final: 0.6336 (mmm) REVERT: 1E 64 GLU cc_start: 0.5756 (pt0) cc_final: 0.5334 (pt0) REVERT: 1E 161 MET cc_start: 0.7422 (tpp) cc_final: 0.7163 (mtp) REVERT: 1E 201 LEU cc_start: 0.8038 (mt) cc_final: 0.7837 (mt) REVERT: 1F 47 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8068 (ptpt) REVERT: 1G 97 GLU cc_start: 0.6959 (tt0) cc_final: 0.6696 (tt0) REVERT: 1H 33 THR cc_start: 0.7367 (OUTLIER) cc_final: 0.6908 (t) REVERT: 1H 40 VAL cc_start: 0.6722 (OUTLIER) cc_final: 0.6494 (p) REVERT: 1K 85 ILE cc_start: 0.2401 (OUTLIER) cc_final: 0.2135 (pt) REVERT: 1N 15 TRP cc_start: 0.8729 (m100) cc_final: 0.8289 (m100) REVERT: 1N 43 GLU cc_start: 0.6325 (pm20) cc_final: 0.5928 (pt0) REVERT: 1N 80 HIS cc_start: 0.7545 (t-90) cc_final: 0.7303 (t-170) REVERT: 1O 13 ASN cc_start: 0.7775 (p0) cc_final: 0.6888 (p0) REVERT: 1P 36 LYS cc_start: 0.9054 (mttt) cc_final: 0.8548 (mmtt) REVERT: 1Q 40 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7860 (ptm160) REVERT: 1Q 117 PHE cc_start: 0.7505 (m-80) cc_final: 0.6853 (m-10) REVERT: 1R 28 LEU cc_start: 0.8644 (tp) cc_final: 0.8343 (tp) REVERT: 1S 10 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6685 (ttp-170) REVERT: 1S 13 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.5511 (ptp-170) REVERT: 1V 77 PHE cc_start: 0.8378 (t80) cc_final: 0.7950 (t80) REVERT: 1Y 25 LYS cc_start: 0.6316 (tppt) cc_final: 0.6036 (tppp) REVERT: 1Z 19 ARG cc_start: 0.6028 (ttm110) cc_final: 0.5821 (ttm110) REVERT: 14 43 PHE cc_start: 0.5081 (t80) cc_final: 0.4105 (p90) REVERT: 17 19 ARG cc_start: 0.8378 (mtp85) cc_final: 0.8092 (mmm-85) REVERT: 19 4 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8306 (ptp-170) REVERT: 19 37 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7629 (tt0) REVERT: 1b 112 ARG cc_start: 0.5139 (ttt180) cc_final: 0.4746 (ttt180) REVERT: 1b 174 GLU cc_start: 0.6953 (tt0) cc_final: 0.6042 (tt0) REVERT: 1d 46 ARG cc_start: 0.6047 (tpt90) cc_final: 0.5594 (ttm170) REVERT: 1d 57 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7321 (tttt) REVERT: 1e 96 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.6051 (tp40) REVERT: 1f 55 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.6972 (m170) REVERT: 1g 49 LEU cc_start: 0.8118 (pp) cc_final: 0.7688 (pp) REVERT: 1h 104 SER cc_start: 0.7356 (t) cc_final: 0.7095 (p) REVERT: 1l 5 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7937 (pt0) REVERT: 1m 8 ILE cc_start: 0.5100 (mp) cc_final: 0.4841 (mp) outliers start: 315 outliers final: 221 residues processed: 1619 average time/residue: 1.3281 time to fit residues: 3720.0081 Evaluate side-chains 1602 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1368 time to evaluate : 6.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1D residue 53 ILE Chi-restraints excluded: chain 1D residue 57 HIS Chi-restraints excluded: chain 1D residue 85 ASN Chi-restraints excluded: chain 1D residue 139 THR Chi-restraints excluded: chain 1D residue 171 VAL Chi-restraints excluded: chain 1D residue 183 VAL Chi-restraints excluded: chain 1D residue 212 TRP Chi-restraints excluded: chain 1E residue 14 ILE Chi-restraints excluded: chain 1E residue 22 ILE Chi-restraints excluded: chain 1E residue 25 THR Chi-restraints excluded: chain 1E residue 51 THR Chi-restraints excluded: chain 1E residue 58 ASN Chi-restraints excluded: chain 1E residue 61 THR Chi-restraints excluded: chain 1E residue 91 THR Chi-restraints excluded: chain 1E residue 109 VAL Chi-restraints excluded: chain 1E residue 113 SER Chi-restraints excluded: chain 1E residue 145 SER Chi-restraints excluded: chain 1E residue 178 VAL Chi-restraints excluded: chain 1E residue 180 VAL Chi-restraints excluded: chain 1E residue 189 VAL Chi-restraints excluded: chain 1E residue 200 ASP Chi-restraints excluded: chain 1E residue 207 VAL Chi-restraints excluded: chain 1F residue 31 VAL Chi-restraints excluded: chain 1F residue 47 LYS Chi-restraints excluded: chain 1F residue 48 THR Chi-restraints excluded: chain 1F residue 70 SER Chi-restraints excluded: chain 1F residue 92 HIS Chi-restraints excluded: chain 1F residue 95 LYS Chi-restraints excluded: chain 1F residue 131 THR Chi-restraints excluded: chain 1F residue 176 ASP Chi-restraints excluded: chain 1G residue 3 LEU Chi-restraints excluded: chain 1G residue 133 GLU Chi-restraints excluded: chain 1G residue 140 ILE Chi-restraints excluded: chain 1H residue 33 THR Chi-restraints excluded: chain 1H residue 36 LEU Chi-restraints excluded: chain 1H residue 37 ASN Chi-restraints excluded: chain 1H residue 40 VAL Chi-restraints excluded: chain 1H residue 66 THR Chi-restraints excluded: chain 1H residue 83 THR Chi-restraints excluded: chain 1H residue 132 LEU Chi-restraints excluded: chain 1H residue 147 LEU Chi-restraints excluded: chain 1I residue 19 VAL Chi-restraints excluded: chain 1I residue 37 VAL Chi-restraints excluded: chain 1I residue 44 ILE Chi-restraints excluded: chain 1J residue 36 ASP Chi-restraints excluded: chain 1J residue 50 VAL Chi-restraints excluded: chain 1J residue 85 SER Chi-restraints excluded: chain 1J residue 108 VAL Chi-restraints excluded: chain 1J residue 123 ILE Chi-restraints excluded: chain 1K residue 10 LEU Chi-restraints excluded: chain 1K residue 59 THR Chi-restraints excluded: chain 1K residue 85 ILE Chi-restraints excluded: chain 1K residue 120 ASP Chi-restraints excluded: chain 1N residue 5 THR Chi-restraints excluded: chain 1N residue 41 LYS Chi-restraints excluded: chain 1N residue 45 THR Chi-restraints excluded: chain 1N residue 64 VAL Chi-restraints excluded: chain 1N residue 76 HIS Chi-restraints excluded: chain 1O residue 4 GLU Chi-restraints excluded: chain 1O residue 29 HIS Chi-restraints excluded: chain 1O residue 57 VAL Chi-restraints excluded: chain 1O residue 61 VAL Chi-restraints excluded: chain 1O residue 65 THR Chi-restraints excluded: chain 1O residue 69 VAL Chi-restraints excluded: chain 1O residue 99 ILE Chi-restraints excluded: chain 1O residue 111 LYS Chi-restraints excluded: chain 1P residue 109 LYS Chi-restraints excluded: chain 1P residue 121 THR Chi-restraints excluded: chain 1Q residue 7 THR Chi-restraints excluded: chain 1Q residue 12 MET Chi-restraints excluded: chain 1Q residue 40 ARG Chi-restraints excluded: chain 1Q residue 42 THR Chi-restraints excluded: chain 1Q residue 110 GLU Chi-restraints excluded: chain 1R residue 1 MET Chi-restraints excluded: chain 1R residue 13 ASN Chi-restraints excluded: chain 1R residue 15 SER Chi-restraints excluded: chain 1R residue 23 ASN Chi-restraints excluded: chain 1R residue 24 MET Chi-restraints excluded: chain 1R residue 33 ILE Chi-restraints excluded: chain 1R residue 37 THR Chi-restraints excluded: chain 1R residue 48 VAL Chi-restraints excluded: chain 1S residue 10 ARG Chi-restraints excluded: chain 1S residue 12 THR Chi-restraints excluded: chain 1S residue 13 ARG Chi-restraints excluded: chain 1S residue 35 ILE Chi-restraints excluded: chain 1S residue 39 VAL Chi-restraints excluded: chain 1S residue 47 VAL Chi-restraints excluded: chain 1S residue 65 THR Chi-restraints excluded: chain 1T residue 7 LEU Chi-restraints excluded: chain 1T residue 47 ILE Chi-restraints excluded: chain 1T residue 79 VAL Chi-restraints excluded: chain 1T residue 85 VAL Chi-restraints excluded: chain 1U residue 8 ILE Chi-restraints excluded: chain 1U residue 24 TYR Chi-restraints excluded: chain 1V residue 14 VAL Chi-restraints excluded: chain 1V residue 22 LEU Chi-restraints excluded: chain 1V residue 33 VAL Chi-restraints excluded: chain 1V residue 54 VAL Chi-restraints excluded: chain 1V residue 60 LYS Chi-restraints excluded: chain 1W residue 22 ASP Chi-restraints excluded: chain 1W residue 49 LYS Chi-restraints excluded: chain 1W residue 74 ILE Chi-restraints excluded: chain 1W residue 77 ASP Chi-restraints excluded: chain 1W residue 96 ILE Chi-restraints excluded: chain 1W residue 105 VAL Chi-restraints excluded: chain 1W residue 108 SER Chi-restraints excluded: chain 1X residue 79 ASP Chi-restraints excluded: chain 1Y residue 33 VAL Chi-restraints excluded: chain 1Y residue 48 VAL Chi-restraints excluded: chain 1Y residue 51 LEU Chi-restraints excluded: chain 1Y residue 57 ILE Chi-restraints excluded: chain 1Y residue 58 VAL Chi-restraints excluded: chain 1Y residue 66 VAL Chi-restraints excluded: chain 1Z residue 60 VAL Chi-restraints excluded: chain 1Z residue 63 ILE Chi-restraints excluded: chain 1Z residue 64 VAL Chi-restraints excluded: chain 1Z residue 77 VAL Chi-restraints excluded: chain 1Z residue 90 ASP Chi-restraints excluded: chain 10 residue 12 SER Chi-restraints excluded: chain 10 residue 13 GLU Chi-restraints excluded: chain 10 residue 32 ILE Chi-restraints excluded: chain 10 residue 42 HIS Chi-restraints excluded: chain 10 residue 49 CYS Chi-restraints excluded: chain 11 residue 3 VAL Chi-restraints excluded: chain 11 residue 12 VAL Chi-restraints excluded: chain 11 residue 15 ASN Chi-restraints excluded: chain 11 residue 39 VAL Chi-restraints excluded: chain 12 residue 11 VAL Chi-restraints excluded: chain 12 residue 19 LEU Chi-restraints excluded: chain 12 residue 21 LEU Chi-restraints excluded: chain 12 residue 42 LEU Chi-restraints excluded: chain 12 residue 55 THR Chi-restraints excluded: chain 13 residue 9 THR Chi-restraints excluded: chain 13 residue 54 VAL Chi-restraints excluded: chain 15 residue 5 ASN Chi-restraints excluded: chain 15 residue 43 THR Chi-restraints excluded: chain 17 residue 9 VAL Chi-restraints excluded: chain 18 residue 6 VAL Chi-restraints excluded: chain 18 residue 53 ASP Chi-restraints excluded: chain 18 residue 56 LEU Chi-restraints excluded: chain 18 residue 61 LEU Chi-restraints excluded: chain 19 residue 4 ARG Chi-restraints excluded: chain 1b residue 41 ASN Chi-restraints excluded: chain 1b residue 45 THR Chi-restraints excluded: chain 1b residue 71 THR Chi-restraints excluded: chain 1b residue 93 HIS Chi-restraints excluded: chain 1b residue 185 ILE Chi-restraints excluded: chain 1b residue 186 VAL Chi-restraints excluded: chain 1c residue 9 ILE Chi-restraints excluded: chain 1c residue 10 ARG Chi-restraints excluded: chain 1c residue 43 THR Chi-restraints excluded: chain 1c residue 55 VAL Chi-restraints excluded: chain 1c residue 114 LEU Chi-restraints excluded: chain 1c residue 181 ILE Chi-restraints excluded: chain 1c residue 199 VAL Chi-restraints excluded: chain 1d residue 57 LYS Chi-restraints excluded: chain 1d residue 61 ARG Chi-restraints excluded: chain 1d residue 116 LEU Chi-restraints excluded: chain 1d residue 142 VAL Chi-restraints excluded: chain 1d residue 158 LEU Chi-restraints excluded: chain 1d residue 172 VAL Chi-restraints excluded: chain 1d residue 200 VAL Chi-restraints excluded: chain 1e residue 17 VAL Chi-restraints excluded: chain 1e residue 31 SER Chi-restraints excluded: chain 1e residue 35 LEU Chi-restraints excluded: chain 1e residue 80 LEU Chi-restraints excluded: chain 1e residue 89 THR Chi-restraints excluded: chain 1e residue 96 GLN Chi-restraints excluded: chain 1e residue 115 GLU Chi-restraints excluded: chain 1e residue 121 ASN Chi-restraints excluded: chain 1f residue 55 HIS Chi-restraints excluded: chain 1g residue 6 ILE Chi-restraints excluded: chain 1g residue 22 LEU Chi-restraints excluded: chain 1g residue 42 VAL Chi-restraints excluded: chain 1g residue 58 LEU Chi-restraints excluded: chain 1g residue 84 TYR Chi-restraints excluded: chain 1g residue 93 VAL Chi-restraints excluded: chain 1g residue 98 LEU Chi-restraints excluded: chain 1g residue 115 MET Chi-restraints excluded: chain 1h residue 10 LEU Chi-restraints excluded: chain 1h residue 33 VAL Chi-restraints excluded: chain 1h residue 47 ASP Chi-restraints excluded: chain 1h residue 58 LEU Chi-restraints excluded: chain 1h residue 88 LYS Chi-restraints excluded: chain 1h residue 103 VAL Chi-restraints excluded: chain 1h residue 124 ILE Chi-restraints excluded: chain 1h residue 128 VAL Chi-restraints excluded: chain 1j residue 50 THR Chi-restraints excluded: chain 1k residue 25 SER Chi-restraints excluded: chain 1k residue 29 THR Chi-restraints excluded: chain 1k residue 58 THR Chi-restraints excluded: chain 1k residue 81 LEU Chi-restraints excluded: chain 1k residue 95 THR Chi-restraints excluded: chain 1k residue 109 ILE Chi-restraints excluded: chain 1k residue 115 ILE Chi-restraints excluded: chain 1l residue 5 GLN Chi-restraints excluded: chain 1l residue 6 LEU Chi-restraints excluded: chain 1l residue 7 VAL Chi-restraints excluded: chain 1l residue 20 VAL Chi-restraints excluded: chain 1l residue 51 VAL Chi-restraints excluded: chain 1l residue 64 SER Chi-restraints excluded: chain 1m residue 24 VAL Chi-restraints excluded: chain 1m residue 33 LEU Chi-restraints excluded: chain 1m residue 64 VAL Chi-restraints excluded: chain 1m residue 73 SER Chi-restraints excluded: chain 1m residue 76 ILE Chi-restraints excluded: chain 1m residue 96 VAL Chi-restraints excluded: chain 1m residue 103 THR Chi-restraints excluded: chain 1m residue 107 THR Chi-restraints excluded: chain 1n residue 67 THR Chi-restraints excluded: chain 1o residue 51 SER Chi-restraints excluded: chain 1o residue 59 VAL Chi-restraints excluded: chain 1p residue 2 VAL Chi-restraints excluded: chain 1p residue 3 THR Chi-restraints excluded: chain 1p residue 19 VAL Chi-restraints excluded: chain 1p residue 29 ASN Chi-restraints excluded: chain 1p residue 36 VAL Chi-restraints excluded: chain 1p residue 61 VAL Chi-restraints excluded: chain 1p residue 66 THR Chi-restraints excluded: chain 1p residue 68 SER Chi-restraints excluded: chain 1p residue 75 ILE Chi-restraints excluded: chain 1q residue 37 ILE Chi-restraints excluded: chain 1q residue 56 ASP Chi-restraints excluded: chain 1r residue 39 VAL Chi-restraints excluded: chain 1r residue 44 THR Chi-restraints excluded: chain 1s residue 3 SER Chi-restraints excluded: chain 1s residue 10 ILE Chi-restraints excluded: chain 1s residue 11 ASP Chi-restraints excluded: chain 1s residue 22 VAL Chi-restraints excluded: chain 1s residue 34 SER Chi-restraints excluded: chain 1s residue 38 THR Chi-restraints excluded: chain 1s residue 59 VAL Chi-restraints excluded: chain 1t residue 11 ILE Chi-restraints excluded: chain 1t residue 19 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 358 optimal weight: 10.0000 chunk 960 optimal weight: 9.9990 chunk 210 optimal weight: 40.0000 chunk 625 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 1067 optimal weight: 20.0000 chunk 885 optimal weight: 0.0970 chunk 494 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 chunk 353 optimal weight: 7.9990 chunk 560 optimal weight: 8.9990 overall best weight: 6.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1D 45 ASN 1D 85 ASN 1E 49 GLN 1F 46 GLN 1F 195 GLN ** 1G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1H 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1N 138 GLN 1O 93 GLN 1P 54 GLN ** 1P 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1R 31 HIS 1T 11 GLN 1W 61 ASN ** 1X 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1Y 44 HIS ** 1Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 15 4 GLN ** 19 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1d 84 ASN 1d 99 ASN 1e 11 GLN 1e 82 HIS 1e 120 HIS ** 1f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.7760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 161532 Z= 0.365 Angle : 0.848 27.115 240827 Z= 0.437 Chirality : 0.044 2.045 30226 Planarity : 0.007 0.132 13517 Dihedral : 23.262 178.658 79659 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.92 % Favored : 90.32 % Rotamer: Outliers : 7.64 % Allowed : 22.86 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % 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: -2.02 (0.10), residues: 6550 helix: -0.36 (0.12), residues: 1938 sheet: -2.22 (0.15), residues: 1065 loop : -1.60 (0.10), residues: 3547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP1g 102 HIS 0.016 0.002 HIS1V 66 PHE 0.027 0.003 PHE1d 106 TYR 0.029 0.003 TYR1h 127 ARG 0.038 0.001 ARG1U 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1821 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 369 poor density : 1452 time to evaluate : 6.237 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: 1D 57 HIS cc_start: 0.7835 (OUTLIER) cc_final: 0.7429 (t-90) REVERT: 1E 64 GLU cc_start: 0.5922 (pt0) cc_final: 0.5513 (pt0) REVERT: 1E 99 GLU cc_start: 0.6577 (mm-30) cc_final: 0.6007 (mm-30) REVERT: 1E 161 MET cc_start: 0.7583 (tpp) cc_final: 0.7238 (mtp) REVERT: 1F 47 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8360 (ptpt) REVERT: 1G 11 VAL cc_start: 0.6951 (t) cc_final: 0.6486 (p) REVERT: 1H 33 THR cc_start: 0.7072 (OUTLIER) cc_final: 0.6741 (t) REVERT: 1O 13 ASN cc_start: 0.7857 (p0) cc_final: 0.6982 (p0) REVERT: 1O 32 TYR cc_start: 0.7107 (OUTLIER) cc_final: 0.6866 (p90) REVERT: 1P 36 LYS cc_start: 0.9041 (mttt) cc_final: 0.8605 (mmtt) REVERT: 1P 82 LEU cc_start: 0.6578 (tt) cc_final: 0.6356 (tt) REVERT: 1Q 40 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7815 (ptm160) REVERT: 1R 28 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8180 (tp) REVERT: 1S 10 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6928 (ttp-170) REVERT: 1S 13 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.5741 (ptp-170) REVERT: 1U 17 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8631 (tp) REVERT: 1Y 25 LYS cc_start: 0.6759 (tppt) cc_final: 0.6549 (tppp) REVERT: 1Z 44 HIS cc_start: 0.6722 (t-90) cc_final: 0.6197 (t70) REVERT: 1Z 48 MET cc_start: 0.7068 (mmp) cc_final: 0.6436 (mmp) REVERT: 17 19 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7979 (mmm-85) REVERT: 19 4 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8626 (ptp-170) REVERT: 19 37 GLN cc_start: 0.8164 (tp-100) cc_final: 0.7627 (tt0) REVERT: 1b 132 GLU cc_start: 0.4003 (pt0) cc_final: 0.3667 (pt0) REVERT: 1b 136 ARG cc_start: 0.6612 (mmp80) cc_final: 0.5004 (ptp-170) REVERT: 1d 46 ARG cc_start: 0.6067 (tpt90) cc_final: 0.5569 (ttm170) REVERT: 1d 116 LEU cc_start: 0.3809 (OUTLIER) cc_final: 0.2841 (tp) REVERT: 1e 96 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6438 (tp40) REVERT: 1f 88 MET cc_start: 0.8665 (ptt) cc_final: 0.8200 (ptt) REVERT: 1g 49 LEU cc_start: 0.8229 (pp) cc_final: 0.7822 (pp) REVERT: 1j 42 LEU cc_start: 0.7316 (mp) cc_final: 0.7082 (mp) REVERT: 1l 87 LYS cc_start: 0.7547 (ttpp) cc_final: 0.7135 (tmtt) REVERT: 1n 13 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.6023 (mtm110) REVERT: 1q 49 ASN cc_start: 0.6722 (OUTLIER) cc_final: 0.6383 (p0) outliers start: 369 outliers final: 269 residues processed: 1633 average time/residue: 1.3301 time to fit residues: 3757.7923 Evaluate side-chains 1639 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1356 time to evaluate : 6.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1D residue 53 ILE Chi-restraints excluded: chain 1D residue 57 HIS Chi-restraints excluded: chain 1D residue 77 VAL Chi-restraints excluded: chain 1D residue 85 ASN Chi-restraints excluded: chain 1D residue 104 LEU Chi-restraints excluded: chain 1D residue 139 THR Chi-restraints excluded: chain 1D residue 140 VAL Chi-restraints excluded: chain 1D residue 171 VAL Chi-restraints excluded: chain 1D residue 183 VAL Chi-restraints excluded: chain 1D residue 212 TRP Chi-restraints excluded: chain 1D residue 249 VAL Chi-restraints excluded: chain 1D residue 261 ARG Chi-restraints excluded: chain 1E residue 14 ILE Chi-restraints excluded: chain 1E residue 25 THR Chi-restraints excluded: chain 1E residue 34 VAL Chi-restraints excluded: chain 1E residue 51 THR Chi-restraints excluded: chain 1E residue 58 ASN Chi-restraints excluded: chain 1E residue 91 THR Chi-restraints excluded: chain 1E residue 109 VAL Chi-restraints excluded: chain 1E residue 113 SER Chi-restraints excluded: chain 1E residue 122 VAL Chi-restraints excluded: chain 1E residue 145 SER Chi-restraints excluded: chain 1E residue 151 THR Chi-restraints excluded: chain 1E residue 177 VAL Chi-restraints excluded: chain 1E residue 180 VAL Chi-restraints excluded: chain 1E residue 189 VAL Chi-restraints excluded: chain 1E residue 200 ASP Chi-restraints excluded: chain 1F residue 18 THR Chi-restraints excluded: chain 1F residue 31 VAL Chi-restraints excluded: chain 1F residue 47 LYS Chi-restraints excluded: chain 1F residue 48 THR Chi-restraints excluded: chain 1F residue 70 SER Chi-restraints excluded: chain 1F residue 84 THR Chi-restraints excluded: chain 1F residue 92 HIS Chi-restraints excluded: chain 1F residue 112 LEU Chi-restraints excluded: chain 1F residue 113 VAL Chi-restraints excluded: chain 1F residue 131 THR Chi-restraints excluded: chain 1F residue 165 HIS Chi-restraints excluded: chain 1F residue 176 ASP Chi-restraints excluded: chain 1G residue 133 GLU Chi-restraints excluded: chain 1G residue 140 ILE Chi-restraints excluded: chain 1H residue 33 THR Chi-restraints excluded: chain 1H residue 36 LEU Chi-restraints excluded: chain 1H residue 37 ASN Chi-restraints excluded: chain 1H residue 40 VAL Chi-restraints excluded: chain 1H residue 42 VAL Chi-restraints excluded: chain 1H residue 46 ASP Chi-restraints excluded: chain 1H residue 48 THR Chi-restraints excluded: chain 1H residue 66 THR Chi-restraints excluded: chain 1H residue 83 THR Chi-restraints excluded: chain 1H residue 88 LEU Chi-restraints excluded: chain 1H residue 89 VAL Chi-restraints excluded: chain 1H residue 132 LEU Chi-restraints excluded: chain 1I residue 1 MET Chi-restraints excluded: chain 1I residue 19 VAL Chi-restraints excluded: chain 1I residue 37 VAL Chi-restraints excluded: chain 1I residue 44 ILE Chi-restraints excluded: chain 1I residue 114 GLU Chi-restraints excluded: chain 1I residue 134 VAL Chi-restraints excluded: chain 1I residue 144 VAL Chi-restraints excluded: chain 1J residue 36 ASP Chi-restraints excluded: chain 1J residue 50 VAL Chi-restraints excluded: chain 1J residue 85 SER Chi-restraints excluded: chain 1J residue 108 VAL Chi-restraints excluded: chain 1K residue 10 LEU Chi-restraints excluded: chain 1K residue 57 VAL Chi-restraints excluded: chain 1K residue 59 THR Chi-restraints excluded: chain 1K residue 120 ASP Chi-restraints excluded: chain 1N residue 30 THR Chi-restraints excluded: chain 1N residue 41 LYS Chi-restraints excluded: chain 1N residue 52 ASP Chi-restraints excluded: chain 1N residue 64 VAL Chi-restraints excluded: chain 1N residue 76 HIS Chi-restraints excluded: chain 1O residue 4 GLU Chi-restraints excluded: chain 1O residue 9 ASN Chi-restraints excluded: chain 1O residue 29 HIS Chi-restraints excluded: chain 1O residue 32 TYR Chi-restraints excluded: chain 1O residue 57 VAL Chi-restraints excluded: chain 1O residue 65 THR Chi-restraints excluded: chain 1O residue 69 VAL Chi-restraints excluded: chain 1Q residue 12 MET Chi-restraints excluded: chain 1Q residue 40 ARG Chi-restraints excluded: chain 1Q residue 42 THR Chi-restraints excluded: chain 1Q residue 115 GLU Chi-restraints excluded: chain 1R residue 1 MET Chi-restraints excluded: chain 1R residue 13 ASN Chi-restraints excluded: chain 1R residue 23 ASN Chi-restraints excluded: chain 1R residue 28 LEU Chi-restraints excluded: chain 1R residue 33 ILE Chi-restraints excluded: chain 1R residue 37 THR Chi-restraints excluded: chain 1S residue 10 ARG Chi-restraints excluded: chain 1S residue 12 THR Chi-restraints excluded: chain 1S residue 13 ARG Chi-restraints excluded: chain 1S residue 27 VAL Chi-restraints excluded: chain 1S residue 39 VAL Chi-restraints excluded: chain 1S residue 47 VAL Chi-restraints excluded: chain 1S residue 65 THR Chi-restraints excluded: chain 1S residue 87 ILE Chi-restraints excluded: chain 1T residue 7 LEU Chi-restraints excluded: chain 1T residue 12 MET Chi-restraints excluded: chain 1T residue 43 GLU Chi-restraints excluded: chain 1T residue 47 ILE Chi-restraints excluded: chain 1T residue 79 VAL Chi-restraints excluded: chain 1T residue 84 SER Chi-restraints excluded: chain 1T residue 85 VAL Chi-restraints excluded: chain 1U residue 8 ILE Chi-restraints excluded: chain 1U residue 17 LEU Chi-restraints excluded: chain 1U residue 24 TYR Chi-restraints excluded: chain 1V residue 14 VAL Chi-restraints excluded: chain 1V residue 19 THR Chi-restraints excluded: chain 1V residue 22 LEU Chi-restraints excluded: chain 1V residue 33 VAL Chi-restraints excluded: chain 1V residue 41 ILE Chi-restraints excluded: chain 1V residue 60 LYS Chi-restraints excluded: chain 1W residue 11 ARG Chi-restraints excluded: chain 1W residue 22 ASP Chi-restraints excluded: chain 1W residue 37 THR Chi-restraints excluded: chain 1W residue 62 ASP Chi-restraints excluded: chain 1W residue 77 ASP Chi-restraints excluded: chain 1W residue 96 ILE Chi-restraints excluded: chain 1W residue 105 VAL Chi-restraints excluded: chain 1W residue 108 SER Chi-restraints excluded: chain 1X residue 22 THR Chi-restraints excluded: chain 1X residue 25 GLU Chi-restraints excluded: chain 1X residue 53 VAL Chi-restraints excluded: chain 1X residue 79 ASP Chi-restraints excluded: chain 1Y residue 4 ILE Chi-restraints excluded: chain 1Y residue 11 ILE Chi-restraints excluded: chain 1Y residue 14 THR Chi-restraints excluded: chain 1Y residue 26 ASN Chi-restraints excluded: chain 1Y residue 33 VAL Chi-restraints excluded: chain 1Y residue 48 VAL Chi-restraints excluded: chain 1Y residue 51 LEU Chi-restraints excluded: chain 1Y residue 57 ILE Chi-restraints excluded: chain 1Y residue 58 VAL Chi-restraints excluded: chain 1Y residue 66 VAL Chi-restraints excluded: chain 1Z residue 47 VAL Chi-restraints excluded: chain 1Z residue 60 VAL Chi-restraints excluded: chain 1Z residue 63 ILE Chi-restraints excluded: chain 1Z residue 64 VAL Chi-restraints excluded: chain 1Z residue 77 VAL Chi-restraints excluded: chain 10 residue 12 SER Chi-restraints excluded: chain 10 residue 32 ILE Chi-restraints excluded: chain 10 residue 42 HIS Chi-restraints excluded: chain 10 residue 47 VAL Chi-restraints excluded: chain 10 residue 49 CYS Chi-restraints excluded: chain 10 residue 63 VAL Chi-restraints excluded: chain 10 residue 78 ILE Chi-restraints excluded: chain 11 residue 3 VAL Chi-restraints excluded: chain 11 residue 12 VAL Chi-restraints excluded: chain 11 residue 13 THR Chi-restraints excluded: chain 11 residue 15 ASN Chi-restraints excluded: chain 11 residue 39 VAL Chi-restraints excluded: chain 12 residue 11 VAL Chi-restraints excluded: chain 12 residue 19 LEU Chi-restraints excluded: chain 12 residue 42 LEU Chi-restraints excluded: chain 12 residue 55 THR Chi-restraints excluded: chain 13 residue 9 THR Chi-restraints excluded: chain 13 residue 30 ARG Chi-restraints excluded: chain 14 residue 17 SER Chi-restraints excluded: chain 15 residue 5 ASN Chi-restraints excluded: chain 15 residue 24 VAL Chi-restraints excluded: chain 15 residue 32 THR Chi-restraints excluded: chain 15 residue 43 THR Chi-restraints excluded: chain 17 residue 9 VAL Chi-restraints excluded: chain 17 residue 43 THR Chi-restraints excluded: chain 18 residue 6 VAL Chi-restraints excluded: chain 18 residue 53 ASP Chi-restraints excluded: chain 18 residue 56 LEU Chi-restraints excluded: chain 19 residue 1 MET Chi-restraints excluded: chain 19 residue 4 ARG Chi-restraints excluded: chain 19 residue 25 VAL Chi-restraints excluded: chain 1b residue 35 ASN Chi-restraints excluded: chain 1b residue 41 ASN Chi-restraints excluded: chain 1b residue 66 ILE Chi-restraints excluded: chain 1b residue 71 THR Chi-restraints excluded: chain 1b residue 152 ASP Chi-restraints excluded: chain 1b residue 162 VAL Chi-restraints excluded: chain 1b residue 185 ILE Chi-restraints excluded: chain 1b residue 188 THR Chi-restraints excluded: chain 1c residue 9 ILE Chi-restraints excluded: chain 1c residue 10 ARG Chi-restraints excluded: chain 1c residue 43 THR Chi-restraints excluded: chain 1c residue 51 VAL Chi-restraints excluded: chain 1c residue 55 VAL Chi-restraints excluded: chain 1c residue 74 ILE Chi-restraints excluded: chain 1c residue 105 VAL Chi-restraints excluded: chain 1c residue 114 LEU Chi-restraints excluded: chain 1c residue 181 ILE Chi-restraints excluded: chain 1c residue 190 THR Chi-restraints excluded: chain 1d residue 61 ARG Chi-restraints excluded: chain 1d residue 73 ASN Chi-restraints excluded: chain 1d residue 87 GLU Chi-restraints excluded: chain 1d residue 116 LEU Chi-restraints excluded: chain 1d residue 158 LEU Chi-restraints excluded: chain 1d residue 197 HIS Chi-restraints excluded: chain 1d residue 200 VAL Chi-restraints excluded: chain 1e residue 17 VAL Chi-restraints excluded: chain 1e residue 72 ASN Chi-restraints excluded: chain 1e residue 80 LEU Chi-restraints excluded: chain 1e residue 89 THR Chi-restraints excluded: chain 1e residue 96 GLN Chi-restraints excluded: chain 1e residue 104 ILE Chi-restraints excluded: chain 1e residue 115 GLU Chi-restraints excluded: chain 1e residue 121 ASN Chi-restraints excluded: chain 1e residue 135 VAL Chi-restraints excluded: chain 1e residue 152 VAL Chi-restraints excluded: chain 1f residue 18 VAL Chi-restraints excluded: chain 1g residue 6 ILE Chi-restraints excluded: chain 1g residue 26 VAL Chi-restraints excluded: chain 1g residue 42 VAL Chi-restraints excluded: chain 1g residue 58 LEU Chi-restraints excluded: chain 1g residue 84 TYR Chi-restraints excluded: chain 1g residue 93 VAL Chi-restraints excluded: chain 1g residue 115 MET Chi-restraints excluded: chain 1h residue 10 LEU Chi-restraints excluded: chain 1h residue 33 VAL Chi-restraints excluded: chain 1h residue 47 ASP Chi-restraints excluded: chain 1h residue 58 LEU Chi-restraints excluded: chain 1h residue 88 LYS Chi-restraints excluded: chain 1h residue 103 VAL Chi-restraints excluded: chain 1i residue 115 VAL Chi-restraints excluded: chain 1j residue 50 THR Chi-restraints excluded: chain 1k residue 25 SER Chi-restraints excluded: chain 1k residue 45 THR Chi-restraints excluded: chain 1k residue 58 THR Chi-restraints excluded: chain 1k residue 81 LEU Chi-restraints excluded: chain 1k residue 95 THR Chi-restraints excluded: chain 1k residue 106 ILE Chi-restraints excluded: chain 1k residue 107 THR Chi-restraints excluded: chain 1k residue 109 ILE Chi-restraints excluded: chain 1k residue 115 ILE Chi-restraints excluded: chain 1l residue 7 VAL Chi-restraints excluded: chain 1l residue 15 VAL Chi-restraints excluded: chain 1l residue 20 VAL Chi-restraints excluded: chain 1l residue 64 SER Chi-restraints excluded: chain 1l residue 86 VAL Chi-restraints excluded: chain 1m residue 24 VAL Chi-restraints excluded: chain 1m residue 33 LEU Chi-restraints excluded: chain 1m residue 76 ILE Chi-restraints excluded: chain 1m residue 96 VAL Chi-restraints excluded: chain 1n residue 13 ARG Chi-restraints excluded: chain 1n residue 67 THR Chi-restraints excluded: chain 1o residue 28 VAL Chi-restraints excluded: chain 1o residue 51 SER Chi-restraints excluded: chain 1o residue 55 LEU Chi-restraints excluded: chain 1o residue 59 VAL Chi-restraints excluded: chain 1o residue 67 ASP Chi-restraints excluded: chain 1o residue 80 LEU Chi-restraints excluded: chain 1o residue 86 LEU Chi-restraints excluded: chain 1p residue 2 VAL Chi-restraints excluded: chain 1p residue 3 THR Chi-restraints excluded: chain 1p residue 29 ASN Chi-restraints excluded: chain 1p residue 34 GLU Chi-restraints excluded: chain 1p residue 36 VAL Chi-restraints excluded: chain 1p residue 42 ILE Chi-restraints excluded: chain 1p residue 50 THR Chi-restraints excluded: chain 1p residue 61 VAL Chi-restraints excluded: chain 1p residue 66 THR Chi-restraints excluded: chain 1p residue 68 SER Chi-restraints excluded: chain 1p residue 75 ILE Chi-restraints excluded: chain 1q residue 37 ILE Chi-restraints excluded: chain 1q residue 49 ASN Chi-restraints excluded: chain 1q residue 56 ASP Chi-restraints excluded: chain 1q residue 78 VAL Chi-restraints excluded: chain 1r residue 23 LYS Chi-restraints excluded: chain 1r residue 30 ASN Chi-restraints excluded: chain 1r residue 39 VAL Chi-restraints excluded: chain 1r residue 44 THR Chi-restraints excluded: chain 1s residue 3 SER Chi-restraints excluded: chain 1s residue 10 ILE Chi-restraints excluded: chain 1s residue 11 ASP Chi-restraints excluded: chain 1s residue 18 VAL Chi-restraints excluded: chain 1s residue 22 VAL Chi-restraints excluded: chain 1s residue 34 SER Chi-restraints excluded: chain 1s residue 38 THR Chi-restraints excluded: chain 1s residue 59 VAL Chi-restraints excluded: chain 1s residue 65 MET Chi-restraints excluded: chain 1s residue 76 THR Chi-restraints excluded: chain 1t residue 11 ILE Chi-restraints excluded: chain 1t residue 19 HIS Chi-restraints excluded: chain 1t residue 22 SER Chi-restraints excluded: chain 1u residue 5 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 1028 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 608 optimal weight: 2.9990 chunk 779 optimal weight: 20.0000 chunk 603 optimal weight: 2.9990 chunk 898 optimal weight: 20.0000 chunk 595 optimal weight: 9.9990 chunk 1063 optimal weight: 40.0000 chunk 665 optimal weight: 10.0000 chunk 648 optimal weight: 0.8980 chunk 490 optimal weight: 0.7980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1H 29 ASN ** 1H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1H 138 GLN ** 1P 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1T 11 GLN ** 1V 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1V 66 HIS 1W 7 HIS ** 1X 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1Y 45 GLN 11 22 ASN ** 13 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1c 184 ASN 1e 11 GLN ** 1f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1f 17 GLN ** 1f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1g 85 GLN ** 1k 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1k 118 ASN ** 1p 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.7901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 161532 Z= 0.187 Angle : 0.684 27.380 240827 Z= 0.365 Chirality : 0.037 2.021 30226 Planarity : 0.006 0.123 13517 Dihedral : 23.177 178.776 79659 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.48 % Favored : 91.77 % Rotamer: Outliers : 4.93 % Allowed : 26.59 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.10), residues: 6550 helix: -0.01 (0.12), residues: 1945 sheet: -1.99 (0.15), residues: 1063 loop : -1.52 (0.10), residues: 3542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP1g 102 HIS 0.016 0.001 HIS1N 77 PHE 0.033 0.002 PHE1R 80 TYR 0.034 0.002 TYR1S 99 ARG 0.015 0.001 ARG1D 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1689 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1451 time to evaluate : 6.447 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: 1D 57 HIS cc_start: 0.7719 (OUTLIER) cc_final: 0.7406 (t-90) REVERT: 1E 64 GLU cc_start: 0.5690 (pt0) cc_final: 0.5349 (pt0) REVERT: 1E 99 GLU cc_start: 0.6277 (mm-30) cc_final: 0.5876 (mm-30) REVERT: 1E 161 MET cc_start: 0.7497 (tpp) cc_final: 0.7150 (mtp) REVERT: 1G 11 VAL cc_start: 0.6899 (t) cc_final: 0.6335 (p) REVERT: 1G 23 SER cc_start: 0.7579 (t) cc_final: 0.7184 (m) REVERT: 1G 95 MET cc_start: 0.7565 (ppp) cc_final: 0.7285 (ppp) REVERT: 1N 13 ARG cc_start: 0.7940 (mtm-85) cc_final: 0.7620 (mtm-85) REVERT: 1O 13 ASN cc_start: 0.7703 (p0) cc_final: 0.6870 (p0) REVERT: 1O 71 ARG cc_start: 0.8320 (tpp80) cc_final: 0.7986 (tpp80) REVERT: 1P 36 LYS cc_start: 0.9073 (mttt) cc_final: 0.8650 (mmtt) REVERT: 1Q 40 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7717 (ptm160) REVERT: 1U 32 ARG cc_start: 0.8229 (mtp-110) cc_final: 0.7984 (mtp85) REVERT: 1Y 25 LYS cc_start: 0.6482 (tppt) cc_final: 0.6250 (tppp) REVERT: 10 62 LYS cc_start: 0.6886 (mmtm) cc_final: 0.6557 (mmtm) REVERT: 12 8 GLU cc_start: 0.7122 (mp0) cc_final: 0.6298 (mt-10) REVERT: 19 4 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8127 (ptp-170) REVERT: 19 37 GLN cc_start: 0.7981 (tp-100) cc_final: 0.7487 (tt0) REVERT: 1b 136 ARG cc_start: 0.6278 (mmp80) cc_final: 0.5145 (ptp-170) REVERT: 1d 13 ARG cc_start: 0.7142 (tpp-160) cc_final: 0.6473 (tpm170) REVERT: 1d 46 ARG cc_start: 0.5965 (tpt90) cc_final: 0.5353 (tpp-160) REVERT: 1d 116 LEU cc_start: 0.4247 (OUTLIER) cc_final: 0.2708 (tt) REVERT: 1e 53 ARG cc_start: 0.7332 (mmt90) cc_final: 0.7079 (mtt-85) REVERT: 1e 96 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.6294 (tp40) REVERT: 1f 68 GLN cc_start: 0.7145 (mp10) cc_final: 0.6599 (mp10) REVERT: 1h 12 ARG cc_start: 0.7740 (ttm110) cc_final: 0.7522 (ttm110) REVERT: 1j 47 GLU cc_start: 0.7732 (mp0) cc_final: 0.7410 (mp0) REVERT: 1l 43 LYS cc_start: 0.7764 (ttmt) cc_final: 0.7445 (mttt) REVERT: 1l 87 LYS cc_start: 0.7486 (ttpp) cc_final: 0.7075 (tmtt) REVERT: 1q 49 ASN cc_start: 0.6483 (p0) cc_final: 0.6156 (p0) REVERT: 1t 28 ARG cc_start: 0.7635 (ptp-110) cc_final: 0.7146 (ttp-110) outliers start: 238 outliers final: 182 residues processed: 1564 average time/residue: 1.3382 time to fit residues: 3610.6950 Evaluate side-chains 1562 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1375 time to evaluate : 6.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1D residue 53 ILE Chi-restraints excluded: chain 1D residue 57 HIS Chi-restraints excluded: chain 1D residue 140 VAL Chi-restraints excluded: chain 1D residue 183 VAL Chi-restraints excluded: chain 1D residue 212 TRP Chi-restraints excluded: chain 1E residue 14 ILE Chi-restraints excluded: chain 1E residue 22 ILE Chi-restraints excluded: chain 1E residue 25 THR Chi-restraints excluded: chain 1E residue 51 THR Chi-restraints excluded: chain 1E residue 58 ASN Chi-restraints excluded: chain 1E residue 91 THR Chi-restraints excluded: chain 1E residue 109 VAL Chi-restraints excluded: chain 1E residue 113 SER Chi-restraints excluded: chain 1E residue 122 VAL Chi-restraints excluded: chain 1E residue 145 SER Chi-restraints excluded: chain 1E residue 177 VAL Chi-restraints excluded: chain 1E residue 180 VAL Chi-restraints excluded: chain 1E residue 189 VAL Chi-restraints excluded: chain 1F residue 18 THR Chi-restraints excluded: chain 1F residue 48 THR Chi-restraints excluded: chain 1F residue 84 THR Chi-restraints excluded: chain 1F residue 92 HIS Chi-restraints excluded: chain 1F residue 131 THR Chi-restraints excluded: chain 1F residue 176 ASP Chi-restraints excluded: chain 1F residue 193 VAL Chi-restraints excluded: chain 1G residue 133 GLU Chi-restraints excluded: chain 1H residue 36 LEU Chi-restraints excluded: chain 1H residue 37 ASN Chi-restraints excluded: chain 1H residue 83 THR Chi-restraints excluded: chain 1H residue 132 LEU Chi-restraints excluded: chain 1H residue 138 GLN Chi-restraints excluded: chain 1I residue 37 VAL Chi-restraints excluded: chain 1I residue 134 VAL Chi-restraints excluded: chain 1J residue 36 ASP Chi-restraints excluded: chain 1J residue 50 VAL Chi-restraints excluded: chain 1J residue 108 VAL Chi-restraints excluded: chain 1K residue 10 LEU Chi-restraints excluded: chain 1K residue 59 THR Chi-restraints excluded: chain 1K residue 97 VAL Chi-restraints excluded: chain 1K residue 120 ASP Chi-restraints excluded: chain 1N residue 5 THR Chi-restraints excluded: chain 1N residue 41 LYS Chi-restraints excluded: chain 1N residue 52 ASP Chi-restraints excluded: chain 1N residue 76 HIS Chi-restraints excluded: chain 1N residue 84 ILE Chi-restraints excluded: chain 1O residue 4 GLU Chi-restraints excluded: chain 1O residue 9 ASN Chi-restraints excluded: chain 1O residue 29 HIS Chi-restraints excluded: chain 1O residue 57 VAL Chi-restraints excluded: chain 1O residue 65 THR Chi-restraints excluded: chain 1Q residue 3 GLN Chi-restraints excluded: chain 1Q residue 12 MET Chi-restraints excluded: chain 1Q residue 40 ARG Chi-restraints excluded: chain 1Q residue 44 ARG Chi-restraints excluded: chain 1Q residue 115 GLU Chi-restraints excluded: chain 1R residue 1 MET Chi-restraints excluded: chain 1R residue 13 ASN Chi-restraints excluded: chain 1R residue 33 ILE Chi-restraints excluded: chain 1R residue 37 THR Chi-restraints excluded: chain 1S residue 35 ILE Chi-restraints excluded: chain 1S residue 47 VAL Chi-restraints excluded: chain 1S residue 87 ILE Chi-restraints excluded: chain 1T residue 7 LEU Chi-restraints excluded: chain 1T residue 15 ASP Chi-restraints excluded: chain 1T residue 43 GLU Chi-restraints excluded: chain 1T residue 79 VAL Chi-restraints excluded: chain 1T residue 85 VAL Chi-restraints excluded: chain 1U residue 8 ILE Chi-restraints excluded: chain 1U residue 82 LEU Chi-restraints excluded: chain 1U residue 110 GLU Chi-restraints excluded: chain 1V residue 22 LEU Chi-restraints excluded: chain 1V residue 32 THR Chi-restraints excluded: chain 1V residue 60 LYS Chi-restraints excluded: chain 1W residue 7 HIS Chi-restraints excluded: chain 1W residue 22 ASP Chi-restraints excluded: chain 1W residue 49 LYS Chi-restraints excluded: chain 1W residue 74 ILE Chi-restraints excluded: chain 1W residue 77 ASP Chi-restraints excluded: chain 1W residue 105 VAL Chi-restraints excluded: chain 1X residue 74 ILE Chi-restraints excluded: chain 1X residue 79 ASP Chi-restraints excluded: chain 1Y residue 14 THR Chi-restraints excluded: chain 1Y residue 33 VAL Chi-restraints excluded: chain 1Y residue 48 VAL Chi-restraints excluded: chain 1Y residue 51 LEU Chi-restraints excluded: chain 1Y residue 57 ILE Chi-restraints excluded: chain 1Y residue 58 VAL Chi-restraints excluded: chain 1Y residue 66 VAL Chi-restraints excluded: chain 1Z residue 63 ILE Chi-restraints excluded: chain 1Z residue 65 VAL Chi-restraints excluded: chain 1Z residue 77 VAL Chi-restraints excluded: chain 10 residue 12 SER Chi-restraints excluded: chain 10 residue 13 GLU Chi-restraints excluded: chain 10 residue 32 ILE Chi-restraints excluded: chain 10 residue 42 HIS Chi-restraints excluded: chain 10 residue 49 CYS Chi-restraints excluded: chain 10 residue 63 VAL Chi-restraints excluded: chain 10 residue 78 ILE Chi-restraints excluded: chain 11 residue 13 THR Chi-restraints excluded: chain 11 residue 39 VAL Chi-restraints excluded: chain 12 residue 11 VAL Chi-restraints excluded: chain 12 residue 19 LEU Chi-restraints excluded: chain 12 residue 42 LEU Chi-restraints excluded: chain 13 residue 9 THR Chi-restraints excluded: chain 14 residue 17 SER Chi-restraints excluded: chain 15 residue 5 ASN Chi-restraints excluded: chain 15 residue 24 VAL Chi-restraints excluded: chain 18 residue 6 VAL Chi-restraints excluded: chain 18 residue 56 LEU Chi-restraints excluded: chain 19 residue 4 ARG Chi-restraints excluded: chain 1b residue 71 THR Chi-restraints excluded: chain 1b residue 152 ASP Chi-restraints excluded: chain 1b residue 185 ILE Chi-restraints excluded: chain 1c residue 10 ARG Chi-restraints excluded: chain 1c residue 51 VAL Chi-restraints excluded: chain 1c residue 55 VAL Chi-restraints excluded: chain 1c residue 105 VAL Chi-restraints excluded: chain 1c residue 181 ILE Chi-restraints excluded: chain 1d residue 87 GLU Chi-restraints excluded: chain 1d residue 99 ASN Chi-restraints excluded: chain 1d residue 116 LEU Chi-restraints excluded: chain 1d residue 142 VAL Chi-restraints excluded: chain 1d residue 158 LEU Chi-restraints excluded: chain 1d residue 172 VAL Chi-restraints excluded: chain 1d residue 197 HIS Chi-restraints excluded: chain 1d residue 200 VAL Chi-restraints excluded: chain 1e residue 72 ASN Chi-restraints excluded: chain 1e residue 80 LEU Chi-restraints excluded: chain 1e residue 96 GLN Chi-restraints excluded: chain 1e residue 102 THR Chi-restraints excluded: chain 1e residue 115 GLU Chi-restraints excluded: chain 1e residue 121 ASN Chi-restraints excluded: chain 1e residue 152 VAL Chi-restraints excluded: chain 1f residue 18 VAL Chi-restraints excluded: chain 1g residue 6 ILE Chi-restraints excluded: chain 1g residue 58 LEU Chi-restraints excluded: chain 1g residue 84 TYR Chi-restraints excluded: chain 1g residue 93 VAL Chi-restraints excluded: chain 1g residue 115 MET Chi-restraints excluded: chain 1h residue 10 LEU Chi-restraints excluded: chain 1h residue 13 ILE Chi-restraints excluded: chain 1h residue 33 VAL Chi-restraints excluded: chain 1h residue 47 ASP Chi-restraints excluded: chain 1h residue 58 LEU Chi-restraints excluded: chain 1h residue 88 LYS Chi-restraints excluded: chain 1h residue 103 VAL Chi-restraints excluded: chain 1i residue 86 LEU Chi-restraints excluded: chain 1j residue 50 THR Chi-restraints excluded: chain 1k residue 25 SER Chi-restraints excluded: chain 1k residue 45 THR Chi-restraints excluded: chain 1k residue 58 THR Chi-restraints excluded: chain 1k residue 63 GLN Chi-restraints excluded: chain 1k residue 81 LEU Chi-restraints excluded: chain 1k residue 109 ILE Chi-restraints excluded: chain 1k residue 115 ILE Chi-restraints excluded: chain 1l residue 20 VAL Chi-restraints excluded: chain 1l residue 64 SER Chi-restraints excluded: chain 1l residue 118 VAL Chi-restraints excluded: chain 1m residue 24 VAL Chi-restraints excluded: chain 1m residue 33 LEU Chi-restraints excluded: chain 1m residue 73 SER Chi-restraints excluded: chain 1m residue 76 ILE Chi-restraints excluded: chain 1o residue 51 SER Chi-restraints excluded: chain 1p residue 3 THR Chi-restraints excluded: chain 1p residue 19 VAL Chi-restraints excluded: chain 1p residue 29 ASN Chi-restraints excluded: chain 1p residue 34 GLU Chi-restraints excluded: chain 1p residue 36 VAL Chi-restraints excluded: chain 1p residue 52 LEU Chi-restraints excluded: chain 1p residue 55 ASP Chi-restraints excluded: chain 1q residue 50 ASN Chi-restraints excluded: chain 1q residue 56 ASP Chi-restraints excluded: chain 1q residue 58 VAL Chi-restraints excluded: chain 1q residue 78 VAL Chi-restraints excluded: chain 1r residue 30 ASN Chi-restraints excluded: chain 1r residue 39 VAL Chi-restraints excluded: chain 1s residue 10 ILE Chi-restraints excluded: chain 1s residue 11 ASP Chi-restraints excluded: chain 1s residue 18 VAL Chi-restraints excluded: chain 1s residue 34 SER Chi-restraints excluded: chain 1s residue 38 THR Chi-restraints excluded: chain 1s residue 65 MET Chi-restraints excluded: chain 1t residue 11 ILE Chi-restraints excluded: chain 1t residue 19 HIS Chi-restraints excluded: chain 1t residue 31 ILE Chi-restraints excluded: chain 1u residue 5 VAL Chi-restraints excluded: chain 1u residue 15 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 657 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 634 optimal weight: 20.0000 chunk 320 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 675 optimal weight: 10.0000 chunk 724 optimal weight: 10.0000 chunk 525 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 835 optimal weight: 9.9990 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1E 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1H 29 ASN ** 1H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1H 138 GLN ** 1O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1P 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1P 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1R 62 ASN 1T 11 GLN ** 1V 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1V 66 HIS ** 1W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1W 57 ASN ** 1X 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1Z 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1e 11 GLN ** 1f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1f 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1p 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1t 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.8588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.200 161532 Z= 0.445 Angle : 0.924 26.952 240827 Z= 0.468 Chirality : 0.047 2.043 30226 Planarity : 0.008 0.133 13517 Dihedral : 23.412 179.832 79659 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 22.09 Ramachandran Plot: Outliers : 0.72 % Allowed : 10.67 % Favored : 88.61 % Rotamer: Outliers : 6.54 % Allowed : 25.91 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.10), residues: 6550 helix: -0.43 (0.12), residues: 1966 sheet: -2.09 (0.14), residues: 1121 loop : -1.91 (0.10), residues: 3463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP1N 15 HIS 0.018 0.002 HIS1b 167 PHE 0.030 0.003 PHE1d 106 TYR 0.034 0.003 TYR1D 82 ARG 0.021 0.001 ARG1d 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1733 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1417 time to evaluate : 6.260 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: 1D 224 MET cc_start: 0.8049 (mmm) cc_final: 0.7677 (mmt) REVERT: 1E 59 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.6014 (tpm170) REVERT: 1E 64 GLU cc_start: 0.5954 (pt0) cc_final: 0.5569 (pt0) REVERT: 1E 99 GLU cc_start: 0.6730 (mm-30) cc_final: 0.6063 (mm-30) REVERT: 1E 161 MET cc_start: 0.7620 (tpp) cc_final: 0.7309 (mtp) REVERT: 1F 47 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8036 (ptpt) REVERT: 1G 11 VAL cc_start: 0.6879 (t) cc_final: 0.6453 (p) REVERT: 1G 23 SER cc_start: 0.7766 (t) cc_final: 0.7245 (m) REVERT: 1H 63 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7497 (mm-40) REVERT: 1O 13 ASN cc_start: 0.7843 (p0) cc_final: 0.6899 (p0) REVERT: 1P 36 LYS cc_start: 0.9084 (mttt) cc_final: 0.8714 (mmtt) REVERT: 1P 109 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7892 (ttmt) REVERT: 1Q 40 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7791 (ptm160) REVERT: 1R 72 ASP cc_start: 0.7698 (t0) cc_final: 0.7002 (t70) REVERT: 1Z 75 GLN cc_start: 0.7230 (pt0) cc_final: 0.7023 (pt0) REVERT: 10 62 LYS cc_start: 0.7171 (mmtm) cc_final: 0.6945 (mmtm) REVERT: 12 8 GLU cc_start: 0.7317 (mp0) cc_final: 0.6541 (mt-10) REVERT: 12 16 THR cc_start: 0.6679 (m) cc_final: 0.6444 (t) REVERT: 19 4 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8818 (ptp-170) REVERT: 19 37 GLN cc_start: 0.8105 (tp-100) cc_final: 0.7574 (tt0) REVERT: 1b 136 ARG cc_start: 0.6872 (mmp80) cc_final: 0.5181 (ptp-170) REVERT: 1d 46 ARG cc_start: 0.6005 (tpt90) cc_final: 0.5514 (ttm170) REVERT: 1d 116 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6048 (tt) REVERT: 1e 44 ARG cc_start: 0.7936 (ptm-80) cc_final: 0.7622 (ptm160) REVERT: 1e 96 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6650 (tp40) REVERT: 1f 79 ARG cc_start: 0.7051 (mtp180) cc_final: 0.6676 (mtm180) REVERT: 1f 88 MET cc_start: 0.8620 (ptt) cc_final: 0.8276 (ptt) REVERT: 1g 49 LEU cc_start: 0.8153 (pp) cc_final: 0.7614 (pp) REVERT: 1k 118 ASN cc_start: 0.6378 (m110) cc_final: 0.6130 (m-40) REVERT: 1l 43 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7552 (mttt) REVERT: 1l 87 LYS cc_start: 0.7803 (ttpp) cc_final: 0.7389 (ttpp) REVERT: 1q 49 ASN cc_start: 0.6647 (OUTLIER) cc_final: 0.6433 (p0) REVERT: 1t 28 ARG cc_start: 0.7818 (ptp-110) cc_final: 0.7241 (ttp-110) outliers start: 316 outliers final: 247 residues processed: 1561 average time/residue: 1.4411 time to fit residues: 3928.5226 Evaluate side-chains 1629 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1374 time to evaluate : 5.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1D residue 53 ILE Chi-restraints excluded: chain 1D residue 139 THR Chi-restraints excluded: chain 1D residue 140 VAL Chi-restraints excluded: chain 1D residue 183 VAL Chi-restraints excluded: chain 1D residue 212 TRP Chi-restraints excluded: chain 1D residue 249 VAL Chi-restraints excluded: chain 1E residue 14 ILE Chi-restraints excluded: chain 1E residue 22 ILE Chi-restraints excluded: chain 1E residue 25 THR Chi-restraints excluded: chain 1E residue 51 THR Chi-restraints excluded: chain 1E residue 58 ASN Chi-restraints excluded: chain 1E residue 59 ARG Chi-restraints excluded: chain 1E residue 60 VAL Chi-restraints excluded: chain 1E residue 91 THR Chi-restraints excluded: chain 1E residue 109 VAL Chi-restraints excluded: chain 1E residue 113 SER Chi-restraints excluded: chain 1E residue 122 VAL Chi-restraints excluded: chain 1E residue 145 SER Chi-restraints excluded: chain 1E residue 151 THR Chi-restraints excluded: chain 1E residue 177 VAL Chi-restraints excluded: chain 1E residue 180 VAL Chi-restraints excluded: chain 1E residue 189 VAL Chi-restraints excluded: chain 1E residue 200 ASP Chi-restraints excluded: chain 1F residue 18 THR Chi-restraints excluded: chain 1F residue 31 VAL Chi-restraints excluded: chain 1F residue 47 LYS Chi-restraints excluded: chain 1F residue 48 THR Chi-restraints excluded: chain 1F residue 70 SER Chi-restraints excluded: chain 1F residue 84 THR Chi-restraints excluded: chain 1F residue 92 HIS Chi-restraints excluded: chain 1F residue 131 THR Chi-restraints excluded: chain 1F residue 165 HIS Chi-restraints excluded: chain 1F residue 176 ASP Chi-restraints excluded: chain 1F residue 193 VAL Chi-restraints excluded: chain 1G residue 122 ASP Chi-restraints excluded: chain 1H residue 36 LEU Chi-restraints excluded: chain 1H residue 37 ASN Chi-restraints excluded: chain 1H residue 42 VAL Chi-restraints excluded: chain 1H residue 66 THR Chi-restraints excluded: chain 1H residue 75 VAL Chi-restraints excluded: chain 1H residue 83 THR Chi-restraints excluded: chain 1H residue 132 LEU Chi-restraints excluded: chain 1I residue 37 VAL Chi-restraints excluded: chain 1I residue 134 VAL Chi-restraints excluded: chain 1J residue 36 ASP Chi-restraints excluded: chain 1J residue 50 VAL Chi-restraints excluded: chain 1J residue 85 SER Chi-restraints excluded: chain 1K residue 10 LEU Chi-restraints excluded: chain 1K residue 59 THR Chi-restraints excluded: chain 1K residue 97 VAL Chi-restraints excluded: chain 1K residue 105 LEU Chi-restraints excluded: chain 1K residue 120 ASP Chi-restraints excluded: chain 1K residue 135 MET Chi-restraints excluded: chain 1N residue 40 HIS Chi-restraints excluded: chain 1N residue 52 ASP Chi-restraints excluded: chain 1N residue 76 HIS Chi-restraints excluded: chain 1O residue 4 GLU Chi-restraints excluded: chain 1O residue 9 ASN Chi-restraints excluded: chain 1O residue 24 VAL Chi-restraints excluded: chain 1O residue 29 HIS Chi-restraints excluded: chain 1O residue 57 VAL Chi-restraints excluded: chain 1O residue 65 THR Chi-restraints excluded: chain 1P residue 61 LEU Chi-restraints excluded: chain 1P residue 109 LYS Chi-restraints excluded: chain 1Q residue 12 MET Chi-restraints excluded: chain 1Q residue 40 ARG Chi-restraints excluded: chain 1Q residue 53 MET Chi-restraints excluded: chain 1Q residue 82 MET Chi-restraints excluded: chain 1Q residue 115 GLU Chi-restraints excluded: chain 1R residue 1 MET Chi-restraints excluded: chain 1R residue 13 ASN Chi-restraints excluded: chain 1R residue 33 ILE Chi-restraints excluded: chain 1R residue 37 THR Chi-restraints excluded: chain 1S residue 12 THR Chi-restraints excluded: chain 1S residue 47 VAL Chi-restraints excluded: chain 1S residue 65 THR Chi-restraints excluded: chain 1S residue 74 VAL Chi-restraints excluded: chain 1S residue 87 ILE Chi-restraints excluded: chain 1T residue 7 LEU Chi-restraints excluded: chain 1T residue 15 ASP Chi-restraints excluded: chain 1T residue 43 GLU Chi-restraints excluded: chain 1T residue 47 ILE Chi-restraints excluded: chain 1T residue 79 VAL Chi-restraints excluded: chain 1T residue 85 VAL Chi-restraints excluded: chain 1U residue 8 ILE Chi-restraints excluded: chain 1U residue 17 LEU Chi-restraints excluded: chain 1U residue 24 TYR Chi-restraints excluded: chain 1U residue 82 LEU Chi-restraints excluded: chain 1V residue 14 VAL Chi-restraints excluded: chain 1V residue 22 LEU Chi-restraints excluded: chain 1V residue 32 THR Chi-restraints excluded: chain 1V residue 33 VAL Chi-restraints excluded: chain 1V residue 60 LYS Chi-restraints excluded: chain 1V residue 75 VAL Chi-restraints excluded: chain 1V residue 86 GLN Chi-restraints excluded: chain 1W residue 22 ASP Chi-restraints excluded: chain 1W residue 49 LYS Chi-restraints excluded: chain 1W residue 62 ASP Chi-restraints excluded: chain 1W residue 77 ASP Chi-restraints excluded: chain 1W residue 81 SER Chi-restraints excluded: chain 1W residue 96 ILE Chi-restraints excluded: chain 1W residue 105 VAL Chi-restraints excluded: chain 1W residue 108 SER Chi-restraints excluded: chain 1X residue 25 GLU Chi-restraints excluded: chain 1X residue 58 VAL Chi-restraints excluded: chain 1X residue 74 ILE Chi-restraints excluded: chain 1X residue 79 ASP Chi-restraints excluded: chain 1Y residue 4 ILE Chi-restraints excluded: chain 1Y residue 5 ARG Chi-restraints excluded: chain 1Y residue 11 ILE Chi-restraints excluded: chain 1Y residue 14 THR Chi-restraints excluded: chain 1Y residue 26 ASN Chi-restraints excluded: chain 1Y residue 48 VAL Chi-restraints excluded: chain 1Y residue 51 LEU Chi-restraints excluded: chain 1Y residue 58 VAL Chi-restraints excluded: chain 1Y residue 64 ILE Chi-restraints excluded: chain 1Y residue 66 VAL Chi-restraints excluded: chain 1Z residue 60 VAL Chi-restraints excluded: chain 1Z residue 63 ILE Chi-restraints excluded: chain 1Z residue 65 VAL Chi-restraints excluded: chain 1Z residue 77 VAL Chi-restraints excluded: chain 10 residue 12 SER Chi-restraints excluded: chain 10 residue 22 PHE Chi-restraints excluded: chain 10 residue 32 ILE Chi-restraints excluded: chain 10 residue 42 HIS Chi-restraints excluded: chain 10 residue 49 CYS Chi-restraints excluded: chain 10 residue 63 VAL Chi-restraints excluded: chain 10 residue 78 ILE Chi-restraints excluded: chain 11 residue 9 LYS Chi-restraints excluded: chain 11 residue 12 VAL Chi-restraints excluded: chain 11 residue 13 THR Chi-restraints excluded: chain 11 residue 15 ASN Chi-restraints excluded: chain 11 residue 22 ASN Chi-restraints excluded: chain 11 residue 39 VAL Chi-restraints excluded: chain 11 residue 58 ILE Chi-restraints excluded: chain 12 residue 11 VAL Chi-restraints excluded: chain 12 residue 19 LEU Chi-restraints excluded: chain 12 residue 42 LEU Chi-restraints excluded: chain 12 residue 55 THR Chi-restraints excluded: chain 13 residue 9 THR Chi-restraints excluded: chain 13 residue 31 ILE Chi-restraints excluded: chain 14 residue 17 SER Chi-restraints excluded: chain 15 residue 5 ASN Chi-restraints excluded: chain 15 residue 24 VAL Chi-restraints excluded: chain 17 residue 9 VAL Chi-restraints excluded: chain 18 residue 6 VAL Chi-restraints excluded: chain 18 residue 56 LEU Chi-restraints excluded: chain 18 residue 60 CYS Chi-restraints excluded: chain 19 residue 4 ARG Chi-restraints excluded: chain 1b residue 35 ASN Chi-restraints excluded: chain 1b residue 41 ASN Chi-restraints excluded: chain 1b residue 48 MET Chi-restraints excluded: chain 1b residue 66 ILE Chi-restraints excluded: chain 1b residue 71 THR Chi-restraints excluded: chain 1b residue 108 GLN Chi-restraints excluded: chain 1b residue 152 ASP Chi-restraints excluded: chain 1b residue 185 ILE Chi-restraints excluded: chain 1c residue 9 ILE Chi-restraints excluded: chain 1c residue 10 ARG Chi-restraints excluded: chain 1c residue 51 VAL Chi-restraints excluded: chain 1c residue 55 VAL Chi-restraints excluded: chain 1c residue 105 VAL Chi-restraints excluded: chain 1c residue 114 LEU Chi-restraints excluded: chain 1c residue 127 VAL Chi-restraints excluded: chain 1c residue 181 ILE Chi-restraints excluded: chain 1d residue 66 VAL Chi-restraints excluded: chain 1d residue 73 ASN Chi-restraints excluded: chain 1d residue 99 ASN Chi-restraints excluded: chain 1d residue 116 LEU Chi-restraints excluded: chain 1d residue 158 LEU Chi-restraints excluded: chain 1d residue 172 VAL Chi-restraints excluded: chain 1d residue 197 HIS Chi-restraints excluded: chain 1d residue 200 VAL Chi-restraints excluded: chain 1e residue 72 ASN Chi-restraints excluded: chain 1e residue 80 LEU Chi-restraints excluded: chain 1e residue 89 THR Chi-restraints excluded: chain 1e residue 96 GLN Chi-restraints excluded: chain 1e residue 104 ILE Chi-restraints excluded: chain 1e residue 115 GLU Chi-restraints excluded: chain 1e residue 121 ASN Chi-restraints excluded: chain 1e residue 152 VAL Chi-restraints excluded: chain 1f residue 18 VAL Chi-restraints excluded: chain 1g residue 6 ILE Chi-restraints excluded: chain 1g residue 58 LEU Chi-restraints excluded: chain 1g residue 84 TYR Chi-restraints excluded: chain 1g residue 93 VAL Chi-restraints excluded: chain 1g residue 98 LEU Chi-restraints excluded: chain 1g residue 100 MET Chi-restraints excluded: chain 1g residue 115 MET Chi-restraints excluded: chain 1h residue 10 LEU Chi-restraints excluded: chain 1h residue 13 ILE Chi-restraints excluded: chain 1h residue 33 VAL Chi-restraints excluded: chain 1h residue 47 ASP Chi-restraints excluded: chain 1h residue 58 LEU Chi-restraints excluded: chain 1h residue 88 LYS Chi-restraints excluded: chain 1h residue 103 VAL Chi-restraints excluded: chain 1h residue 124 ILE Chi-restraints excluded: chain 1h residue 125 ILE Chi-restraints excluded: chain 1i residue 64 ILE Chi-restraints excluded: chain 1i residue 86 LEU Chi-restraints excluded: chain 1j residue 50 THR Chi-restraints excluded: chain 1k residue 25 SER Chi-restraints excluded: chain 1k residue 30 ILE Chi-restraints excluded: chain 1k residue 45 THR Chi-restraints excluded: chain 1k residue 58 THR Chi-restraints excluded: chain 1k residue 63 GLN Chi-restraints excluded: chain 1k residue 95 THR Chi-restraints excluded: chain 1k residue 106 ILE Chi-restraints excluded: chain 1k residue 107 THR Chi-restraints excluded: chain 1k residue 109 ILE Chi-restraints excluded: chain 1k residue 115 ILE Chi-restraints excluded: chain 1l residue 7 VAL Chi-restraints excluded: chain 1l residue 20 VAL Chi-restraints excluded: chain 1m residue 24 VAL Chi-restraints excluded: chain 1m residue 33 LEU Chi-restraints excluded: chain 1m residue 73 SER Chi-restraints excluded: chain 1m residue 76 ILE Chi-restraints excluded: chain 1m residue 96 VAL Chi-restraints excluded: chain 1n residue 58 SER Chi-restraints excluded: chain 1o residue 28 VAL Chi-restraints excluded: chain 1o residue 59 VAL Chi-restraints excluded: chain 1o residue 67 ASP Chi-restraints excluded: chain 1o residue 80 LEU Chi-restraints excluded: chain 1p residue 3 THR Chi-restraints excluded: chain 1p residue 19 VAL Chi-restraints excluded: chain 1p residue 29 ASN Chi-restraints excluded: chain 1p residue 36 VAL Chi-restraints excluded: chain 1p residue 52 LEU Chi-restraints excluded: chain 1p residue 55 ASP Chi-restraints excluded: chain 1p residue 61 VAL Chi-restraints excluded: chain 1p residue 66 THR Chi-restraints excluded: chain 1p residue 68 SER Chi-restraints excluded: chain 1q residue 20 ILE Chi-restraints excluded: chain 1q residue 37 ILE Chi-restraints excluded: chain 1q residue 49 ASN Chi-restraints excluded: chain 1q residue 56 ASP Chi-restraints excluded: chain 1q residue 58 VAL Chi-restraints excluded: chain 1q residue 78 VAL Chi-restraints excluded: chain 1r residue 23 LYS Chi-restraints excluded: chain 1r residue 30 ASN Chi-restraints excluded: chain 1r residue 39 VAL Chi-restraints excluded: chain 1r residue 44 THR Chi-restraints excluded: chain 1s residue 3 SER Chi-restraints excluded: chain 1s residue 10 ILE Chi-restraints excluded: chain 1s residue 11 ASP Chi-restraints excluded: chain 1s residue 18 VAL Chi-restraints excluded: chain 1s residue 22 VAL Chi-restraints excluded: chain 1s residue 38 THR Chi-restraints excluded: chain 1s residue 65 MET Chi-restraints excluded: chain 1t residue 11 ILE Chi-restraints excluded: chain 1t residue 19 HIS Chi-restraints excluded: chain 1t residue 39 GLU Chi-restraints excluded: chain 1t residue 56 ILE Chi-restraints excluded: chain 1u residue 5 VAL Chi-restraints excluded: chain 1u residue 15 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 967 optimal weight: 6.9990 chunk 1018 optimal weight: 5.9990 chunk 929 optimal weight: 7.9990 chunk 990 optimal weight: 0.8980 chunk 596 optimal weight: 5.9990 chunk 431 optimal weight: 40.0000 chunk 777 optimal weight: 20.0000 chunk 304 optimal weight: 8.9990 chunk 895 optimal weight: 6.9990 chunk 936 optimal weight: 0.6980 chunk 987 optimal weight: 4.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1E 94 GLN ** 1F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1H 29 ASN ** 1H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1N 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1O 89 ASN ** 1O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1P 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1T 11 GLN ** 1V 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1V 66 HIS 1W 7 HIS 1W 31 GLN 1W 57 ASN 1X 15 HIS ** 1Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1Y 68 ASN ** 13 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1c 101 ASN 1e 11 GLN 1e 82 HIS ** 1f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1p 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1t 47 GLN 1t 51 ASN ** 1t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.8649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 161532 Z= 0.223 Angle : 0.730 27.137 240827 Z= 0.386 Chirality : 0.039 2.028 30226 Planarity : 0.006 0.125 13517 Dihedral : 23.296 179.917 79659 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.23 % Favored : 91.07 % Rotamer: Outliers : 4.85 % Allowed : 28.49 % Favored : 66.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.10), residues: 6550 helix: -0.10 (0.12), residues: 1959 sheet: -1.96 (0.15), residues: 1078 loop : -1.80 (0.10), residues: 3513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP1s 33 HIS 0.017 0.002 HIS1N 77 PHE 0.022 0.002 PHE1n 73 TYR 0.025 0.002 TYR1S 99 ARG 0.015 0.001 ARG1q 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1668 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1434 time to evaluate : 6.389 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: 1D 42 ARG cc_start: 0.7387 (mtt90) cc_final: 0.7035 (mtt-85) REVERT: 1D 224 MET cc_start: 0.7909 (mmm) cc_final: 0.7677 (mmt) REVERT: 1E 64 GLU cc_start: 0.5746 (pt0) cc_final: 0.5431 (pt0) REVERT: 1F 47 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7947 (ptpt) REVERT: 1F 51 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6455 (tt0) REVERT: 1G 23 SER cc_start: 0.7548 (t) cc_final: 0.7042 (m) REVERT: 1N 43 GLU cc_start: 0.6813 (pm20) cc_final: 0.6283 (pt0) REVERT: 1O 13 ASN cc_start: 0.7668 (p0) cc_final: 0.6877 (p0) REVERT: 1P 36 LYS cc_start: 0.9109 (mttt) cc_final: 0.8664 (mmtt) REVERT: 1Q 40 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7762 (ptm160) REVERT: 1R 72 ASP cc_start: 0.7377 (t0) cc_final: 0.6521 (t0) REVERT: 1R 107 ASN cc_start: 0.8289 (t0) cc_final: 0.7583 (t0) REVERT: 1S 112 GLU cc_start: 0.6737 (pp20) cc_final: 0.5941 (pp20) REVERT: 1U 31 TYR cc_start: 0.8563 (t80) cc_final: 0.8226 (t80) REVERT: 1Z 75 GLN cc_start: 0.7265 (pt0) cc_final: 0.7048 (pt0) REVERT: 12 8 GLU cc_start: 0.7118 (mp0) cc_final: 0.6256 (mt-10) REVERT: 13 5 LYS cc_start: 0.8454 (mmtt) cc_final: 0.7737 (mmtm) REVERT: 19 4 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8280 (ptp-170) REVERT: 19 37 GLN cc_start: 0.8038 (tp-100) cc_final: 0.7488 (tt0) REVERT: 1b 136 ARG cc_start: 0.6354 (mmp80) cc_final: 0.5127 (ptp-170) REVERT: 1d 13 ARG cc_start: 0.7386 (tpp-160) cc_final: 0.6808 (tpm170) REVERT: 1d 46 ARG cc_start: 0.6015 (tpt90) cc_final: 0.5314 (tpp-160) REVERT: 1d 99 ASN cc_start: 0.7085 (t0) cc_final: 0.6864 (t0) REVERT: 1d 116 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.5416 (tt) REVERT: 1e 44 ARG cc_start: 0.7757 (ptm-80) cc_final: 0.7532 (ptm160) REVERT: 1e 53 ARG cc_start: 0.7405 (mmt90) cc_final: 0.7180 (mtt-85) REVERT: 1e 96 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6453 (tt0) REVERT: 1f 79 ARG cc_start: 0.6820 (mtp180) cc_final: 0.6552 (mtm180) REVERT: 1g 49 LEU cc_start: 0.8094 (pp) cc_final: 0.7563 (pp) REVERT: 1j 47 GLU cc_start: 0.7739 (mp0) cc_final: 0.7479 (mp0) REVERT: 1k 81 LEU cc_start: 0.6298 (pp) cc_final: 0.5783 (pp) REVERT: 1l 35 ARG cc_start: 0.7891 (tpt90) cc_final: 0.7609 (tpt-90) REVERT: 1l 43 LYS cc_start: 0.7956 (ttmt) cc_final: 0.7602 (mttt) REVERT: 1l 87 LYS cc_start: 0.7565 (ttpp) cc_final: 0.7224 (ttpp) REVERT: 1l 110 LYS cc_start: 0.6754 (mmtm) cc_final: 0.6390 (mptt) REVERT: 1o 14 PHE cc_start: 0.7553 (m-80) cc_final: 0.7254 (m-10) REVERT: 1t 28 ARG cc_start: 0.7584 (ptp-110) cc_final: 0.7137 (ttp-110) outliers start: 234 outliers final: 199 residues processed: 1542 average time/residue: 1.2986 time to fit residues: 3465.5681 Evaluate side-chains 1588 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1384 time to evaluate : 6.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1D residue 53 ILE Chi-restraints excluded: chain 1D residue 139 THR Chi-restraints excluded: chain 1D residue 140 VAL Chi-restraints excluded: chain 1D residue 183 VAL Chi-restraints excluded: chain 1D residue 212 TRP Chi-restraints excluded: chain 1E residue 14 ILE Chi-restraints excluded: chain 1E residue 22 ILE Chi-restraints excluded: chain 1E residue 25 THR Chi-restraints excluded: chain 1E residue 51 THR Chi-restraints excluded: chain 1E residue 58 ASN Chi-restraints excluded: chain 1E residue 109 VAL Chi-restraints excluded: chain 1E residue 113 SER Chi-restraints excluded: chain 1E residue 122 VAL Chi-restraints excluded: chain 1E residue 145 SER Chi-restraints excluded: chain 1E residue 177 VAL Chi-restraints excluded: chain 1E residue 180 VAL Chi-restraints excluded: chain 1E residue 189 VAL Chi-restraints excluded: chain 1E residue 200 ASP Chi-restraints excluded: chain 1F residue 18 THR Chi-restraints excluded: chain 1F residue 31 VAL Chi-restraints excluded: chain 1F residue 47 LYS Chi-restraints excluded: chain 1F residue 48 THR Chi-restraints excluded: chain 1F residue 84 THR Chi-restraints excluded: chain 1F residue 92 HIS Chi-restraints excluded: chain 1F residue 131 THR Chi-restraints excluded: chain 1F residue 176 ASP Chi-restraints excluded: chain 1G residue 122 ASP Chi-restraints excluded: chain 1H residue 36 LEU Chi-restraints excluded: chain 1H residue 37 ASN Chi-restraints excluded: chain 1H residue 71 LEU Chi-restraints excluded: chain 1H residue 83 THR Chi-restraints excluded: chain 1H residue 132 LEU Chi-restraints excluded: chain 1I residue 37 VAL Chi-restraints excluded: chain 1I residue 44 ILE Chi-restraints excluded: chain 1I residue 134 VAL Chi-restraints excluded: chain 1J residue 36 ASP Chi-restraints excluded: chain 1J residue 50 VAL Chi-restraints excluded: chain 1J residue 85 SER Chi-restraints excluded: chain 1K residue 10 LEU Chi-restraints excluded: chain 1K residue 59 THR Chi-restraints excluded: chain 1K residue 120 ASP Chi-restraints excluded: chain 1N residue 52 ASP Chi-restraints excluded: chain 1N residue 76 HIS Chi-restraints excluded: chain 1O residue 4 GLU Chi-restraints excluded: chain 1O residue 9 ASN Chi-restraints excluded: chain 1O residue 24 VAL Chi-restraints excluded: chain 1O residue 29 HIS Chi-restraints excluded: chain 1O residue 65 THR Chi-restraints excluded: chain 1P residue 61 LEU Chi-restraints excluded: chain 1P residue 77 ILE Chi-restraints excluded: chain 1Q residue 12 MET Chi-restraints excluded: chain 1Q residue 40 ARG Chi-restraints excluded: chain 1Q residue 44 ARG Chi-restraints excluded: chain 1Q residue 82 MET Chi-restraints excluded: chain 1Q residue 115 GLU Chi-restraints excluded: chain 1R residue 1 MET Chi-restraints excluded: chain 1R residue 13 ASN Chi-restraints excluded: chain 1R residue 33 ILE Chi-restraints excluded: chain 1R residue 37 THR Chi-restraints excluded: chain 1R residue 53 THR Chi-restraints excluded: chain 1S residue 12 THR Chi-restraints excluded: chain 1S residue 35 ILE Chi-restraints excluded: chain 1S residue 47 VAL Chi-restraints excluded: chain 1S residue 65 THR Chi-restraints excluded: chain 1S residue 74 VAL Chi-restraints excluded: chain 1S residue 87 ILE Chi-restraints excluded: chain 1T residue 7 LEU Chi-restraints excluded: chain 1T residue 15 ASP Chi-restraints excluded: chain 1T residue 43 GLU Chi-restraints excluded: chain 1T residue 47 ILE Chi-restraints excluded: chain 1T residue 79 VAL Chi-restraints excluded: chain 1T residue 85 VAL Chi-restraints excluded: chain 1T residue 109 ILE Chi-restraints excluded: chain 1U residue 8 ILE Chi-restraints excluded: chain 1U residue 82 LEU Chi-restraints excluded: chain 1U residue 110 GLU Chi-restraints excluded: chain 1V residue 22 LEU Chi-restraints excluded: chain 1V residue 32 THR Chi-restraints excluded: chain 1V residue 60 LYS Chi-restraints excluded: chain 1W residue 22 ASP Chi-restraints excluded: chain 1W residue 31 GLN Chi-restraints excluded: chain 1W residue 49 LYS Chi-restraints excluded: chain 1W residue 62 ASP Chi-restraints excluded: chain 1W residue 74 ILE Chi-restraints excluded: chain 1W residue 77 ASP Chi-restraints excluded: chain 1W residue 105 VAL Chi-restraints excluded: chain 1X residue 74 ILE Chi-restraints excluded: chain 1X residue 79 ASP Chi-restraints excluded: chain 1Y residue 5 ARG Chi-restraints excluded: chain 1Y residue 11 ILE Chi-restraints excluded: chain 1Y residue 14 THR Chi-restraints excluded: chain 1Y residue 48 VAL Chi-restraints excluded: chain 1Y residue 51 LEU Chi-restraints excluded: chain 1Y residue 58 VAL Chi-restraints excluded: chain 1Y residue 64 ILE Chi-restraints excluded: chain 1Y residue 66 VAL Chi-restraints excluded: chain 1Z residue 63 ILE Chi-restraints excluded: chain 1Z residue 65 VAL Chi-restraints excluded: chain 1Z residue 77 VAL Chi-restraints excluded: chain 10 residue 12 SER Chi-restraints excluded: chain 10 residue 13 GLU Chi-restraints excluded: chain 10 residue 32 ILE Chi-restraints excluded: chain 10 residue 42 HIS Chi-restraints excluded: chain 10 residue 49 CYS Chi-restraints excluded: chain 10 residue 63 VAL Chi-restraints excluded: chain 10 residue 78 ILE Chi-restraints excluded: chain 11 residue 13 THR Chi-restraints excluded: chain 11 residue 39 VAL Chi-restraints excluded: chain 12 residue 11 VAL Chi-restraints excluded: chain 12 residue 19 LEU Chi-restraints excluded: chain 12 residue 42 LEU Chi-restraints excluded: chain 12 residue 55 THR Chi-restraints excluded: chain 13 residue 9 THR Chi-restraints excluded: chain 14 residue 17 SER Chi-restraints excluded: chain 15 residue 5 ASN Chi-restraints excluded: chain 15 residue 24 VAL Chi-restraints excluded: chain 18 residue 6 VAL Chi-restraints excluded: chain 18 residue 53 ASP Chi-restraints excluded: chain 18 residue 56 LEU Chi-restraints excluded: chain 18 residue 60 CYS Chi-restraints excluded: chain 19 residue 4 ARG Chi-restraints excluded: chain 1b residue 26 MET Chi-restraints excluded: chain 1b residue 71 THR Chi-restraints excluded: chain 1b residue 152 ASP Chi-restraints excluded: chain 1b residue 185 ILE Chi-restraints excluded: chain 1c residue 9 ILE Chi-restraints excluded: chain 1c residue 10 ARG Chi-restraints excluded: chain 1c residue 51 VAL Chi-restraints excluded: chain 1c residue 55 VAL Chi-restraints excluded: chain 1c residue 105 VAL Chi-restraints excluded: chain 1c residue 115 VAL Chi-restraints excluded: chain 1c residue 127 VAL Chi-restraints excluded: chain 1c residue 181 ILE Chi-restraints excluded: chain 1d residue 66 VAL Chi-restraints excluded: chain 1d residue 73 ASN Chi-restraints excluded: chain 1d residue 116 LEU Chi-restraints excluded: chain 1d residue 158 LEU Chi-restraints excluded: chain 1d residue 172 VAL Chi-restraints excluded: chain 1d residue 197 HIS Chi-restraints excluded: chain 1d residue 200 VAL Chi-restraints excluded: chain 1e residue 72 ASN Chi-restraints excluded: chain 1e residue 80 LEU Chi-restraints excluded: chain 1e residue 96 GLN Chi-restraints excluded: chain 1e residue 115 GLU Chi-restraints excluded: chain 1e residue 121 ASN Chi-restraints excluded: chain 1e residue 152 VAL Chi-restraints excluded: chain 1f residue 18 VAL Chi-restraints excluded: chain 1g residue 6 ILE Chi-restraints excluded: chain 1g residue 58 LEU Chi-restraints excluded: chain 1g residue 84 TYR Chi-restraints excluded: chain 1g residue 93 VAL Chi-restraints excluded: chain 1g residue 115 MET Chi-restraints excluded: chain 1h residue 13 ILE Chi-restraints excluded: chain 1h residue 33 VAL Chi-restraints excluded: chain 1h residue 47 ASP Chi-restraints excluded: chain 1h residue 58 LEU Chi-restraints excluded: chain 1h residue 88 LYS Chi-restraints excluded: chain 1h residue 103 VAL Chi-restraints excluded: chain 1i residue 86 LEU Chi-restraints excluded: chain 1j residue 50 THR Chi-restraints excluded: chain 1k residue 25 SER Chi-restraints excluded: chain 1k residue 45 THR Chi-restraints excluded: chain 1k residue 58 THR Chi-restraints excluded: chain 1k residue 63 GLN Chi-restraints excluded: chain 1k residue 95 THR Chi-restraints excluded: chain 1k residue 107 THR Chi-restraints excluded: chain 1k residue 109 ILE Chi-restraints excluded: chain 1k residue 115 ILE Chi-restraints excluded: chain 1l residue 20 VAL Chi-restraints excluded: chain 1m residue 24 VAL Chi-restraints excluded: chain 1m residue 33 LEU Chi-restraints excluded: chain 1m residue 55 LEU Chi-restraints excluded: chain 1m residue 73 SER Chi-restraints excluded: chain 1m residue 76 ILE Chi-restraints excluded: chain 1m residue 107 THR Chi-restraints excluded: chain 1n residue 58 SER Chi-restraints excluded: chain 1o residue 51 SER Chi-restraints excluded: chain 1o residue 80 LEU Chi-restraints excluded: chain 1p residue 2 VAL Chi-restraints excluded: chain 1p residue 3 THR Chi-restraints excluded: chain 1p residue 19 VAL Chi-restraints excluded: chain 1p residue 29 ASN Chi-restraints excluded: chain 1p residue 36 VAL Chi-restraints excluded: chain 1p residue 55 ASP Chi-restraints excluded: chain 1p residue 61 VAL Chi-restraints excluded: chain 1p residue 66 THR Chi-restraints excluded: chain 1p residue 68 SER Chi-restraints excluded: chain 1q residue 37 ILE Chi-restraints excluded: chain 1q residue 56 ASP Chi-restraints excluded: chain 1q residue 58 VAL Chi-restraints excluded: chain 1q residue 78 VAL Chi-restraints excluded: chain 1r residue 39 VAL Chi-restraints excluded: chain 1r residue 44 THR Chi-restraints excluded: chain 1s residue 3 SER Chi-restraints excluded: chain 1s residue 10 ILE Chi-restraints excluded: chain 1s residue 11 ASP Chi-restraints excluded: chain 1s residue 18 VAL Chi-restraints excluded: chain 1s residue 22 VAL Chi-restraints excluded: chain 1s residue 34 SER Chi-restraints excluded: chain 1s residue 38 THR Chi-restraints excluded: chain 1t residue 11 ILE Chi-restraints excluded: chain 1t residue 19 HIS Chi-restraints excluded: chain 1u residue 5 VAL Chi-restraints excluded: chain 1u residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 650 optimal weight: 9.9990 chunk 1047 optimal weight: 6.9990 chunk 639 optimal weight: 8.9990 chunk 496 optimal weight: 9.9990 chunk 728 optimal weight: 10.0000 chunk 1098 optimal weight: 20.0000 chunk 1011 optimal weight: 0.9990 chunk 875 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 675 optimal weight: 10.0000 chunk 536 optimal weight: 8.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1N 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1O 93 GLN ** 1P 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1V 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1V 66 HIS 1W 7 HIS ** 1X 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1e 11 GLN ** 1f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1k 118 ASN ** 1o 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1p 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.8732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 161532 Z= 0.296 Angle : 0.780 27.011 240827 Z= 0.406 Chirality : 0.041 2.035 30226 Planarity : 0.007 0.127 13517 Dihedral : 23.276 179.879 79659 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.70 % Allowed : 9.73 % Favored : 89.57 % Rotamer: Outliers : 4.78 % Allowed : 28.87 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.10), residues: 6550 helix: -0.19 (0.12), residues: 1975 sheet: -1.99 (0.15), residues: 1101 loop : -1.84 (0.10), residues: 3474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.004 TRP1N 15 HIS 0.021 0.002 HIS1N 77 PHE 0.063 0.002 PHE1b 89 TYR 0.033 0.003 TYR1G 142 ARG 0.012 0.001 ARG1h 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13100 Ramachandran restraints generated. 6550 Oldfield, 0 Emsley, 6550 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1628 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1397 time to evaluate : 6.285 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: 1D 52 HIS cc_start: 0.7612 (m170) cc_final: 0.7290 (m170) REVERT: 1D 224 MET cc_start: 0.7989 (mmm) cc_final: 0.7730 (mmt) REVERT: 1E 64 GLU cc_start: 0.5842 (pt0) cc_final: 0.5511 (pt0) REVERT: 1F 47 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7957 (ptpt) REVERT: 1G 23 SER cc_start: 0.7595 (t) cc_final: 0.7089 (m) REVERT: 1G 95 MET cc_start: 0.7838 (ppp) cc_final: 0.6846 (ppp) REVERT: 1G 146 ASP cc_start: 0.6634 (m-30) cc_final: 0.6419 (m-30) REVERT: 1N 43 GLU cc_start: 0.6838 (pm20) cc_final: 0.6292 (pt0) REVERT: 1O 13 ASN cc_start: 0.7749 (p0) cc_final: 0.6873 (p0) REVERT: 1P 36 LYS cc_start: 0.9142 (mttt) cc_final: 0.8699 (mmtt) REVERT: 1Q 40 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7765 (ptm160) REVERT: 1R 72 ASP cc_start: 0.7320 (t0) cc_final: 0.6722 (t70) REVERT: 1R 107 ASN cc_start: 0.8339 (t0) cc_final: 0.7655 (t0) REVERT: 1S 112 GLU cc_start: 0.6771 (pp20) cc_final: 0.5991 (pp20) REVERT: 1T 50 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7493 (ttt-90) REVERT: 1U 31 TYR cc_start: 0.8581 (t80) cc_final: 0.8304 (t80) REVERT: 1Z 1 MET cc_start: 0.4878 (tpp) cc_final: 0.4410 (tmm) REVERT: 1Z 75 GLN cc_start: 0.7163 (pt0) cc_final: 0.6955 (pt0) REVERT: 12 8 GLU cc_start: 0.7094 (mp0) cc_final: 0.6306 (mt-10) REVERT: 13 5 LYS cc_start: 0.8479 (mmtt) cc_final: 0.7745 (mmtm) REVERT: 19 4 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8314 (ptp-170) REVERT: 19 37 GLN cc_start: 0.8050 (tp-100) cc_final: 0.7489 (tt0) REVERT: 1b 103 TRP cc_start: 0.6501 (t-100) cc_final: 0.6254 (t-100) REVERT: 1b 136 ARG cc_start: 0.6442 (mmp80) cc_final: 0.5112 (ptp-170) REVERT: 1d 13 ARG cc_start: 0.7481 (tpp-160) cc_final: 0.6877 (tpm170) REVERT: 1d 46 ARG cc_start: 0.6001 (tpt90) cc_final: 0.5536 (ttm170) REVERT: 1d 158 LEU cc_start: 0.2184 (OUTLIER) cc_final: 0.1094 (pp) REVERT: 1e 44 ARG cc_start: 0.7851 (ptm-80) cc_final: 0.7635 (ptm160) REVERT: 1e 53 ARG cc_start: 0.7351 (mmt90) cc_final: 0.7102 (mtt-85) REVERT: 1e 96 GLN cc_start: 0.7152 (OUTLIER) cc_final: 0.6491 (tt0) REVERT: 1e 110 MET cc_start: 0.7751 (tmm) cc_final: 0.7521 (tmm) REVERT: 1f 79 ARG cc_start: 0.6905 (mtp180) cc_final: 0.6584 (mtm180) REVERT: 1g 49 LEU cc_start: 0.8125 (pp) cc_final: 0.7576 (pp) REVERT: 1j 47 GLU cc_start: 0.7773 (mp0) cc_final: 0.7477 (mp0) REVERT: 1l 35 ARG cc_start: 0.7988 (tpt90) cc_final: 0.7703 (tpt-90) REVERT: 1l 43 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7608 (mttt) REVERT: 1l 87 LYS cc_start: 0.7626 (ttpp) cc_final: 0.7237 (ttpp) REVERT: 1o 83 ARG cc_start: 0.6283 (ttm170) cc_final: 0.5975 (ttp-110) REVERT: 1t 28 ARG cc_start: 0.7695 (ptp-110) cc_final: 0.7133 (ttp-110) outliers start: 231 outliers final: 209 residues processed: 1513 average time/residue: 1.3674 time to fit residues: 3607.3991 Evaluate side-chains 1585 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1370 time to evaluate : 6.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1D residue 53 ILE Chi-restraints excluded: chain 1D residue 139 THR Chi-restraints excluded: chain 1D residue 140 VAL Chi-restraints excluded: chain 1D residue 183 VAL Chi-restraints excluded: chain 1D residue 212 TRP Chi-restraints excluded: chain 1E residue 14 ILE Chi-restraints excluded: chain 1E residue 22 ILE Chi-restraints excluded: chain 1E residue 25 THR Chi-restraints excluded: chain 1E residue 51 THR Chi-restraints excluded: chain 1E residue 58 ASN Chi-restraints excluded: chain 1E residue 60 VAL Chi-restraints excluded: chain 1E residue 84 LEU Chi-restraints excluded: chain 1E residue 91 THR Chi-restraints excluded: chain 1E residue 109 VAL Chi-restraints excluded: chain 1E residue 113 SER Chi-restraints excluded: chain 1E residue 122 VAL Chi-restraints excluded: chain 1E residue 145 SER Chi-restraints excluded: chain 1E residue 177 VAL Chi-restraints excluded: chain 1E residue 180 VAL Chi-restraints excluded: chain 1E residue 189 VAL Chi-restraints excluded: chain 1E residue 200 ASP Chi-restraints excluded: chain 1F residue 14 VAL Chi-restraints excluded: chain 1F residue 18 THR Chi-restraints excluded: chain 1F residue 31 VAL Chi-restraints excluded: chain 1F residue 47 LYS Chi-restraints excluded: chain 1F residue 48 THR Chi-restraints excluded: chain 1F residue 84 THR Chi-restraints excluded: chain 1F residue 92 HIS Chi-restraints excluded: chain 1F residue 131 THR Chi-restraints excluded: chain 1F residue 176 ASP Chi-restraints excluded: chain 1G residue 122 ASP Chi-restraints excluded: chain 1G residue 151 LEU Chi-restraints excluded: chain 1H residue 36 LEU Chi-restraints excluded: chain 1H residue 37 ASN Chi-restraints excluded: chain 1H residue 83 THR Chi-restraints excluded: chain 1H residue 132 LEU Chi-restraints excluded: chain 1I residue 37 VAL Chi-restraints excluded: chain 1J residue 36 ASP Chi-restraints excluded: chain 1J residue 50 VAL Chi-restraints excluded: chain 1J residue 85 SER Chi-restraints excluded: chain 1K residue 10 LEU Chi-restraints excluded: chain 1K residue 59 THR Chi-restraints excluded: chain 1K residue 97 VAL Chi-restraints excluded: chain 1K residue 120 ASP Chi-restraints excluded: chain 1K residue 138 VAL Chi-restraints excluded: chain 1N residue 11 VAL Chi-restraints excluded: chain 1N residue 76 HIS Chi-restraints excluded: chain 1O residue 4 GLU Chi-restraints excluded: chain 1O residue 9 ASN Chi-restraints excluded: chain 1O residue 29 HIS Chi-restraints excluded: chain 1O residue 65 THR Chi-restraints excluded: chain 1P residue 61 LEU Chi-restraints excluded: chain 1Q residue 12 MET Chi-restraints excluded: chain 1Q residue 40 ARG Chi-restraints excluded: chain 1Q residue 44 ARG Chi-restraints excluded: chain 1Q residue 82 MET Chi-restraints excluded: chain 1Q residue 115 GLU Chi-restraints excluded: chain 1R residue 1 MET Chi-restraints excluded: chain 1R residue 13 ASN Chi-restraints excluded: chain 1R residue 23 ASN Chi-restraints excluded: chain 1R residue 33 ILE Chi-restraints excluded: chain 1R residue 37 THR Chi-restraints excluded: chain 1R residue 53 THR Chi-restraints excluded: chain 1S residue 12 THR Chi-restraints excluded: chain 1S residue 35 ILE Chi-restraints excluded: chain 1S residue 47 VAL Chi-restraints excluded: chain 1S residue 65 THR Chi-restraints excluded: chain 1S residue 74 VAL Chi-restraints excluded: chain 1S residue 87 ILE Chi-restraints excluded: chain 1T residue 7 LEU Chi-restraints excluded: chain 1T residue 15 ASP Chi-restraints excluded: chain 1T residue 23 ASP Chi-restraints excluded: chain 1T residue 43 GLU Chi-restraints excluded: chain 1T residue 47 ILE Chi-restraints excluded: chain 1T residue 50 ARG Chi-restraints excluded: chain 1T residue 79 VAL Chi-restraints excluded: chain 1T residue 85 VAL Chi-restraints excluded: chain 1T residue 109 ILE Chi-restraints excluded: chain 1U residue 8 ILE Chi-restraints excluded: chain 1U residue 82 LEU Chi-restraints excluded: chain 1V residue 22 LEU Chi-restraints excluded: chain 1V residue 32 THR Chi-restraints excluded: chain 1V residue 60 LYS Chi-restraints excluded: chain 1W residue 7 HIS Chi-restraints excluded: chain 1W residue 22 ASP Chi-restraints excluded: chain 1W residue 49 LYS Chi-restraints excluded: chain 1W residue 62 ASP Chi-restraints excluded: chain 1W residue 74 ILE Chi-restraints excluded: chain 1W residue 77 ASP Chi-restraints excluded: chain 1W residue 81 SER Chi-restraints excluded: chain 1W residue 96 ILE Chi-restraints excluded: chain 1W residue 105 VAL Chi-restraints excluded: chain 1X residue 74 ILE Chi-restraints excluded: chain 1Y residue 5 ARG Chi-restraints excluded: chain 1Y residue 11 ILE Chi-restraints excluded: chain 1Y residue 48 VAL Chi-restraints excluded: chain 1Y residue 51 LEU Chi-restraints excluded: chain 1Y residue 58 VAL Chi-restraints excluded: chain 1Y residue 64 ILE Chi-restraints excluded: chain 1Y residue 66 VAL Chi-restraints excluded: chain 1Z residue 60 VAL Chi-restraints excluded: chain 1Z residue 63 ILE Chi-restraints excluded: chain 1Z residue 65 VAL Chi-restraints excluded: chain 1Z residue 77 VAL Chi-restraints excluded: chain 10 residue 12 SER Chi-restraints excluded: chain 10 residue 13 GLU Chi-restraints excluded: chain 10 residue 32 ILE Chi-restraints excluded: chain 10 residue 42 HIS Chi-restraints excluded: chain 10 residue 49 CYS Chi-restraints excluded: chain 10 residue 63 VAL Chi-restraints excluded: chain 10 residue 78 ILE Chi-restraints excluded: chain 11 residue 13 THR Chi-restraints excluded: chain 11 residue 15 ASN Chi-restraints excluded: chain 11 residue 39 VAL Chi-restraints excluded: chain 12 residue 11 VAL Chi-restraints excluded: chain 12 residue 19 LEU Chi-restraints excluded: chain 12 residue 42 LEU Chi-restraints excluded: chain 12 residue 55 THR Chi-restraints excluded: chain 13 residue 9 THR Chi-restraints excluded: chain 14 residue 17 SER Chi-restraints excluded: chain 15 residue 5 ASN Chi-restraints excluded: chain 15 residue 24 VAL Chi-restraints excluded: chain 15 residue 43 THR Chi-restraints excluded: chain 18 residue 6 VAL Chi-restraints excluded: chain 18 residue 53 ASP Chi-restraints excluded: chain 18 residue 56 LEU Chi-restraints excluded: chain 18 residue 60 CYS Chi-restraints excluded: chain 19 residue 4 ARG Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 1b residue 26 MET Chi-restraints excluded: chain 1b residue 71 THR Chi-restraints excluded: chain 1b residue 185 ILE Chi-restraints excluded: chain 1b residue 188 THR Chi-restraints excluded: chain 1c residue 9 ILE Chi-restraints excluded: chain 1c residue 10 ARG Chi-restraints excluded: chain 1c residue 43 THR Chi-restraints excluded: chain 1c residue 51 VAL Chi-restraints excluded: chain 1c residue 55 VAL Chi-restraints excluded: chain 1c residue 105 VAL Chi-restraints excluded: chain 1c residue 115 VAL Chi-restraints excluded: chain 1c residue 127 VAL Chi-restraints excluded: chain 1c residue 181 ILE Chi-restraints excluded: chain 1d residue 66 VAL Chi-restraints excluded: chain 1d residue 73 ASN Chi-restraints excluded: chain 1d residue 116 LEU Chi-restraints excluded: chain 1d residue 158 LEU Chi-restraints excluded: chain 1d residue 172 VAL Chi-restraints excluded: chain 1d residue 197 HIS Chi-restraints excluded: chain 1d residue 200 VAL Chi-restraints excluded: chain 1e residue 25 LYS Chi-restraints excluded: chain 1e residue 72 ASN Chi-restraints excluded: chain 1e residue 80 LEU Chi-restraints excluded: chain 1e residue 89 THR Chi-restraints excluded: chain 1e residue 96 GLN Chi-restraints excluded: chain 1e residue 115 GLU Chi-restraints excluded: chain 1e residue 121 ASN Chi-restraints excluded: chain 1e residue 152 VAL Chi-restraints excluded: chain 1f residue 18 VAL Chi-restraints excluded: chain 1g residue 6 ILE Chi-restraints excluded: chain 1g residue 58 LEU Chi-restraints excluded: chain 1g residue 84 TYR Chi-restraints excluded: chain 1g residue 93 VAL Chi-restraints excluded: chain 1g residue 115 MET Chi-restraints excluded: chain 1h residue 13 ILE Chi-restraints excluded: chain 1h residue 33 VAL Chi-restraints excluded: chain 1h residue 47 ASP Chi-restraints excluded: chain 1h residue 58 LEU Chi-restraints excluded: chain 1h residue 62 LEU Chi-restraints excluded: chain 1h residue 88 LYS Chi-restraints excluded: chain 1h residue 103 VAL Chi-restraints excluded: chain 1h residue 123 GLU Chi-restraints excluded: chain 1i residue 86 LEU Chi-restraints excluded: chain 1j residue 50 THR Chi-restraints excluded: chain 1k residue 25 SER Chi-restraints excluded: chain 1k residue 30 ILE Chi-restraints excluded: chain 1k residue 45 THR Chi-restraints excluded: chain 1k residue 58 THR Chi-restraints excluded: chain 1k residue 63 GLN Chi-restraints excluded: chain 1k residue 109 ILE Chi-restraints excluded: chain 1k residue 115 ILE Chi-restraints excluded: chain 1l residue 20 VAL Chi-restraints excluded: chain 1l residue 51 VAL Chi-restraints excluded: chain 1m residue 24 VAL Chi-restraints excluded: chain 1m residue 33 LEU Chi-restraints excluded: chain 1m residue 73 SER Chi-restraints excluded: chain 1m residue 76 ILE Chi-restraints excluded: chain 1m residue 96 VAL Chi-restraints excluded: chain 1n residue 12 LYS Chi-restraints excluded: chain 1n residue 58 SER Chi-restraints excluded: chain 1o residue 51 SER Chi-restraints excluded: chain 1o residue 80 LEU Chi-restraints excluded: chain 1p residue 2 VAL Chi-restraints excluded: chain 1p residue 3 THR Chi-restraints excluded: chain 1p residue 19 VAL Chi-restraints excluded: chain 1p residue 29 ASN Chi-restraints excluded: chain 1p residue 36 VAL Chi-restraints excluded: chain 1p residue 55 ASP Chi-restraints excluded: chain 1p residue 61 VAL Chi-restraints excluded: chain 1p residue 66 THR Chi-restraints excluded: chain 1p residue 68 SER Chi-restraints excluded: chain 1q residue 56 ASP Chi-restraints excluded: chain 1q residue 58 VAL Chi-restraints excluded: chain 1q residue 78 VAL Chi-restraints excluded: chain 1r residue 39 VAL Chi-restraints excluded: chain 1r residue 44 THR Chi-restraints excluded: chain 1s residue 10 ILE Chi-restraints excluded: chain 1s residue 11 ASP Chi-restraints excluded: chain 1s residue 18 VAL Chi-restraints excluded: chain 1s residue 34 SER Chi-restraints excluded: chain 1s residue 38 THR Chi-restraints excluded: chain 1s residue 65 MET Chi-restraints excluded: chain 1t residue 11 ILE Chi-restraints excluded: chain 1t residue 19 HIS Chi-restraints excluded: chain 1u residue 5 VAL Chi-restraints excluded: chain 1u residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 695 optimal weight: 10.0000 chunk 932 optimal weight: 0.9990 chunk 268 optimal weight: 10.0000 chunk 806 optimal weight: 0.0670 chunk 129 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 876 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 899 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 overall best weight: 5.8130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1T 11 GLN ** 1V 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1V 66 HIS 1X 15 HIS ** 1Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1d 70 GLN 1d 99 ASN 1e 11 GLN ** 1f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1k 118 ASN ** 1p 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.114159 restraints weight = 295552.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116666 restraints weight = 142426.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.116807 restraints weight = 71701.463| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.8813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 161532 Z= 0.313 Angle : 0.793 26.960 240827 Z= 0.412 Chirality : 0.042 2.037 30226 Planarity : 0.007 0.128 13517 Dihedral : 23.293 179.914 79659 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.08 % Favored : 89.28 % Rotamer: Outliers : 5.22 % Allowed : 29.03 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.10), residues: 6550 helix: -0.27 (0.12), residues: 1994 sheet: -1.92 (0.15), residues: 1106 loop : -1.91 (0.10), residues: 3450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.131 0.004 TRP1N 15 HIS 0.097 0.003 HIS1W 7 PHE 0.040 0.002 PHE1b 89 TYR 0.033 0.003 TYR1G 142 ARG 0.019 0.001 ARG1W 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47680.94 seconds wall clock time: 828 minutes 39.00 seconds (49719.00 seconds total)