Starting phenix.real_space_refine on Wed Apr 17 07:50:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcr_8237/04_2024/5kcr_8237_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcr_8237/04_2024/5kcr_8237.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcr_8237/04_2024/5kcr_8237_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcr_8237/04_2024/5kcr_8237_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcr_8237/04_2024/5kcr_8237_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcr_8237/04_2024/5kcr_8237.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcr_8237/04_2024/5kcr_8237.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcr_8237/04_2024/5kcr_8237_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kcr_8237/04_2024/5kcr_8237_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4653 5.49 5 S 149 5.16 5 Cl 2 4.86 5 C 73266 2.51 5 N 27107 2.21 5 O 40511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1D ARG 52": "NH1" <-> "NH2" Residue "1D ARG 63": "NH1" <-> "NH2" Residue "1D ARG 80": "NH1" <-> "NH2" Residue "1D ARG 133": "NH1" <-> "NH2" Residue "1D TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D ARG 167": "NH1" <-> "NH2" Residue "1D ARG 177": "NH1" <-> "NH2" Residue "1D ARG 182": "NH1" <-> "NH2" Residue "1D ARG 189": "NH1" <-> "NH2" Residue "1D ARG 203": "NH1" <-> "NH2" Residue "1D ARG 212": "NH1" <-> "NH2" 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 TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F ARG 162": "NH1" <-> "NH2" Residue "1F ARG 170": "NH1" <-> "NH2" Residue "1G ARG 71": "NH1" <-> "NH2" Residue "1G ARG 92": "NH1" <-> "NH2" Residue "1G ARG 102": "NH1" <-> "NH2" Residue "1G ARG 110": "NH1" <-> "NH2" Residue "1G ARG 112": "NH1" <-> "NH2" Residue "1G ARG 115": "NH1" <-> "NH2" Residue "1G ARG 133": "NH1" <-> "NH2" Residue "1H ARG 3": "NH1" <-> "NH2" Residue "1H ARG 153": "NH1" <-> "NH2" Residue "1H ARG 163": "NH1" <-> "NH2" Residue "1H ARG 170": "NH1" <-> "NH2" Residue "1I ARG 27": "NH1" <-> "NH2" Residue "1K PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1N ARG 13": "NH1" <-> "NH2" Residue "1N ARG 37": "NH1" <-> "NH2" Residue "1N ARG 96": "NH1" <-> "NH2" Residue "1N ARG 120": "NH1" <-> "NH2" 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 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 81": "NH1" <-> "NH2" Residue "1Q ARG 81": "NH1" <-> "NH2" Residue "1Q TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 21": "NH1" <-> "NH2" Residue "1T ARG 39": "NH1" <-> "NH2" Residue "1T PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1T PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1T ARG 62": "NH1" <-> "NH2" Residue "1T ARG 89": "NH1" <-> "NH2" Residue "1T ARG 101": "NH1" <-> "NH2" Residue "1T ARG 109": "NH1" <-> "NH2" Residue "1U ARG 3": "NH1" <-> "NH2" Residue "1U ARG 6": "NH1" <-> "NH2" Residue "1U ARG 13": "NH1" <-> "NH2" Residue "1U ARG 33": "NH1" <-> "NH2" Residue "1U ARG 48": "NH1" <-> "NH2" Residue "1U ARG 70": "NH1" <-> "NH2" 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 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 6": "NH1" <-> "NH2" Residue "1Y ARG 7": "NH1" <-> "NH2" Residue "1Y ARG 82": "NH1" <-> "NH2" Residue "1Y ARG 86": "NH1" <-> "NH2" Residue "1Y ARG 94": "NH1" <-> "NH2" Residue "11 ARG 3": "NH1" <-> "NH2" Residue "11 ARG 11": "NH1" <-> "NH2" Residue "11 ARG 18": "NH1" <-> "NH2" Residue "11 ARG 37": "NH1" <-> "NH2" Residue "11 ARG 50": "NH1" <-> "NH2" Residue "11 ARG 57": "NH1" <-> "NH2" Residue "11 ARG 74": "NH1" <-> "NH2" Residue "11 TYR 78": "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 11": "NH1" <-> "NH2" Residue "13 ARG 30": "NH1" <-> "NH2" Residue "13 ARG 45": "NH1" <-> "NH2" Residue "13 PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "15 ARG 10": "NH1" <-> "NH2" Residue "15 ARG 16": "NH1" <-> "NH2" Residue "15 ARG 52": "NH1" <-> "NH2" Residue "16 ARG 44": "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 13": "NH1" <-> "NH2" Residue "18 ARG 30": "NH1" <-> "NH2" Residue "18 ARG 40": "NH1" <-> "NH2" Residue "18 ARG 42": "NH1" <-> "NH2" Residue "19 ARG 24": "NH1" <-> "NH2" Residue "1b PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1b PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1c PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1c ARG 131": "NH1" <-> "NH2" Residue "1e PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1h PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1i ARG 124": "NH1" <-> "NH2" Residue "1l ARG 56": "NH1" <-> "NH2" Residue "1p ARG 28": "NH1" <-> "NH2" Residue "1p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1u PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 145689 Number of models: 1 Model: "" Number of chains: 57 Chain: "1A" Number of atoms: 62361 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2897, 62209 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 7, 'rna2p_pur': 279, 'rna2p_pyr': 145, 'rna3p': 17, 'rna3p_pur': 1385, 'rna3p_pyr': 1064} Link IDs: {'rna2p': 431, 'rna3p': 2465} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 10 Conformer: "B" Number of residues, atoms: 2897, 62209 Classifications: {'RNA': 2897} Modifications used: {'rna2p': 7, 'rna2p_pur': 280, 'rna2p_pyr': 144, 'rna3p': 17, 'rna3p_pur': 1384, 'rna3p_pyr': 1065} Link IDs: {'rna2p': 431, 'rna3p': 2465} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 10 bond proxies already assigned to first conformer: 69499 Chain: "1B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} 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: 1576 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1576 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: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1404 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "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: "1I" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "1J" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1023 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 128} Chain: "1K" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 979 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} 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: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "1P" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "1Q" Number of atoms: 1090 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} bond proxies already assigned to first conformer: 1075 Chain: "1R" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 993 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "1S" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "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: {'PCIS': 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: 591 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 575 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: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "13" Number of atoms: 463 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Conformer: "B" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} bond proxies already assigned to first conformer: 439 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: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "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: 33015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33015 Classifications: {'RNA': 1539} Modifications used: {'rna2p_pur': 119, 'rna2p_pyr': 87, 'rna3p_pur': 755, 'rna3p_pyr': 578} Link IDs: {'rna2p': 206, 'rna3p': 1332} Chain: "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: {'PTRANS': 7, '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: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} 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: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "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: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "1o" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 710 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 87} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} 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: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1v" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "1x" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1861 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 40, 'rna3p_pyr': 36} Link IDs: {'rna2p': 10, 'rna3p': 76} Chain: "1A" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 95 Unusual residues: {'6UQ': 1} Classifications: {'undetermined': 1} Chain: "19" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 91901 SG CYS19 11 115.959 149.714 220.674 1.00139.09 S ATOM 91926 SG CYS19 14 114.135 152.696 219.673 1.00136.57 S ATOM 92029 SG CYS19 27 118.009 152.848 221.112 1.00131.38 S Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" P A A1A 404 " occ=0.60 ... (42 atoms not shown) pdb=" C4 B A1A 404 " occ=0.40 residue: pdb=" P A U1A2884 " occ=0.53 ... (38 atoms not shown) pdb=" C6 B U1A2884 " occ=0.47 residue: pdb=" P A G1A2885 " occ=0.53 ... (44 atoms not shown) pdb=" C4 B G1A2885 " occ=0.47 residue: pdb=" P A A1A2886 " occ=0.53 ... (42 atoms not shown) pdb=" C4 B A1A2886 " occ=0.47 residue: pdb=" P A A1A2887 " occ=0.53 ... (42 atoms not shown) pdb=" C4 B A1A2887 " occ=0.47 residue: pdb=" P A C1A2888 " occ=0.53 ... (38 atoms not shown) pdb=" C6 B C1A2888 " occ=0.47 residue: pdb=" N AMEQ1E 150 " occ=0.49 ... (18 atoms not shown) pdb=" NE2BMEQ1E 150 " occ=0.51 residue: pdb=" N AARG10 41 " occ=0.51 ... (20 atoms not shown) pdb=" NH2BARG10 41 " occ=0.49 residue: pdb=" N AALA13 2 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA13 2 " occ=0.50 residue: pdb=" N ALYS13 3 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS13 3 " occ=0.50 Time building chain proxies: 77.43, per 1000 atoms: 0.53 Number of scatterers: 145689 At special positions: 0 Unit cell: (267.028, 280.324, 285.864, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Cl 2 17.00 S 149 16.00 P 4653 15.00 O 40511 8.00 N 27107 7.00 C 73266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 62.86 Conformation dependent library (CDL) restraints added in 7.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN19 101 " pdb="ZN ZN19 101 " - pdb=" SG CYS19 14 " pdb="ZN ZN19 101 " - pdb=" SG CYS19 27 " pdb="ZN ZN19 101 " - pdb=" SG CYS19 11 " pdb="ZN ZN19 101 " - pdb=" ND1 HIS19 33 " Number of angles added : 3 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10768 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: 177 helices and 68 sheets defined 38.6% alpha, 17.9% beta 1535 base pairs and 2619 stacking pairs defined. Time for finding SS restraints: 76.30 Creating SS restraints... Processing helix chain '1D' and resid 10 through 17 removed outlier: 4.982A pdb=" N HIS1D 15 " --> pdb=" O PRO1D 11 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL1D 16 " --> pdb=" O GLY1D 12 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL1D 17 " --> pdb=" O ARG1D 13 " (cutoff:3.500A) Processing helix chain '1D' and resid 30 through 35 removed outlier: 4.225A pdb=" N LEU1D 34 " --> pdb=" O PHE1D 30 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLU1D 35 " --> pdb=" O ALA1D 31 " (cutoff:3.500A) No H-bonds generated for 'chain '1D' and resid 30 through 35' Processing helix chain '1D' and resid 131 through 136 removed outlier: 3.812A pdb=" N ILE1D 135 " --> pdb=" O PRO1D 131 " (cutoff:3.500A) Proline residue: 1D 136 - end of helix No H-bonds generated for 'chain '1D' and resid 131 through 136' Processing helix chain '1D' and resid 207 through 215 removed outlier: 3.966A pdb=" N ALA1D 211 " --> pdb=" O LYS1D 207 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG1D 214 " --> pdb=" O ALA1D 210 " (cutoff:3.500A) Processing helix chain '1D' and resid 221 through 226 removed outlier: 3.867A pdb=" N MET1D 225 " --> pdb=" O ARG1D 221 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASN1D 226 " --> pdb=" O GLY1D 222 " (cutoff:3.500A) No H-bonds generated for 'chain '1D' and resid 221 through 226' Processing helix chain '1D' and resid 260 through 268 removed outlier: 4.925A pdb=" N LYS1D 265 " --> pdb=" O LYS1D 261 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE1D 266 " --> pdb=" O ARG1D 262 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE1D 267 " --> pdb=" O THR1D 263 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N VAL1D 268 " --> pdb=" O ASP1D 264 " (cutoff:3.500A) Processing helix chain '1E' and resid 56 through 61 removed outlier: 5.256A pdb=" N THR1E 61 " --> pdb=" O ALA1E 57 " (cutoff:3.500A) Processing helix chain '1E' and resid 62 through 72 removed outlier: 3.514A pdb=" N ALA1E 71 " --> pdb=" O HIS1E 67 " (cutoff:3.500A) Processing helix chain '1E' and resid 98 through 103 removed outlier: 4.367A pdb=" N ALA1E 102 " --> pdb=" O VAL1E 98 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP1E 103 " --> pdb=" O GLU1E 99 " (cutoff:3.500A) No H-bonds generated for 'chain '1E' and resid 98 through 103' Processing helix chain '1E' and resid 120 through 125 Processing helix chain '1E' and resid 39 through 44 Processing helix chain '1F' and resid 15 through 20 Processing helix chain '1F' and resid 24 through 40 removed outlier: 3.706A pdb=" N ARG1F 40 " --> pdb=" O ALA1F 36 " (cutoff:3.500A) Processing helix chain '1F' and resid 97 through 116 Processing helix chain '1F' and resid 130 through 142 removed outlier: 3.518A pdb=" N LEU1F 134 " --> pdb=" O LYS1F 130 " (cutoff:3.500A) Processing helix chain '1F' and resid 154 through 163 removed outlier: 4.618A pdb=" N ASN1F 163 " --> pdb=" O LEU1F 159 " (cutoff:3.500A) Processing helix chain '1F' and resid 176 through 183 removed outlier: 3.527A pdb=" N ILE1F 181 " --> pdb=" O PRO1F 177 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE1F 183 " --> pdb=" O SER1F 179 " (cutoff:3.500A) Processing helix chain '1F' and resid 189 through 201 Processing helix chain '1G' and resid 2 through 21 removed outlier: 4.526A pdb=" N VAL1G 13 " --> pdb=" O LYS1G 9 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LYS1G 14 " --> pdb=" O ASP1G 10 " (cutoff:3.500A) Processing helix chain '1G' and resid 42 through 47 removed outlier: 3.650A pdb=" N ASP1G 46 " --> pdb=" O GLU1G 42 " (cutoff:3.500A) Processing helix chain '1G' and resid 48 through 62 Processing helix chain '1G' and resid 93 through 105 Processing helix chain '1G' and resid 106 through 111 removed outlier: 3.582A pdb=" N ARG1G 110 " --> pdb=" O ILE1G 106 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE1G 111 " --> pdb=" O ALA1G 107 " (cutoff:3.500A) No H-bonds generated for 'chain '1G' and resid 106 through 111' Processing helix chain '1G' and resid 162 through 174 removed outlier: 3.601A pdb=" N PHE1G 173 " --> pdb=" O LEU1G 169 " (cutoff:3.500A) Processing helix chain '1G' and resid 134 through 139 removed outlier: 3.505A pdb=" N PHE1G 138 " --> pdb=" O GLN1G 135 " (cutoff:3.500A) Proline residue: 1G 139 - end of helix Processing helix chain '1H' and resid 2 through 8 removed outlier: 3.938A pdb=" N ALA1H 7 " --> pdb=" O ARG1H 3 " (cutoff:3.500A) Proline residue: 1H 8 - end of helix Processing helix chain '1H' and resid 60 through 81 Processing helix chain '1H' and resid 137 through 153 removed outlier: 3.684A pdb=" N TYR1H 151 " --> pdb=" O ASP1H 147 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG1H 152 " --> pdb=" O LEU1H 148 " (cutoff:3.500A) Processing helix chain '1I' and resid 22 through 29 Processing helix chain '1I' and resid 40 through 76 removed outlier: 3.662A pdb=" N ALA1I 67 " --> pdb=" O ALA1I 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN1I 73 " --> pdb=" O ALA1I 69 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU1I 75 " --> pdb=" O LYS1I 71 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU1I 76 " --> pdb=" O ILE1I 72 " (cutoff:3.500A) Processing helix chain '1I' and resid 95 through 107 removed outlier: 3.565A pdb=" N ALA1I 105 " --> pdb=" O ASP1I 101 " (cutoff:3.500A) Processing helix chain '1I' and resid 111 through 116 removed outlier: 3.859A pdb=" N VAL1I 115 " --> pdb=" O ALA1I 111 " (cutoff:3.500A) removed outlier: 5.706A 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 4 through 22 removed outlier: 3.662A pdb=" N GLY1J 21 " --> pdb=" O GLU1J 17 " (cutoff:3.500A) Processing helix chain '1J' and resid 34 through 49 Processing helix chain '1J' and resid 56 through 68 removed outlier: 3.634A pdb=" N ARG1J 62 " --> pdb=" O THR1J 58 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY1J 66 " --> pdb=" O ARG1J 62 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR1J 67 " --> pdb=" O ALA1J 63 " (cutoff:3.500A) Proline residue: 1J 68 - end of helix Processing helix chain '1J' and resid 72 through 77 removed outlier: 3.720A pdb=" N PHE1J 76 " --> pdb=" O LEU1J 72 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL1J 77 " --> pdb=" O LYS1J 73 " (cutoff:3.500A) No H-bonds generated for 'chain '1J' and resid 72 through 77' Processing helix chain '1J' and resid 90 through 104 removed outlier: 5.814A pdb=" N ARG1J 94 " --> pdb=" O GLY1J 90 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS1J 97 " --> pdb=" O ALA1J 93 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU1J 98 " --> pdb=" O ARG1J 94 " (cutoff:3.500A) Processing helix chain '1J' and resid 123 through 129 Processing helix chain '1K' and resid 24 through 32 removed outlier: 4.694A pdb=" N GLN1K 31 " --> pdb=" O ALA1K 27 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY1K 32 " --> pdb=" O LEU1K 28 " (cutoff:3.500A) Processing helix chain '1K' and resid 34 through 47 removed outlier: 3.580A pdb=" N PHE1K 38 " --> pdb=" O ASN1K 34 " (cutoff:3.500A) Processing helix chain '1K' and resid 75 through 85 Processing helix chain '1K' and resid 102 through 115 Processing helix chain '1K' and resid 121 through 137 removed outlier: 3.610A pdb=" N GLY1K 137 " --> pdb=" O ALA1K 133 " (cutoff:3.500A) Processing helix chain '1N' and resid 24 through 38 removed outlier: 4.086A pdb=" N GLU1N 31 " --> pdb=" O ARG1N 27 " (cutoff:3.500A) Processing helix chain '1N' and resid 88 through 96 Processing helix chain '1N' and resid 97 through 110 removed outlier: 4.157A pdb=" N ILE1N 101 " --> pdb=" O PRO1N 97 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET1N 108 " --> pdb=" O ALA1N 104 " (cutoff:3.500A) Proline residue: 1N 110 - end of helix Processing helix chain '1N' and resid 112 through 122 removed outlier: 3.989A pdb=" N LYS1N 121 " --> pdb=" O ALA1N 117 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU1N 122 " --> pdb=" O MET1N 118 " (cutoff:3.500A) Processing helix chain '1O' and resid 104 through 109 removed outlier: 4.724A pdb=" N ARG1O 108 " --> pdb=" O THR1O 104 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N SER1O 109 " --> pdb=" O ARG1O 105 " (cutoff:3.500A) No H-bonds generated for 'chain '1O' and resid 104 through 109' Processing helix chain '1O' and resid 112 through 119 removed outlier: 3.539A pdb=" N ILE1O 116 " --> pdb=" O PHE1O 112 " (cutoff:3.500A) Processing helix chain '1P' and resid 56 through 62 Proline residue: 1P 62 - end of helix Processing helix chain '1P' and resid 68 through 75 removed outlier: 4.060A pdb=" N ALA1P 72 " --> pdb=" O SER1P 68 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE1P 73 " --> pdb=" O ARG1P 69 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ALA1P 75 " --> pdb=" O ALA1P 71 " (cutoff:3.500A) Processing helix chain '1P' and resid 78 through 85 removed outlier: 3.870A pdb=" N LEU1P 82 " --> pdb=" O ARG1P 78 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA1P 83 " --> pdb=" O LEU1P 79 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS1P 84 " --> pdb=" O SER1P 80 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL1P 85 " --> pdb=" O ASP1P 81 " (cutoff:3.500A) No H-bonds generated for 'chain '1P' and resid 78 through 85' Processing helix chain '1P' and resid 91 through 99 Processing helix chain '1P' and resid 128 through 139 removed outlier: 3.705A pdb=" N GLY1P 139 " --> pdb=" O ILE1P 135 " (cutoff:3.500A) Processing helix chain '1Q' and resid 42 through 58 removed outlier: 4.051A pdb=" N ARG1Q 50 " --> pdb=" O ILE1Q 46 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ARG1Q 51 " --> pdb=" O GLU1Q 47 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA1Q 52 " --> pdb=" O ALA1Q 48 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ARG1Q 55 " --> pdb=" O ARG1Q 51 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS1Q 58 " --> pdb=" O THR1Q 54 " (cutoff:3.500A) Processing helix chain '1Q' and resid 109 through 125 removed outlier: 4.157A pdb=" N LYS1Q 123 " --> pdb=" O LEU1Q 119 " (cutoff:3.500A) removed outlier: 3.914A 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 32 Processing helix chain '1R' and resid 38 through 57 removed outlier: 3.516A pdb=" N ARG1R 45 " --> pdb=" O ALA1R 41 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG1R 46 " --> pdb=" O LYS1R 42 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL1R 47 " --> pdb=" O GLU1R 43 " (cutoff:3.500A) Proline residue: 1R 50 - end of helix removed outlier: 4.574A pdb=" N THR1R 57 " --> pdb=" O THR1R 53 " (cutoff:3.500A) Processing helix chain '1R' and resid 59 through 71 Processing helix chain '1R' and resid 72 through 88 removed outlier: 5.053A pdb=" N GLY1R 84 " --> pdb=" O PHE1R 80 " (cutoff:3.500A) Proline residue: 1R 85 - end of helix Processing helix chain '1R' and resid 119 through 125 removed outlier: 3.516A pdb=" N ALA1R 124 " --> pdb=" O GLU1R 120 " (cutoff:3.500A) Processing helix chain '1S' and resid 2 through 22 removed outlier: 4.705A pdb=" N ARG1S 13 " --> pdb=" O ARG1S 9 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA1S 14 " --> pdb=" O ARG1S 10 " (cutoff:3.500A) Processing helix chain '1S' and resid 55 through 63 removed outlier: 4.828A pdb=" N GLN1S 61 " --> pdb=" O ALA1S 57 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU1S 62 " --> pdb=" O ILE1S 58 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LYS1S 63 " --> pdb=" O ALA1S 59 " (cutoff:3.500A) Processing helix chain '1S' and resid 67 through 86 removed outlier: 3.629A pdb=" N LYS1S 85 " --> pdb=" O ARG1S 81 " (cutoff:3.500A) Processing helix chain '1S' and resid 101 through 114 removed outlier: 3.680A pdb=" N GLY1S 114 " --> pdb=" O ALA1S 110 " (cutoff:3.500A) Processing helix chain '1T' and resid 2 through 14 removed outlier: 3.532A pdb=" N GLU1T 11 " --> pdb=" O GLN1T 7 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN1T 12 " --> pdb=" O LEU1T 8 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LYS1T 14 " --> pdb=" O GLN1T 10 " (cutoff:3.500A) Processing helix chain '1T' and resid 97 through 104 removed outlier: 4.658A pdb=" N ARG1T 101 " --> pdb=" O LEU1T 97 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLU1T 102 " --> pdb=" O TYR1T 98 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG1T 103 " --> pdb=" O TYR1T 99 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N THR1T 104 " --> pdb=" O LEU1T 100 " (cutoff:3.500A) No H-bonds generated for 'chain '1T' and resid 97 through 104' Processing helix chain '1U' and resid 6 through 22 removed outlier: 3.538A pdb=" N ALA1U 12 " --> pdb=" O VAL1U 8 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN1U 20 " --> pdb=" O LYS1U 16 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS1U 22 " --> pdb=" O LEU1U 18 " (cutoff:3.500A) Processing helix chain '1U' and resid 26 through 31 removed outlier: 3.888A pdb=" N ARG1U 30 " --> pdb=" O GLY1U 26 " (cutoff:3.500A) Processing helix chain '1U' and resid 32 through 37 removed outlier: 3.591A pdb=" N GLN1U 37 " --> pdb=" O ARG1U 33 " (cutoff:3.500A) Processing helix chain '1U' and resid 39 through 73 removed outlier: 3.787A pdb=" N ARG1U 51 " --> pdb=" O TYR1U 47 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS1U 54 " --> pdb=" O ARG1U 50 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG1U 55 " --> pdb=" O ARG1U 51 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG1U 58 " --> pdb=" O LYS1U 54 " (cutoff:3.500A) Processing helix chain '1U' and resid 75 through 87 Processing helix chain '1U' and resid 91 through 102 Processing helix chain '1U' and resid 103 through 118 Processing helix chain '1W' and resid 13 through 25 removed outlier: 4.030A pdb=" N VAL1W 20 " --> pdb=" O LYS1W 16 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU1W 23 " --> pdb=" O LEU1W 19 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE1W 24 " --> pdb=" O VAL1W 20 " (cutoff:3.500A) Processing helix chain '1W' and resid 28 through 39 Processing helix chain '1W' and resid 41 through 61 removed outlier: 3.600A pdb=" N VAL1W 45 " --> pdb=" O LYS1W 41 " (cutoff:3.500A) Processing helix chain '1X' and resid 3 through 11 removed outlier: 3.791A pdb=" N LYS1X 9 " --> pdb=" O GLU1X 5 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU1X 11 " --> pdb=" O LEU1X 7 " (cutoff:3.500A) Processing helix chain '1X' and resid 17 through 27 Processing helix chain '1X' and resid 39 through 51 Processing helix chain '1Y' and resid 66 through 71 removed outlier: 3.964A pdb=" N VAL1Y 70 " --> pdb=" O GLN1Y 66 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ALA1Y 71 " --> pdb=" O VAL1Y 67 " (cutoff:3.500A) No H-bonds generated for 'chain '1Y' and resid 66 through 71' Processing helix chain '1Z' and resid 13 through 24 Processing helix chain '1Z' and resid 43 through 53 removed outlier: 4.433A pdb=" N LYS1Z 53 " --> pdb=" O ASN1Z 49 " (cutoff:3.500A) Processing helix chain '1Z' and resid 54 through 59 removed outlier: 3.741A pdb=" N SER1Z 58 " --> pdb=" O ALA1Z 54 " (cutoff:3.500A) Processing helix chain '11' and resid 52 through 63 Processing helix chain '11' and resid 64 through 75 Processing helix chain '12' and resid 2 through 10 removed outlier: 6.051A pdb=" N LEU12 6 " --> pdb=" O LYS12 2 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG12 7 " --> pdb=" O ALA12 3 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS12 9 " --> pdb=" O GLU12 5 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N SER12 10 " --> pdb=" O LEU12 6 " (cutoff:3.500A) Processing helix chain '12' and resid 11 through 35 Processing helix chain '12' and resid 40 through 63 removed outlier: 4.638A pdb=" N LYS12 44 " --> pdb=" O SER12 40 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN12 45 " --> pdb=" O HIS12 41 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA12 63 " --> pdb=" O GLU12 59 " (cutoff:3.500A) Processing helix chain '13' and resid 17 through 28 Processing helix chain '13' and resid 41 through 52 removed outlier: 3.560A pdb=" N MET13 47 " --> pdb=" O ALA13 43 " (cutoff:3.500A) Processing helix chain '15' and resid 9 through 18 Processing helix chain '17' and resid 8 through 16 Processing helix chain '17' and resid 17 through 25 removed outlier: 4.180A pdb=" N THR17 24 " --> pdb=" O ALA17 20 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LYS17 25 " --> pdb=" O ARG17 21 " (cutoff:3.500A) Processing helix chain '17' and resid 26 through 38 Processing helix chain '18' and resid 7 through 14 removed outlier: 3.532A pdb=" N LYS18 12 " --> pdb=" O ARG18 8 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG18 13 " --> pdb=" O GLY18 9 " (cutoff:3.500A) Processing helix chain '18' and resid 32 through 37 removed outlier: 4.730A pdb=" N LYS18 36 " --> pdb=" O ILE18 32 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ALA18 37 " --> pdb=" O LEU18 33 " (cutoff:3.500A) No H-bonds generated for 'chain '18' and resid 32 through 37' Processing helix chain '18' and resid 38 through 46 Proline residue: 18 46 - end of helix Processing helix chain '18' and resid 51 through 63 removed outlier: 4.723A pdb=" N GLY18 56 " --> pdb=" O LYS18 52 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU18 57 " --> pdb=" O GLY18 53 " (cutoff:3.500A) Proline residue: 18 63 - end of helix Processing helix chain '1b' and resid 24 through 29 removed outlier: 3.918A pdb=" N LYS1b 28 " --> pdb=" O ASN1b 24 " (cutoff:3.500A) Proline residue: 1b 29 - end of helix No H-bonds generated for 'chain '1b' and resid 24 through 29' Processing helix chain '1b' and resid 42 through 64 Proline residue: 1b 48 - end of helix removed outlier: 4.263A pdb=" N GLU1b 56 " --> pdb=" O GLU1b 52 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU1b 57 " --> pdb=" O ALA1b 53 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS1b 59 " --> pdb=" O ALA1b 55 " (cutoff:3.500A) Processing helix chain '1b' and resid 76 through 82 removed outlier: 4.203A pdb=" N LYS1b 81 " --> pdb=" O SER1b 77 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP1b 82 " --> pdb=" O GLU1b 78 " (cutoff:3.500A) Processing helix chain '1b' and resid 99 through 104 Processing helix chain '1b' and resid 105 through 123 removed outlier: 4.684A pdb=" N GLN1b 109 " --> pdb=" O LYS1b 105 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER1b 110 " --> pdb=" O THR1b 106 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR1b 119 " --> pdb=" O LYS1b 115 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN1b 120 " --> pdb=" O ASP1b 116 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLN1b 122 " --> pdb=" O GLU1b 118 " (cutoff:3.500A) Processing helix chain '1b' and resid 130 through 148 removed outlier: 3.624A pdb=" N ALA1b 134 " --> pdb=" O THR1b 130 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG1b 137 " --> pdb=" O GLU1b 133 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU1b 140 " --> pdb=" O MET1b 136 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU1b 141 " --> pdb=" O ARG1b 137 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU1b 142 " --> pdb=" O THR1b 138 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS1b 143 " --> pdb=" O ARG1b 139 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER1b 147 " --> pdb=" O LYS1b 143 " (cutoff:3.500A) Processing helix chain '1b' and resid 150 through 155 removed outlier: 3.832A pdb=" N MET1b 154 " --> pdb=" O GLY1b 150 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY1b 155 " --> pdb=" O ILE1b 151 " (cutoff:3.500A) No H-bonds generated for 'chain '1b' and resid 150 through 155' Processing helix chain '1b' and resid 169 through 180 removed outlier: 3.654A pdb=" N GLU1b 175 " --> pdb=" O ILE1b 171 " (cutoff:3.500A) Processing helix chain '1b' and resid 206 through 223 removed outlier: 3.551A pdb=" N TYR1b 213 " --> pdb=" O ALA1b 209 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR1b 220 " --> pdb=" O ALA1b 216 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG1b 222 " --> pdb=" O ALA1b 218 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLU1b 223 " --> pdb=" O ALA1b 219 " (cutoff:3.500A) Processing helix chain '1c' and resid 6 through 13 removed outlier: 3.666A pdb=" N ILE1c 10 " --> pdb=" O HIS1c 6 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG1c 11 " --> pdb=" O PRO1c 7 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU1c 12 " --> pdb=" O ASN1c 8 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLY1c 13 " --> pdb=" O GLY1c 9 " (cutoff:3.500A) No H-bonds generated for 'chain '1c' and resid 6 through 13' Processing helix chain '1c' and resid 28 through 48 Processing helix chain '1c' and resid 72 through 78 removed outlier: 3.671A pdb=" N VAL1c 76 " --> pdb=" O ARG1c 72 " (cutoff:3.500A) Processing helix chain '1c' and resid 81 through 96 removed outlier: 4.291A pdb=" N LYS1c 86 " --> pdb=" O GLU1c 82 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU1c 87 " --> pdb=" O ASP1c 83 " (cutoff:3.500A) Processing helix chain '1c' and resid 108 through 113 removed outlier: 4.426A pdb=" N ASP1c 112 " --> pdb=" O LYS1c 108 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ALA1c 113 " --> pdb=" O PRO1c 109 " (cutoff:3.500A) No H-bonds generated for 'chain '1c' and resid 108 through 113' Processing helix chain '1c' and resid 114 through 127 removed outlier: 3.785A pdb=" N GLU1c 125 " --> pdb=" O THR1c 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG1c 126 " --> pdb=" O SER1c 122 " (cutoff:3.500A) Processing helix chain '1c' and resid 129 through 145 removed outlier: 4.221A pdb=" N ALA1c 141 " --> pdb=" O ALA1c 137 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU1c 144 " --> pdb=" O ASN1c 140 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY1c 145 " --> pdb=" O ALA1c 141 " (cutoff:3.500A) Processing helix chain '1d' and resid 7 through 16 removed outlier: 4.552A pdb=" N LEU1d 11 " --> pdb=" O PRO1d 7 " (cutoff:3.500A) Processing helix chain '1d' and resid 49 through 66 removed outlier: 4.043A pdb=" N LYS1d 58 " --> pdb=" O GLN1d 54 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR1d 65 " --> pdb=" O VAL1d 61 " (cutoff:3.500A) Processing helix chain '1d' and resid 68 through 83 removed outlier: 5.480A pdb=" N LYS1d 83 " --> pdb=" O ALA1d 79 " (cutoff:3.500A) Processing helix chain '1d' and resid 85 through 97 removed outlier: 3.719A pdb=" N LEU1d 91 " --> pdb=" O GLY1d 87 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG1d 97 " --> pdb=" O LEU1d 93 " (cutoff:3.500A) Processing helix chain '1d' and resid 98 through 106 Processing helix chain '1d' and resid 110 through 121 removed outlier: 4.012A pdb=" N LYS1d 121 " --> pdb=" O LEU1d 117 " (cutoff:3.500A) Processing helix chain '1d' and resid 152 through 166 removed outlier: 5.443A pdb=" N LYS1d 156 " --> pdb=" O GLN1d 152 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA1d 157 " --> pdb=" O SER1d 153 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN1d 164 " --> pdb=" O GLU1d 160 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG1d 165 " --> pdb=" O LEU1d 161 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU1d 166 " --> pdb=" O ALA1d 162 " (cutoff:3.500A) Processing helix chain '1d' and resid 187 through 192 removed outlier: 3.960A pdb=" N LEU1d 191 " --> pdb=" O GLU1d 187 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N SER1d 192 " --> pdb=" O ARG1d 188 " (cutoff:3.500A) No H-bonds generated for 'chain '1d' and resid 187 through 192' Processing helix chain '1d' and resid 196 through 206 removed outlier: 4.431A pdb=" N ILE1d 200 " --> pdb=" O ASN1d 196 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL1d 201 " --> pdb=" O GLU1d 197 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER1d 205 " --> pdb=" O VAL1d 201 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS1d 206 " --> pdb=" O GLU1d 202 " (cutoff:3.500A) Processing helix chain '1e' and resid 55 through 71 removed outlier: 3.921A pdb=" N ARG1e 69 " --> pdb=" O GLU1e 65 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASN1e 70 " --> pdb=" O LYS1e 66 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N MET1e 71 " --> pdb=" O ALA1e 67 " (cutoff:3.500A) Processing helix chain '1e' and resid 109 through 119 removed outlier: 6.367A pdb=" N ALA1e 113 " --> pdb=" O GLY1e 109 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY1e 119 " --> pdb=" O LEU1e 115 " (cutoff:3.500A) Processing helix chain '1e' and resid 132 through 148 removed outlier: 4.876A pdb=" N ARG1e 138 " --> pdb=" O ILE1e 134 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE1e 141 " --> pdb=" O VAL1e 137 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLY1e 143 " --> pdb=" O ALA1e 139 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN1e 146 " --> pdb=" O ASP1e 142 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET1e 147 " --> pdb=" O GLY1e 143 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASN1e 148 " --> pdb=" O LEU1e 144 " (cutoff:3.500A) Processing helix chain '1e' and resid 149 through 156 removed outlier: 3.776A pdb=" N ALA1e 154 " --> pdb=" O PRO1e 150 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ALA1e 155 " --> pdb=" O GLU1e 151 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS1e 156 " --> pdb=" O MET1e 152 " (cutoff:3.500A) Processing helix chain '1f' and resid 14 through 33 removed outlier: 4.518A pdb=" N VAL1f 18 " --> pdb=" O GLN1f 14 " (cutoff:3.500A) Proline residue: 1f 19 - end of helix removed outlier: 3.756A pdb=" N GLU1f 23 " --> pdb=" O PRO1f 19 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG1f 24 " --> pdb=" O GLY1f 20 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA1f 28 " --> pdb=" O ARG1f 24 " (cutoff:3.500A) Processing helix chain '1f' and resid 67 through 82 removed outlier: 3.736A pdb=" N GLU1f 73 " --> pdb=" O GLU1f 69 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASP1f 82 " --> pdb=" O PHE1f 78 " (cutoff:3.500A) Processing helix chain '1g' and resid 20 through 31 removed outlier: 3.587A pdb=" N ALA1g 24 " --> pdb=" O SER1g 20 " (cutoff:3.500A) Processing helix chain '1g' and resid 35 through 54 removed outlier: 3.701A pdb=" N SER1g 45 " --> pdb=" O SER1g 41 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU1g 50 " --> pdb=" O ALA1g 46 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN1g 52 " --> pdb=" O GLU1g 48 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG1g 53 " --> pdb=" O THR1g 49 " (cutoff:3.500A) Processing helix chain '1g' and resid 58 through 70 removed outlier: 4.456A pdb=" N PHE1g 62 " --> pdb=" O GLU1g 58 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU1g 63 " --> pdb=" O LEU1g 59 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN1g 68 " --> pdb=" O VAL1g 64 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL1g 69 " --> pdb=" O ALA1g 65 " (cutoff:3.500A) Processing helix chain '1g' and resid 92 through 112 removed outlier: 3.832A pdb=" N ASN1g 97 " --> pdb=" O PRO1g 93 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA1g 98 " --> pdb=" O VAL1g 94 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA1g 100 " --> pdb=" O ARG1g 96 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY1g 112 " --> pdb=" O ALA1g 108 " (cutoff:3.500A) Processing helix chain '1g' and resid 115 through 130 removed outlier: 3.513A pdb=" N ALA1g 128 " --> pdb=" O LEU1g 124 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU1g 129 " --> pdb=" O SER1g 125 " (cutoff:3.500A) Processing helix chain '1g' and resid 132 through 150 removed outlier: 3.570A pdb=" N LYS1g 149 " --> pdb=" O ALA1g 145 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA1g 150 " --> pdb=" O GLU1g 146 " (cutoff:3.500A) Processing helix chain '1h' and resid 5 through 21 removed outlier: 3.521A pdb=" N ASN1h 21 " --> pdb=" O GLY1h 17 " (cutoff:3.500A) Processing helix chain '1h' and resid 30 through 44 removed outlier: 3.983A pdb=" N GLU1h 43 " --> pdb=" O VAL1h 39 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY1h 44 " --> pdb=" O LEU1h 40 " (cutoff:3.500A) Processing helix chain '1h' and resid 112 through 120 Processing helix chain '1i' and resid 34 through 39 removed outlier: 3.512A pdb=" N TYR1i 38 " --> pdb=" O SER1i 34 " (cutoff:3.500A) Processing helix chain '1i' and resid 46 through 54 Proline residue: 1i 51 - end of helix removed outlier: 4.026A pdb=" N LEU1i 54 " --> pdb=" O GLN1i 50 " (cutoff:3.500A) Processing helix chain '1i' and resid 71 through 88 removed outlier: 4.830A pdb=" N MET1i 88 " --> pdb=" O THR1i 84 " (cutoff:3.500A) Processing helix chain '1i' and resid 92 through 102 removed outlier: 4.122A pdb=" N SER1i 96 " --> pdb=" O GLU1i 92 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU1i 97 " --> pdb=" O SER1i 93 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS1i 100 " --> pdb=" O SER1i 96 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA1i 101 " --> pdb=" O GLU1i 97 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY1i 102 " --> pdb=" O LEU1i 98 " (cutoff:3.500A) Processing helix chain '1j' and resid 14 through 33 removed outlier: 3.535A pdb=" N ASP1j 19 " --> pdb=" O HIS1j 15 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN1j 20 " --> pdb=" O ARG1j 16 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU1j 24 " --> pdb=" O GLN1j 20 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE1j 25 " --> pdb=" O ALA1j 21 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU1j 27 " --> pdb=" O ALA1j 23 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA1j 29 " --> pdb=" O ILE1j 25 " (cutoff:3.500A) Processing helix chain '1j' and resid 80 through 89 removed outlier: 3.683A pdb=" N ALA1j 86 " --> pdb=" O LYS1j 82 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET1j 88 " --> pdb=" O VAL1j 84 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG1j 89 " --> pdb=" O ASP1j 85 " (cutoff:3.500A) Processing helix chain '1k' and resid 46 through 51 removed outlier: 4.080A pdb=" N GLY1k 51 " --> pdb=" O ALA1k 47 " (cutoff:3.500A) Processing helix chain '1k' and resid 54 through 59 removed outlier: 4.681A pdb=" N SER1k 58 " --> pdb=" O GLY1k 54 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR1k 59 " --> pdb=" O SER1k 55 " (cutoff:3.500A) No H-bonds generated for 'chain '1k' and resid 54 through 59' Processing helix chain '1k' and resid 60 through 75 removed outlier: 4.983A pdb=" N ALA1k 73 " --> pdb=" O ARG1k 69 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N VAL1k 74 " --> pdb=" O CYS1k 70 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS1k 75 " --> pdb=" O ALA1k 71 " (cutoff:3.500A) Processing helix chain '1k' and resid 92 through 104 removed outlier: 4.489A pdb=" N THR1k 96 " --> pdb=" O GLY1k 92 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE1k 97 " --> pdb=" O ARG1k 93 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA1k 99 " --> pdb=" O SER1k 95 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU1k 100 " --> pdb=" O THR1k 96 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN1k 101 " --> pdb=" O ILE1k 97 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA1k 102 " --> pdb=" O ARG1k 98 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY1k 104 " --> pdb=" O LEU1k 100 " (cutoff:3.500A) Processing helix chain '1l' and resid 3 through 10 removed outlier: 3.615A pdb=" N LEU1l 7 " --> pdb=" O THR1l 3 " (cutoff:3.500A) Processing helix chain '1l' and resid 113 through 118 removed outlier: 4.318A pdb=" N TYR1l 117 " --> pdb=" O ALA1l 113 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY1l 118 " --> pdb=" O ARG1l 114 " (cutoff:3.500A) No H-bonds generated for 'chain '1l' and resid 113 through 118' Processing helix chain '1m' and resid 14 through 22 removed outlier: 4.093A pdb=" N THR1m 20 " --> pdb=" O VAL1m 16 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE1m 22 " --> pdb=" O ALA1m 18 " (cutoff:3.500A) Processing helix chain '1m' and resid 26 through 38 removed outlier: 3.645A pdb=" N ALA1m 36 " --> pdb=" O ALA1m 32 " (cutoff:3.500A) Processing helix chain '1m' and resid 49 through 64 removed outlier: 4.109A pdb=" N ASP1m 54 " --> pdb=" O GLU1m 50 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR1m 55 " --> pdb=" O GLY1m 51 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU1m 56 " --> pdb=" O GLN1m 52 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU1m 59 " --> pdb=" O THR1m 55 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL1m 60 " --> pdb=" O LEU1m 56 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE1m 63 " --> pdb=" O GLU1m 59 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL1m 64 " --> pdb=" O VAL1m 60 " (cutoff:3.500A) Processing helix chain '1m' and resid 66 through 84 removed outlier: 3.729A pdb=" N ARG1m 70 " --> pdb=" O GLU1m 66 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER1m 76 " --> pdb=" O GLU1m 72 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP1m 82 " --> pdb=" O LYS1m 78 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY1m 84 " --> pdb=" O LEU1m 80 " (cutoff:3.500A) Processing helix chain '1m' and resid 85 through 94 removed outlier: 4.823A pdb=" N GLY1m 94 " --> pdb=" O ARG1m 90 " (cutoff:3.500A) Processing helix chain '1n' and resid 3 through 25 removed outlier: 4.498A pdb=" N ASP1n 18 " --> pdb=" O VAL1n 14 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS1n 19 " --> pdb=" O ALA1n 15 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR1n 20 " --> pdb=" O LEU1n 16 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE1n 21 " --> pdb=" O ALA1n 17 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA1n 22 " --> pdb=" O ASP1n 18 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS1n 23 " --> pdb=" O LYS1n 19 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG1n 24 " --> pdb=" O TYR1n 20 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA1n 25 " --> pdb=" O PHE1n 21 " (cutoff:3.500A) Processing helix chain '1n' and resid 26 through 34 removed outlier: 3.917A pdb=" N ILE1n 30 " --> pdb=" O GLU1n 26 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE1n 31 " --> pdb=" O LEU1n 27 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER1n 32 " --> pdb=" O LYS1n 28 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP1n 33 " --> pdb=" O ALA1n 29 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL1n 34 " --> pdb=" O ILE1n 30 " (cutoff:3.500A) No H-bonds generated for 'chain '1n' and resid 26 through 34' Processing helix chain '1n' and resid 43 through 49 removed outlier: 5.296A pdb=" N LYS1n 47 " --> pdb=" O ASN1n 43 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN1n 49 " --> pdb=" O VAL1n 45 " (cutoff:3.500A) Processing helix chain '1n' and resid 80 through 91 removed outlier: 4.085A pdb=" N ARG1n 90 " --> pdb=" O GLU1n 86 " (cutoff:3.500A) Processing helix chain '1o' and resid 4 through 16 removed outlier: 3.541A pdb=" N GLU1o 14 " --> pdb=" O LYS1o 10 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY1o 16 " --> pdb=" O VAL1o 12 " (cutoff:3.500A) Processing helix chain '1o' and resid 24 through 44 removed outlier: 4.219A pdb=" N GLY1o 41 " --> pdb=" O ASN1o 37 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS1o 42 " --> pdb=" O HIS1o 38 " (cutoff:3.500A) Processing helix chain '1o' and resid 49 through 74 removed outlier: 3.971A pdb=" N GLY1o 55 " --> pdb=" O HIS1o 51 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS1o 73 " --> pdb=" O TYR1o 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP1o 74 " --> pdb=" O LEU1o 70 " (cutoff:3.500A) Processing helix chain '1o' and resid 75 through 86 Processing helix chain '1p' and resid 53 through 64 removed outlier: 3.724A pdb=" N ILE1p 57 " --> pdb=" O ASP1p 53 " (cutoff:3.500A) Processing helix chain '1p' and resid 68 through 79 Processing helix chain '1r' and resid 25 through 34 removed outlier: 4.045A pdb=" N ASN1r 31 " --> pdb=" O ALA1r 27 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR1r 32 " --> pdb=" O THR1r 28 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE1r 33 " --> pdb=" O LEU1r 29 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR1r 34 " --> pdb=" O LYS1r 30 " (cutoff:3.500A) Processing helix chain '1r' and resid 41 through 46 removed outlier: 3.672A pdb=" N THR1r 45 " --> pdb=" O PRO1r 41 " (cutoff:3.500A) Processing helix chain '1r' and resid 48 through 66 Processing helix chain '1s' and resid 12 through 25 removed outlier: 3.788A pdb=" N LYS1s 18 " --> pdb=" O HIS1s 14 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU1s 24 " --> pdb=" O GLU1s 20 " (cutoff:3.500A) Processing helix chain '1s' and resid 70 through 76 removed outlier: 4.688A pdb=" N PHE1s 74 " --> pdb=" O LYS1s 70 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA1s 75 " --> pdb=" O LEU1s 71 " (cutoff:3.500A) Proline residue: 1s 76 - end of helix No H-bonds generated for 'chain '1s' and resid 70 through 76' Processing helix chain '1t' and resid 6 through 42 removed outlier: 4.582A pdb=" N ARG1t 10 " --> pdb=" O SER1t 6 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE1t 12 " --> pdb=" O LYS1t 8 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU1t 15 " --> pdb=" O ALA1t 11 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER1t 23 " --> pdb=" O LYS1t 19 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG1t 24 " --> pdb=" O HIS1t 20 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY1t 42 " --> pdb=" O ALA1t 38 " (cutoff:3.500A) Processing helix chain '1t' and resid 43 through 65 Proline residue: 1t 56 - end of helix Processing helix chain '1t' and resid 68 through 87 removed outlier: 4.457A pdb=" N ALA1t 72 " --> pdb=" O HIS1t 68 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ALA1t 73 " --> pdb=" O LYS1t 69 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN1t 78 " --> pdb=" O ARG1t 74 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN1t 84 " --> pdb=" O THR1t 80 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU1t 86 " --> pdb=" O GLN1t 82 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA1t 87 " --> pdb=" O ILE1t 83 " (cutoff:3.500A) Processing helix chain '1u' and resid 17 through 24 removed outlier: 4.693A pdb=" N ARG1u 21 " --> pdb=" O ARG1u 17 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU1u 24 " --> pdb=" O LYS1u 20 " (cutoff:3.500A) Processing helix chain '1u' and resid 27 through 34 removed outlier: 5.375A pdb=" N GLU1u 31 " --> pdb=" O GLY1u 27 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG1u 34 " --> pdb=" O ALA1u 30 " (cutoff:3.500A) Processing helix chain '1u' and resid 39 through 53 removed outlier: 6.484A pdb=" N THR1u 43 " --> pdb=" O GLU1u 39 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS1u 46 " --> pdb=" O THR1u 42 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL1u 53 " --> pdb=" O LYS1u 49 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '1D' and resid 75 through 78 removed outlier: 4.752A pdb=" N ASP1D 114 " --> pdb=" O VAL1D 78 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '1D' and resid 80 through 83 removed outlier: 3.629A pdb=" N ARG1D 80 " --> pdb=" O LEU1D 93 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '1D' and resid 138 through 142 removed outlier: 4.002A pdb=" N SER1D 139 " --> pdb=" O ILE1D 164 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR1D 173 " --> pdb=" O VAL1D 165 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU1D 180 " --> pdb=" O LEU1D 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '1E' and resid 11 through 16 removed outlier: 4.399A pdb=" N VAL1E 20 " --> pdb=" O THR1E 16 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL1E 26 " --> pdb=" O VAL1E 9 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER1E 199 " --> pdb=" O LYS1E 8 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASP1E 200 " --> pdb=" O THR1E 112 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR1E 112 " --> pdb=" O ASP1E 200 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU1E 168 " --> pdb=" O SER1E 113 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '1E' and resid 79 through 84 removed outlier: 5.817A pdb=" N ARG1E 46 " --> pdb=" O LEU1E 84 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN1E 49 " --> pdb=" O THR1E 35 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLN1E 94 " --> pdb=" O VAL1E 34 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '1E' and resid 179 through 182 Processing sheet with id= 7, first strand: chain '1E' and resid 24 through 28 Processing sheet with id= 8, first strand: chain '1E' and resid 105 through 108 removed outlier: 6.606A pdb=" N LYS1E 105 " --> pdb=" O VAL1E 177 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '1F' and resid 1 through 5 removed outlier: 4.336A pdb=" N SER1F 10 " --> pdb=" O LEU1F 5 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '1F' and resid 117 through 120 removed outlier: 5.498A pdb=" N ARG1F 117 " --> pdb=" O ASP1F 184 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '1G' and resid 65 through 69 removed outlier: 7.831A pdb=" N ILE1G 85 " --> pdb=" O VAL1G 40 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLY1G 39 " --> pdb=" O GLY1G 151 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY1G 151 " --> pdb=" O GLY1G 39 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N THR1G 158 " --> pdb=" O GLY1G 126 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLY1G 126 " --> pdb=" O THR1G 158 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '1H' and resid 16 through 19 Processing sheet with id= 13, first strand: chain '1H' and resid 41 through 45 Processing sheet with id= 14, first strand: chain '1H' and resid 82 through 89 removed outlier: 6.133A pdb=" N THR1H 129 " --> pdb=" O LEU1H 89 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '1H' and resid 94 through 98 Processing sheet with id= 16, first strand: chain '1I' and resid 17 through 21 removed outlier: 4.739A pdb=" N ASP1I 17 " --> pdb=" O LEU1I 5 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN1I 2 " --> pdb=" O ALA1I 39 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '1I' and resid 77 through 80 removed outlier: 3.697A pdb=" N ILE1I 80 " --> pdb=" O ASN1I 145 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '1J' and resid 50 through 54 removed outlier: 4.049A pdb=" N SER1J 24 " --> pdb=" O SER1J 85 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL1J 27 " --> pdb=" O LYS1J 109 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASP1J 29 " --> pdb=" O GLU1J 107 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU1J 107 " --> pdb=" O ASP1J 29 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '1K' and resid 8 through 13 removed outlier: 4.085A pdb=" N SER1K 66 " --> pdb=" O TYR1K 62 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '1N' and resid 14 through 19 Processing sheet with id= 21, first strand: chain '1N' and resid 74 through 78 removed outlier: 7.584A pdb=" N GLY1N 83 " --> pdb=" O THR1N 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '1O' and resid 17 through 21 removed outlier: 6.561A pdb=" N ARG1O 17 " --> pdb=" O VAL1O 10 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL1O 10 " --> pdb=" O ARG1O 17 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR1O 6 " --> pdb=" O CYS1O 21 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN1O 82 " --> pdb=" O MET1O 7 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '1O' and resid 38 through 41 Processing sheet with id= 24, first strand: chain '1Q' and resid 37 through 40 No H-bonds generated for sheet with id= 24 Processing sheet with id= 25, first strand: chain '1Q' and resid 62 through 65 removed outlier: 6.493A pdb=" N LEU1Q 33 " --> pdb=" O LEU1Q 102 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS1Q 100 " --> pdb=" O ALA1Q 35 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '1Q' and resid 30 through 36 removed outlier: 7.967A pdb=" N SER1Q 30 " --> pdb=" O LYS1Q 133 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS1Q 127 " --> pdb=" O VAL1Q 36 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '1R' and resid 33 through 37 removed outlier: 4.844A pdb=" N MET1R 110 " --> pdb=" O CYS1R 100 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N TYR1R 94 " --> pdb=" O VAL1R 116 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '1S' and resid 49 through 52 removed outlier: 3.535A pdb=" N VAL1S 49 " --> pdb=" O VAL1S 39 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '1T' and resid 38 through 45 removed outlier: 6.497A pdb=" N THR1T 25 " --> pdb=" O LYS1T 87 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '1T' and resid 49 through 52 removed outlier: 3.760A pdb=" N ALA1T 49 " --> pdb=" O THR1T 60 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N SER1T 57 " --> pdb=" O THR1T 76 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '1V' and resid 11 through 15 removed outlier: 3.615A pdb=" N MET1V 40 " --> pdb=" O VAL1V 4 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU1V 39 " --> pdb=" O GLY1V 50 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU1V 46 " --> pdb=" O ASN1V 43 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '1V' and resid 18 through 23 removed outlier: 4.007A pdb=" N GLN1V 18 " --> pdb=" O ILE1V 98 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP1V 95 " --> pdb=" O VAL1V 64 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS1V 60 " --> pdb=" O THR1V 99 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLU1V 31 " --> pdb=" O VAL1V 63 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '1V' and resid 57 through 60 Processing sheet with id= 34, first strand: chain '1V' and resid 65 through 68 removed outlier: 3.503A pdb=" N ALA1V 65 " --> pdb=" O ASP1V 95 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '1V' and resid 71 through 78 removed outlier: 4.238A pdb=" N TYR1V 83 " --> pdb=" O ARG1V 78 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain '1W' and resid 2 through 8 Processing sheet with id= 37, first strand: chain '1X' and resid 28 through 33 removed outlier: 6.137A pdb=" N ASN1X 28 " --> pdb=" O LEU1X 87 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N LYS1X 66 " --> pdb=" O ARG1X 77 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP1X 79 " --> pdb=" O LYS1X 64 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LYS1X 64 " --> pdb=" O ASP1X 79 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LYS1X 81 " --> pdb=" O VAL1X 62 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL1X 62 " --> pdb=" O LYS1X 81 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA1X 83 " --> pdb=" O THR1X 60 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR1X 60 " --> pdb=" O ALA1X 83 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL1X 85 " --> pdb=" O VAL1X 58 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL1X 58 " --> pdb=" O VAL1X 85 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '1Y' and resid 82 through 86 removed outlier: 7.156A pdb=" N ARG1Y 82 " --> pdb=" O LYS1Y 97 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ARG1Y 94 " --> pdb=" O ILE1Y 103 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU1Y 101 " --> pdb=" O PHE1Y 96 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain '1Z' and resid 69 through 72 removed outlier: 6.572A pdb=" N ALA1Z 39 " --> pdb=" O ARG1Z 9 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE1Z 89 " --> pdb=" O PRO1Z 27 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain '10' and resid 51 through 54 removed outlier: 4.257A pdb=" N THR10 58 " --> pdb=" O GLY10 54 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '10' and resid 65 through 71 Processing sheet with id= 42, first strand: chain '11' and resid 12 through 19 removed outlier: 4.668A pdb=" N ASN11 23 " --> pdb=" O SER11 19 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '11' and resid 34 through 41 Processing sheet with id= 44, first strand: chain '13' and resid 34 through 39 removed outlier: 4.424A pdb=" N HIS13 34 " --> pdb=" O GLN13 9 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N MET13 54 " --> pdb=" O THR13 10 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '15' and resid 29 through 32 removed outlier: 4.187A pdb=" N GLU15 36 " --> pdb=" O ASP15 31 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '16' and resid 19 through 24 removed outlier: 5.934A pdb=" N HIS16 19 " --> pdb=" O SER16 13 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE16 48 " --> pdb=" O SER16 14 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU16 34 " --> pdb=" O GLU16 51 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '18' and resid 22 through 25 No H-bonds generated for sheet with id= 47 Processing sheet with id= 48, first strand: chain '19' and resid 1 through 5 removed outlier: 5.352A pdb=" N ILE19 23 " --> pdb=" O GLN19 37 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER19 28 " --> pdb=" O ASN19 13 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ASN19 13 " --> pdb=" O SER19 28 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '1b' and resid 89 through 92 removed outlier: 6.499A pdb=" N PHE1b 90 " --> pdb=" O ILE1b 67 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU1b 68 " --> pdb=" O ALA1b 160 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL1b 163 " --> pdb=" O PHE1b 184 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '1c' and resid 53 through 59 removed outlier: 6.673A pdb=" N GLU1c 58 " --> pdb=" O ARG1c 65 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE1c 64 " --> pdb=" O PRO1c 98 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL1c 66 " --> pdb=" O GLN1c 100 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain '1c' and resid 167 through 171 removed outlier: 3.688A pdb=" N THR1c 191 " --> pdb=" O GLY1c 194 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS1c 204 " --> pdb=" O ASP1c 181 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP1c 181 " --> pdb=" O LYS1c 204 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain '1d' and resid 141 through 144 removed outlier: 4.181A pdb=" N ASP1d 141 " --> pdb=" O PHE1d 182 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain '1e' and resid 17 through 25 removed outlier: 6.285A pdb=" N ILE1e 30 " --> pdb=" O LYS1e 23 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA1e 35 " --> pdb=" O GLY1e 51 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY1e 51 " --> pdb=" O ALA1e 35 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain '1e' and resid 83 through 88 removed outlier: 7.503A pdb=" N HIS1e 83 " --> pdb=" O PRO1e 98 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain '1f' and resid 39 through 42 removed outlier: 3.634A pdb=" N GLU1f 40 " --> pdb=" O LEU1f 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP1f 42 " --> pdb=" O TYR1f 59 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N TYR1f 59 " --> pdb=" O TRP1f 42 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL1f 60 " --> pdb=" O PHE1f 8 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE1f 8 " --> pdb=" O VAL1f 60 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE1f 6 " --> pdb=" O MET1f 62 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N HIS1f 3 " --> pdb=" O THR1f 92 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR1f 92 " --> pdb=" O HIS1f 3 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL1f 7 " --> pdb=" O MET1f 88 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARG1f 86 " --> pdb=" O MET1f 9 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain '1f' and resid 43 through 47 removed outlier: 3.689A pdb=" N GLY1f 43 " --> pdb=" O TYR1f 59 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU1f 47 " --> pdb=" O HIS1f 55 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N HIS1f 55 " --> pdb=" O LEU1f 47 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain '1g' and resid 73 through 79 removed outlier: 6.400A pdb=" N TYR1g 85 " --> pdb=" O ARG1g 78 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain '1h' and resid 23 through 29 removed outlier: 6.095A pdb=" N ALA1h 23 " --> pdb=" O LEU1h 63 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL1h 25 " --> pdb=" O LEU1h 61 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP1h 48 " --> pdb=" O THR1h 62 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain '1h' and resid 74 through 77 removed outlier: 3.806A pdb=" N CYS1h 127 " --> pdb=" O VAL1h 103 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE1h 101 " --> pdb=" O VAL1h 129 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain '1i' and resid 5 through 11 removed outlier: 4.303A pdb=" N GLY1i 10 " --> pdb=" O ALA1i 17 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS1i 22 " --> pdb=" O ASP1i 62 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain '1j' and resid 44 through 52 removed outlier: 6.540A pdb=" N ILE1j 8 " --> pdb=" O VAL1j 74 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN1j 99 " --> pdb=" O ARG1j 9 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain '1k' and resid 42 through 45 removed outlier: 3.659A pdb=" N ASN1k 81 " --> pdb=" O SER1k 17 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN1k 109 " --> pdb=" O LEU1k 82 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLY1k 88 " --> pdb=" O VAL1k 113 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain '1l' and resid 29 through 32 removed outlier: 4.928A pdb=" N LEU1l 81 " --> pdb=" O VAL1l 98 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N HIS1l 96 " --> pdb=" O ARG1l 83 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '1l' and resid 36 through 41 removed outlier: 5.496A pdb=" N LYS1l 51 " --> pdb=" O ILE1l 67 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE1l 67 " --> pdb=" O LYS1l 51 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE1l 61 " --> pdb=" O LEU1l 57 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '1p' and resid 4 through 10 removed outlier: 5.761A pdb=" N PHE1p 16 " --> pdb=" O HIS1p 9 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '1q' and resid 7 through 11 removed outlier: 3.547A pdb=" N LEU1q 8 " --> pdb=" O ILE1q 61 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLU1q 60 " --> pdb=" O VAL1q 76 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '1q' and resid 19 through 30 removed outlier: 5.048A pdb=" N LYS1q 19 " --> pdb=" O ASP1q 48 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP1q 48 " --> pdb=" O LYS1q 19 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '1s' and resid 48 through 52 removed outlier: 4.062A pdb=" N ILE1s 49 " --> pdb=" O VAL1s 60 " (cutoff:3.500A) 1774 hydrogen bonds defined for protein. 5238 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3851 hydrogen bonds 6030 hydrogen bond angles 0 basepair planarities 1535 basepair parallelities 2622 stacking parallelities Total time for adding SS restraints: 236.09 Time building geometry restraints manager: 68.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 15741 1.32 - 1.45: 68500 1.45 - 1.57: 64482 1.57 - 1.69: 9304 1.69 - 1.82: 271 Bond restraints: 158298 Sorted by residual: bond pdb=" CCM 6UQ1A3001 " pdb=" OCS 6UQ1A3001 " ideal model delta sigma weight residual 0.761 1.420 -0.659 2.00e-02 2.50e+03 1.09e+03 bond pdb=" CCM 6UQ1A3001 " pdb=" CCN 6UQ1A3001 " ideal model delta sigma weight residual 1.081 1.520 -0.439 2.00e-02 2.50e+03 4.83e+02 bond pdb=" CBF 6UQ1A3001 " pdb=" CBG 6UQ1A3001 " ideal model delta sigma weight residual 1.123 1.527 -0.404 2.00e-02 2.50e+03 4.08e+02 bond pdb=" CCR 6UQ1A3001 " pdb=" OCQ 6UQ1A3001 " ideal model delta sigma weight residual 1.065 1.463 -0.398 2.00e-02 2.50e+03 3.97e+02 bond pdb=" CCJ 6UQ1A3001 " pdb=" OCP 6UQ1A3001 " ideal model delta sigma weight residual 1.124 1.474 -0.350 2.00e-02 2.50e+03 3.06e+02 ... (remaining 158293 not shown) Histogram of bond angle deviations from ideal: 96.53 - 104.69: 20889 104.69 - 112.84: 96437 112.84 - 120.99: 75210 120.99 - 129.14: 40042 129.14 - 137.30: 4227 Bond angle restraints: 236805 Sorted by residual: angle pdb=" C2' G7M1A2069 " pdb=" C1' G7M1A2069 " pdb=" N9 G7M1A2069 " ideal model delta sigma weight residual 112.00 96.53 15.47 1.50e+00 4.44e-01 1.06e+02 angle pdb=" N VAL1Q 36 " pdb=" CA VAL1Q 36 " pdb=" C VAL1Q 36 " ideal model delta sigma weight residual 112.96 104.58 8.38 1.00e+00 1.00e+00 7.03e+01 angle pdb=" N TYR1J 132 " pdb=" CA TYR1J 132 " pdb=" C TYR1J 132 " ideal model delta sigma weight residual 111.69 120.51 -8.82 1.23e+00 6.61e-01 5.14e+01 angle pdb=" C1' 2MA1A2503 " pdb=" N9 2MA1A2503 " pdb=" C8 2MA1A2503 " ideal model delta sigma weight residual 106.32 126.76 -20.44 3.00e+00 1.11e-01 4.64e+01 angle pdb=" C TYR1J 132 " pdb=" N GLU1J 133 " pdb=" CA GLU1J 133 " ideal model delta sigma weight residual 121.70 133.55 -11.85 1.80e+00 3.09e-01 4.34e+01 ... (remaining 236800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 90057 35.88 - 71.76: 9974 71.76 - 107.63: 1299 107.63 - 143.51: 29 143.51 - 179.39: 20 Dihedral angle restraints: 101379 sinusoidal: 84685 harmonic: 16694 Sorted by residual: dihedral pdb=" O4' U1A 545 " pdb=" C1' U1A 545 " pdb=" N1 U1A 545 " pdb=" C2 U1A 545 " ideal model delta sinusoidal sigma weight residual 200.00 48.55 151.45 1 1.50e+01 4.44e-03 8.01e+01 dihedral pdb=" O4' U1A2321 " pdb=" C1' U1A2321 " pdb=" N1 U1A2321 " pdb=" C2 U1A2321 " ideal model delta sinusoidal sigma weight residual 200.00 52.38 147.62 1 1.50e+01 4.44e-03 7.87e+01 dihedral pdb=" O4' U1A1174 " pdb=" C1' U1A1174 " pdb=" N1 U1A1174 " pdb=" C2 U1A1174 " ideal model delta sinusoidal sigma weight residual -160.00 -16.65 -143.35 1 1.50e+01 4.44e-03 7.69e+01 ... (remaining 101376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.064: 30224 1.064 - 2.128: 0 2.128 - 3.193: 0 3.193 - 4.257: 2 4.257 - 5.321: 3 Chirality restraints: 30229 Sorted by residual: chirality pdb=" CCJ 6UQ1A3001 " pdb=" CCL 6UQ1A3001 " pdb=" OCI 6UQ1A3001 " pdb=" OCK 6UQ1A3001 " both_signs ideal model delta sigma weight residual False -2.70 2.62 -5.32 2.00e-01 2.50e+01 7.08e+02 chirality pdb=" CCN 6UQ1A3001 " pdb=" CCM 6UQ1A3001 " pdb=" CCO 6UQ1A3001 " pdb=" CDA 6UQ1A3001 " both_signs ideal model delta sigma weight residual False -2.36 2.55 -4.92 2.00e-01 2.50e+01 6.04e+02 chirality pdb=" CAX 6UQ1A3001 " pdb=" CAW 6UQ1A3001 " pdb=" OAY 6UQ1A3001 " pdb=" OBB 6UQ1A3001 " both_signs ideal model delta sigma weight residual False -2.06 2.28 -4.34 2.00e-01 2.50e+01 4.71e+02 ... (remaining 30226 not shown) Planarity restraints: 12697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG1A2445 " -0.050 2.00e-02 2.50e+03 6.02e-01 8.14e+03 pdb=" C4' 2MG1A2445 " -0.441 2.00e-02 2.50e+03 pdb=" O4' 2MG1A2445 " -0.693 2.00e-02 2.50e+03 pdb=" C3' 2MG1A2445 " 0.602 2.00e-02 2.50e+03 pdb=" O3' 2MG1A2445 " 0.609 2.00e-02 2.50e+03 pdb=" C2' 2MG1A2445 " 0.198 2.00e-02 2.50e+03 pdb=" O2' 2MG1A2445 " -0.941 2.00e-02 2.50e+03 pdb=" C1' 2MG1A2445 " -0.219 2.00e-02 2.50e+03 pdb=" N9 2MG1A2445 " 0.934 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC1A2498 " 0.074 2.00e-02 2.50e+03 5.97e-01 8.03e+03 pdb=" C4' OMC1A2498 " 0.435 2.00e-02 2.50e+03 pdb=" O4' OMC1A2498 " 0.581 2.00e-02 2.50e+03 pdb=" C3' OMC1A2498 " -0.597 2.00e-02 2.50e+03 pdb=" O3' OMC1A2498 " -0.655 2.00e-02 2.50e+03 pdb=" C2' OMC1A2498 " -0.164 2.00e-02 2.50e+03 pdb=" O2' OMC1A2498 " 1.002 2.00e-02 2.50e+03 pdb=" C1' OMC1A2498 " 0.225 2.00e-02 2.50e+03 pdb=" N1 OMC1A2498 " -0.901 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG1A2251 " 0.027 2.00e-02 2.50e+03 5.86e-01 7.73e+03 pdb=" C4' OMG1A2251 " 0.451 2.00e-02 2.50e+03 pdb=" O4' OMG1A2251 " 0.694 2.00e-02 2.50e+03 pdb=" C3' OMG1A2251 " -0.588 2.00e-02 2.50e+03 pdb=" O3' OMG1A2251 " -0.575 2.00e-02 2.50e+03 pdb=" C2' OMG1A2251 " -0.221 2.00e-02 2.50e+03 pdb=" O2' OMG1A2251 " 0.903 2.00e-02 2.50e+03 pdb=" C1' OMG1A2251 " 0.214 2.00e-02 2.50e+03 pdb=" N9 OMG1A2251 " -0.905 2.00e-02 2.50e+03 ... (remaining 12694 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 2418 2.60 - 3.18: 114874 3.18 - 3.75: 287197 3.75 - 4.33: 400115 4.33 - 4.90: 529481 Nonbonded interactions: 1334085 Sorted by model distance: nonbonded pdb=" OP1 G1A1799 " pdb=" NH1 ARG1D 258 " model vdw 2.027 2.520 nonbonded pdb=" OH TYR16 21 " pdb=" O PHE16 39 " model vdw 2.035 2.440 nonbonded pdb=" O2' G1a1124 " pdb=" N6 A1a1145 " model vdw 2.065 2.520 nonbonded pdb=" OP2 A1a 10 " pdb=" OG1 THR1e 131 " model vdw 2.075 2.440 nonbonded pdb=" O2' A1A1508 " pdb=" O4' A1A1509 " model vdw 2.080 2.440 ... (remaining 1334080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.620 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: 16.270 Check model and map are aligned: 1.520 Set scattering table: 0.970 Process input model: 580.480 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.480 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 610.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 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 0.659 158298 Z= 0.359 Angle : 0.620 20.440 236805 Z= 0.331 Chirality : 0.066 5.321 30229 Planarity : 0.015 0.602 12697 Dihedral : 22.215 179.389 90611 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 1.65 % Allowed : 5.65 % Favored : 92.69 % Rotamer: Outliers : 0.46 % Allowed : 1.32 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.53 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.10), residues: 5756 helix: -2.62 (0.09), residues: 1790 sheet: -1.86 (0.15), residues: 1048 loop : -0.91 (0.11), residues: 2918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP1F 78 HIS 0.005 0.001 HIS10 57 PHE 0.026 0.002 PHE1Y 95 TYR 0.025 0.002 TYR1N 53 ARG 0.007 0.001 ARG1k 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2529 residues out of total 4763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 2509 time to evaluate : 6.054 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: 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 28 LYS cc_start: 0.7727 (mptt) cc_final: 0.7420 (mttp) REVERT: 1D 74 ILE cc_start: 0.8755 (mt) cc_final: 0.8399 (mt) REVERT: 1D 84 ASP cc_start: 0.8350 (t0) cc_final: 0.7913 (t0) REVERT: 1D 181 MET cc_start: 0.8490 (mmt) cc_final: 0.8060 (mmm) REVERT: 1D 201 MET cc_start: 0.8645 (ptm) cc_final: 0.8426 (ptm) REVERT: 1D 220 VAL cc_start: 0.9304 (t) cc_final: 0.9088 (m) REVERT: 1E 36 GLN cc_start: 0.7969 (tt0) cc_final: 0.7457 (tt0) REVERT: 1E 42 ASN cc_start: 0.8391 (t0) cc_final: 0.8112 (p0) REVERT: 1E 43 ASP cc_start: 0.7555 (m-30) cc_final: 0.7163 (m-30) REVERT: 1E 48 ILE cc_start: 0.8675 (pt) cc_final: 0.8463 (pt) REVERT: 1E 174 SER cc_start: 0.8712 (m) cc_final: 0.8420 (p) REVERT: 1E 190 LYS cc_start: 0.8424 (tttt) cc_final: 0.8061 (tttm) REVERT: 1E 204 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8509 (mtpp) REVERT: 1F 19 PHE cc_start: 0.8230 (m-80) cc_final: 0.7598 (m-80) REVERT: 1F 41 GLN cc_start: 0.7661 (tt0) cc_final: 0.7356 (tt0) REVERT: 1F 59 PRO cc_start: 0.8997 (Cg_exo) cc_final: 0.8713 (Cg_endo) REVERT: 1F 70 SER cc_start: 0.7933 (p) cc_final: 0.7524 (p) REVERT: 1F 111 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7373 (tp30) REVERT: 1F 115 GLN cc_start: 0.8181 (mm-40) cc_final: 0.6734 (mm110) REVERT: 1F 136 GLN cc_start: 0.8200 (tp40) cc_final: 0.7931 (tp40) REVERT: 1F 156 ASN cc_start: 0.8109 (m-40) cc_final: 0.7767 (m-40) REVERT: 1F 176 ASP cc_start: 0.8321 (p0) cc_final: 0.7632 (p0) REVERT: 1F 186 VAL cc_start: 0.9431 (t) cc_final: 0.9039 (p) REVERT: 1F 194 LYS cc_start: 0.8898 (ttpp) cc_final: 0.8599 (tptp) REVERT: 1G 20 PHE cc_start: 0.7876 (m-80) cc_final: 0.7105 (m-80) REVERT: 1G 33 LYS cc_start: 0.7434 (pttt) cc_final: 0.7084 (pttt) REVERT: 1G 98 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6775 (tm-30) REVERT: 1G 163 ASP cc_start: 0.7985 (m-30) cc_final: 0.7714 (m-30) REVERT: 1H 104 ASN cc_start: 0.8039 (m110) cc_final: 0.7731 (p0) REVERT: 1H 130 GLU cc_start: 0.7853 (tt0) cc_final: 0.7589 (mt-10) REVERT: 1H 132 VAL cc_start: 0.9006 (t) cc_final: 0.8733 (p) REVERT: 1I 1 MET cc_start: 0.6960 (ttm) cc_final: 0.6715 (ptm) REVERT: 1K 106 LEU cc_start: 0.4902 (mt) cc_final: 0.4610 (mt) REVERT: 1N 68 LYS cc_start: 0.8186 (mtmt) cc_final: 0.7639 (mtmm) REVERT: 1N 106 LYS cc_start: 0.8916 (tttt) cc_final: 0.8349 (ttmt) REVERT: 1N 142 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7576 (tp) REVERT: 1O 2 ILE cc_start: 0.8730 (mm) cc_final: 0.8412 (mt) REVERT: 1O 3 GLN cc_start: 0.8249 (pt0) cc_final: 0.7951 (pt0) REVERT: 1O 78 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7572 (mtp85) REVERT: 1P 68 SER cc_start: 0.8369 (t) cc_final: 0.8090 (p) REVERT: 1P 79 LEU cc_start: 0.8811 (mt) cc_final: 0.7908 (tp) REVERT: 1P 84 LYS cc_start: 0.8463 (mttt) cc_final: 0.8106 (tttt) REVERT: 1P 91 ASP cc_start: 0.7372 (m-30) cc_final: 0.6738 (m-30) REVERT: 1Q 73 ILE cc_start: 0.9299 (mm) cc_final: 0.8902 (mt) REVERT: 1Q 101 VAL cc_start: 0.8986 (t) cc_final: 0.8593 (m) REVERT: 1R 5 LYS cc_start: 0.8490 (mttt) cc_final: 0.8201 (mmmm) REVERT: 1R 6 SER cc_start: 0.8132 (m) cc_final: 0.7892 (t) REVERT: 1R 24 MET cc_start: 0.7839 (ttm) cc_final: 0.7390 (ttm) REVERT: 1S 2 ASP cc_start: 0.6994 (p0) cc_final: 0.5943 (t70) REVERT: 1S 8 ILE cc_start: 0.8837 (mt) cc_final: 0.8583 (tt) REVERT: 1S 29 HIS cc_start: 0.8966 (t70) cc_final: 0.8744 (t70) REVERT: 1S 45 SER cc_start: 0.8673 (m) cc_final: 0.8305 (t) REVERT: 1S 53 THR cc_start: 0.8510 (p) cc_final: 0.8282 (p) REVERT: 1T 5 ILE cc_start: 0.8904 (mt) cc_final: 0.8686 (mt) REVERT: 1T 8 LEU cc_start: 0.8895 (mt) cc_final: 0.8576 (mm) REVERT: 1T 81 VAL cc_start: 0.8166 (t) cc_final: 0.7740 (p) REVERT: 1U 45 TYR cc_start: 0.7770 (m-10) cc_final: 0.7366 (m-80) REVERT: 1U 47 TYR cc_start: 0.8798 (t80) cc_final: 0.8519 (t80) REVERT: 1U 98 ILE cc_start: 0.8817 (mt) cc_final: 0.7778 (mt) REVERT: 1U 101 PHE cc_start: 0.7326 (m-80) cc_final: 0.7076 (m-80) REVERT: 1V 29 THR cc_start: 0.6980 (m) cc_final: 0.6549 (t) REVERT: 1V 32 THR cc_start: 0.6991 (m) cc_final: 0.6734 (m) REVERT: 1V 41 ILE cc_start: 0.8094 (mt) cc_final: 0.7400 (mm) REVERT: 1V 85 LYS cc_start: 0.7569 (pttt) cc_final: 0.7348 (ptmt) REVERT: 1W 30 SER cc_start: 0.8526 (p) cc_final: 0.7399 (m) REVERT: 1X 27 SER cc_start: 0.8751 (t) cc_final: 0.8467 (t) REVERT: 1X 43 ILE cc_start: 0.9268 (mt) cc_final: 0.8933 (tp) REVERT: 1X 82 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7871 (mtpp) REVERT: 1X 86 THR cc_start: 0.8927 (m) cc_final: 0.8531 (p) REVERT: 1Y 81 ASP cc_start: 0.7718 (t0) cc_final: 0.7408 (m-30) REVERT: 1Y 83 VAL cc_start: 0.8477 (t) cc_final: 0.8205 (t) REVERT: 1Z 2 PHE cc_start: 0.7003 (m-80) cc_final: 0.5560 (m-80) REVERT: 1Z 3 THR cc_start: 0.8911 (m) cc_final: 0.8239 (p) REVERT: 10 31 VAL cc_start: 0.8976 (m) cc_final: 0.8484 (m) REVERT: 10 50 ASN cc_start: 0.7691 (m-40) cc_final: 0.7459 (m-40) REVERT: 11 32 ASN cc_start: 0.8740 (t0) cc_final: 0.7774 (t0) REVERT: 11 33 LEU cc_start: 0.9088 (mt) cc_final: 0.8786 (mt) REVERT: 11 51 VAL cc_start: 0.9521 (m) cc_final: 0.9073 (p) REVERT: 12 14 LEU cc_start: 0.8445 (mt) cc_final: 0.8089 (tp) REVERT: 12 46 VAL cc_start: 0.8611 (t) cc_final: 0.8159 (t) REVERT: 15 36 GLU cc_start: 0.6870 (mt-10) cc_final: 0.6238 (mt-10) REVERT: 16 38 LYS cc_start: 0.7133 (mttm) cc_final: 0.6818 (mmtm) REVERT: 19 13 ASN cc_start: 0.9031 (m110) cc_final: 0.8806 (m-40) REVERT: 19 22 VAL cc_start: 0.8189 (t) cc_final: 0.7879 (p) REVERT: 19 30 GLU cc_start: 0.7868 (tp30) cc_final: 0.7649 (mp0) REVERT: 19 32 LYS cc_start: 0.7722 (mttt) cc_final: 0.7007 (mtpp) REVERT: 1b 31 ILE cc_start: 0.8451 (mt) cc_final: 0.8199 (tt) REVERT: 1b 151 ILE cc_start: 0.7295 (tt) cc_final: 0.6520 (tt) REVERT: 1b 200 ILE cc_start: 0.7185 (mp) cc_final: 0.6966 (mp) REVERT: 1c 12 LEU cc_start: 0.8899 (mt) cc_final: 0.8657 (mt) REVERT: 1c 36 ASP cc_start: 0.8701 (m-30) cc_final: 0.8349 (m-30) REVERT: 1c 38 LYS cc_start: 0.8882 (mmtp) cc_final: 0.8639 (mmmm) REVERT: 1c 42 TYR cc_start: 0.8859 (t80) cc_final: 0.8627 (t80) REVERT: 1c 45 LYS cc_start: 0.8820 (tttt) cc_final: 0.8456 (tttt) REVERT: 1c 46 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7661 (mm-30) REVERT: 1c 69 HIS cc_start: 0.8449 (m-70) cc_final: 0.7566 (m170) REVERT: 1c 86 LYS cc_start: 0.8964 (pttp) cc_final: 0.8652 (pttp) REVERT: 1c 134 MET cc_start: 0.8061 (mtp) cc_final: 0.7837 (mtm) REVERT: 1c 136 ARG cc_start: 0.7841 (mtt-85) cc_final: 0.7581 (mtm-85) REVERT: 1c 184 TYR cc_start: 0.7851 (t80) cc_final: 0.7201 (t80) REVERT: 1d 21 LEU cc_start: 0.8219 (mt) cc_final: 0.7988 (mt) REVERT: 1d 54 GLN cc_start: 0.7522 (mm-40) cc_final: 0.7306 (mm-40) REVERT: 1d 61 VAL cc_start: 0.9323 (t) cc_final: 0.9114 (p) REVERT: 1d 100 ASN cc_start: 0.8440 (t0) cc_final: 0.7885 (t0) REVERT: 1d 141 ASP cc_start: 0.7769 (m-30) cc_final: 0.7430 (m-30) REVERT: 1e 124 LEU cc_start: 0.8702 (mt) cc_final: 0.8412 (mp) REVERT: 1f 14 GLN cc_start: 0.8742 (mt0) cc_final: 0.8233 (pt0) REVERT: 1f 68 GLN cc_start: 0.7788 (pt0) cc_final: 0.7387 (mt0) REVERT: 1f 84 VAL cc_start: 0.8660 (p) cc_final: 0.8416 (p) REVERT: 1g 31 MET cc_start: 0.7686 (ttp) cc_final: 0.7275 (ttp) REVERT: 1g 33 ASP cc_start: 0.8144 (m-30) cc_final: 0.7824 (t0) REVERT: 1g 41 SER cc_start: 0.9025 (m) cc_final: 0.8680 (p) REVERT: 1g 42 ILE cc_start: 0.8896 (mt) cc_final: 0.8674 (mt) REVERT: 1g 69 VAL cc_start: 0.8898 (m) cc_final: 0.8687 (p) REVERT: 1g 72 THR cc_start: 0.7420 (m) cc_final: 0.7180 (m) REVERT: 1g 122 ASN cc_start: 0.8435 (m-40) cc_final: 0.7802 (m110) REVERT: 1g 143 ARG cc_start: 0.7477 (mtt90) cc_final: 0.6856 (mtm110) REVERT: 1h 27 MET cc_start: 0.8001 (ptp) cc_final: 0.7536 (ptp) REVERT: 1h 59 LEU cc_start: 0.7882 (tp) cc_final: 0.7440 (tt) REVERT: 1h 62 THR cc_start: 0.9492 (m) cc_final: 0.8778 (p) REVERT: 1i 79 ILE cc_start: 0.9248 (mt) cc_final: 0.8984 (tp) REVERT: 1i 103 PHE cc_start: 0.7717 (m-10) cc_final: 0.7339 (m-80) REVERT: 1j 18 ILE cc_start: 0.7922 (tt) cc_final: 0.7625 (tt) REVERT: 1k 14 LYS cc_start: 0.8674 (tptp) cc_final: 0.8454 (mmmt) REVERT: 1k 20 VAL cc_start: 0.8546 (t) cc_final: 0.7983 (p) REVERT: 1k 40 ASN cc_start: 0.8705 (m-40) cc_final: 0.7818 (t0) REVERT: 1k 61 PHE cc_start: 0.8073 (t80) cc_final: 0.7608 (t80) REVERT: 1k 68 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7988 (mt-10) REVERT: 1k 74 VAL cc_start: 0.6981 (m) cc_final: 0.6185 (p) REVERT: 1k 84 VAL cc_start: 0.6932 (t) cc_final: 0.6361 (m) REVERT: 1k 97 ILE cc_start: 0.8625 (pt) cc_final: 0.8389 (mt) REVERT: 1k 107 ILE cc_start: 0.7395 (tt) cc_final: 0.7175 (tp) REVERT: 1l 21 VAL cc_start: 0.7719 (m) cc_final: 0.7484 (m) REVERT: 1l 67 ILE cc_start: 0.8535 (mt) cc_final: 0.8261 (mt) REVERT: 1l 89 ASP cc_start: 0.7258 (t70) cc_final: 0.6876 (t0) REVERT: 1m 23 TYR cc_start: 0.8367 (t80) cc_final: 0.8052 (t80) REVERT: 1m 64 VAL cc_start: 0.8759 (t) cc_final: 0.8194 (p) REVERT: 1m 85 CYS cc_start: 0.8138 (p) cc_final: 0.7456 (t) REVERT: 1m 97 VAL cc_start: 0.8643 (t) cc_final: 0.8151 (p) REVERT: 1n 80 SER cc_start: 0.8223 (m) cc_final: 0.8010 (p) REVERT: 1n 83 LYS cc_start: 0.8978 (mmmt) cc_final: 0.8599 (tppp) REVERT: 1o 35 GLN cc_start: 0.8122 (tp40) cc_final: 0.7125 (tp-100) REVERT: 1p 2 VAL cc_start: 0.7478 (m) cc_final: 0.6560 (m) REVERT: 1p 3 THR cc_start: 0.6483 (m) cc_final: 0.6203 (t) REVERT: 1p 55 ASP cc_start: 0.8446 (m-30) cc_final: 0.8177 (t0) REVERT: 1q 72 SER cc_start: 0.7314 (m) cc_final: 0.6594 (p) REVERT: 1s 13 LEU cc_start: 0.8284 (tt) cc_final: 0.8061 (tt) REVERT: 1s 17 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7842 (mtmt) REVERT: 1s 35 SER cc_start: 0.8578 (t) cc_final: 0.7666 (t) REVERT: 1s 63 THR cc_start: 0.7757 (m) cc_final: 0.7443 (p) REVERT: 1s 66 MET cc_start: 0.7900 (mmt) cc_final: 0.7396 (mtp) REVERT: 1t 57 ILE cc_start: 0.8621 (tp) cc_final: 0.8374 (tt) REVERT: 1t 80 THR cc_start: 0.8873 (m) cc_final: 0.8653 (m) outliers start: 20 outliers final: 4 residues processed: 2517 average time/residue: 1.3212 time to fit residues: 5494.7303 Evaluate side-chains 1659 residues out of total 4763 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1654 time to evaluate : 5.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1G residue 154 ILE Chi-restraints excluded: chain 1N residue 142 ILE Chi-restraints excluded: chain 1Q residue 54 THR Chi-restraints excluded: chain 1R residue 33 ILE Chi-restraints excluded: chain 1d residue 191 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1024 random chunks: chunk 864 optimal weight: 10.0000 chunk 776 optimal weight: 10.0000 chunk 430 optimal weight: 4.9990 chunk 265 optimal weight: 20.0000 chunk 523 optimal weight: 9.9990 chunk 414 optimal weight: 40.0000 chunk 802 optimal weight: 6.9990 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 7.9990 chunk 597 optimal weight: 9.9990 chunk 929 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: