Starting phenix.real_space_refine (version: dev) on Sat Apr 16 04:33:23 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/04_2022/6q95_4475_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/04_2022/6q95_4475.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/04_2022/6q95_4475_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/04_2022/6q95_4475_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/04_2022/6q95_4475_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/04_2022/6q95_4475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/04_2022/6q95_4475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/04_2022/6q95_4475_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/04_2022/6q95_4475_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "g GLU 12": "OE1" <-> "OE2" Residue "g GLU 116": "OE1" <-> "OE2" Residue "g GLU 119": "OE1" <-> "OE2" Residue "g GLU 128": "OE1" <-> "OE2" Residue "g GLU 231": "OE1" <-> "OE2" Residue "h GLU 19": "OE1" <-> "OE2" Residue "h GLU 35": "OE1" <-> "OE2" Residue "h GLU 44": "OE1" <-> "OE2" Residue "h GLU 58": "OE1" <-> "OE2" Residue "h GLU 122": "OE1" <-> "OE2" Residue "h GLU 143": "OE1" <-> "OE2" Residue "i ARG 3": "NH1" <-> "NH2" Residue "i GLU 15": "OE1" <-> "OE2" Residue "i GLU 60": "OE1" <-> "OE2" Residue "i PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 98": "OE1" <-> "OE2" Residue "i ARG 118": "NH1" <-> "NH2" Residue "j GLU 79": "OE1" <-> "OE2" Residue "j GLU 111": "OE1" <-> "OE2" Residue "j GLU 137": "OE1" <-> "OE2" Residue "k GLU 95": "OE1" <-> "OE2" Residue "m GLU 34": "OE1" <-> "OE2" Residue "m GLU 42": "OE1" <-> "OE2" Residue "m GLU 99": "OE1" <-> "OE2" Residue "n GLU 12": "OE1" <-> "OE2" Residue "p GLU 92": "OE1" <-> "OE2" Residue "r GLU 8": "OE1" <-> "OE2" Residue "r GLU 73": "OE1" <-> "OE2" Residue "t GLU 73": "OE1" <-> "OE2" Residue "y ARG 89": "NH1" <-> "NH2" Residue "W ARG 32": "NH1" <-> "NH2" Residue "X ARG 11": "NH1" <-> "NH2" Residue "X ARG 20": "NH1" <-> "NH2" Residue "Y GLU 27": "OE1" <-> "OE2" Residue "Z GLU 48": "OE1" <-> "OE2" Residue "a GLU 30": "OE1" <-> "OE2" Residue "a ARG 48": "NH1" <-> "NH2" Residue "a ARG 55": "NH1" <-> "NH2" Residue "c TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "B TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 58": "NH1" <-> "NH2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 161": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "E GLU 14": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "J GLU 68": "OE1" <-> "OE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "K GLU 9": "OE1" <-> "OE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L ARG 102": "NH1" <-> "NH2" Residue "L ARG 111": "NH1" <-> "NH2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "M GLU 80": "OE1" <-> "OE2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 88": "NH1" <-> "NH2" Residue "N GLU 102": "OE1" <-> "OE2" Residue "O GLU 43": "OE1" <-> "OE2" Residue "O GLU 103": "OE1" <-> "OE2" Residue "P GLU 36": "OE1" <-> "OE2" Residue "P GLU 134": "OE1" <-> "OE2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q ARG 64": "NH1" <-> "NH2" Residue "Q GLU 89": "OE1" <-> "OE2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "V GLU 13": "OE1" <-> "OE2" Residue "V GLU 84": "OE1" <-> "OE2" Residue "5 GLU 15": "OE1" <-> "OE2" Residue "5 GLU 21": "OE1" <-> "OE2" Residue "5 GLU 85": "OE1" <-> "OE2" Residue "5 GLU 94": "OE1" <-> "OE2" Residue "5 ARG 129": "NH1" <-> "NH2" Residue "5 ARG 130": "NH1" <-> "NH2" Residue "5 GLU 143": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 154751 Number of models: 1 Model: "" Number of chains: 84 Chain: "2" Number of atoms: 32329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1504, 32329 Classifications: {'RNA': 1504} Modifications used: {'5*END': 1, 'rna2p_pur': 111, 'rna3p_pur': 743, 'rna2p_pyr': 79, 'rna3p_pyr': 571} Link IDs: {'rna3p': 1313, 'rna2p': 190} Chain breaks: 7 Chain: "g" Number of atoms: 1901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1901 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "h" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1613 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1703 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "j" Number of atoms: 1147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1147 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 8, 'TRANS': 142} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "k" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 843 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "l" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1257 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 148} Chain: "m" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1116 Classifications: {'peptide': 138} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 128} Chain: "n" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1011 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "o" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 6, 'TRANS': 92} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 885 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "q" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "r" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 955 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain breaks: 2 Chain: "s" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "t" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 734 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "u" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 701 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "v" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 824 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 574 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "x" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 630 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 2 Chain: "y" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 763 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "z" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 209 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "7" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1645 Classifications: {'RNA': 77} Modifications used: {'rna3p': 1, 'rna2p_pyr': 4, 'p5*END': 1, 'rna3p_pur': 31, 'rna3p_pyr': 33, 'rna2p_pur': 8} Link IDs: {'rna3p': 65, 'rna2p': 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "8" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1616 Classifications: {'RNA': 76} Modifications used: {'rna2p_pyr': 3, 'rna3p_pyr': 37, 'p5*END': 1, 'rna3p_pur': 30, 'rna2p_pur': 6} Link IDs: {'rna3p': 66, 'rna2p': 9} Chain: "9" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'rna3p_pyr': 3, 'rna2p_pur': 1, 'rna3p_pur': 1, 'rna2p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "W" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 650 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 82} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "X" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 693 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 4, 'TRANS': 84} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 421 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 1, 'TRANS': 49} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 4, 'TRANS': 55} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 464 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "b" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 459 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 49} Chain: "c" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 381 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 419 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 508 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "1" Number of atoms: 60977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2831, 60977 Classifications: {'RNA': 2831} Modifications used: {'5*END': 1, 'rna2p_pur': 273, 'rna3p_pur': 1387, 'rna2p_pyr': 129, 'rna3p_pyr': 1042} Link IDs: {'rna3p': 2428, 'rna2p': 402} Chain breaks: 22 Chain: "3" Number of atoms: 2551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2551 Classifications: {'RNA': 119} Modifications used: {'rna3p_pyr': 51, 'rna2p_pur': 3, 'rna3p_pur': 62, 'rna2p_pyr': 3, '5*END': 1} Link IDs: {'rna3p': 112, 'rna2p': 6} Chain: "A" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1142 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 273 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 155 Chain: "B" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2105 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 19, 'TRANS': 250, 'PCIS': 2} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1564 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 15, 'TRANS': 188, 'PCIS': 1} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1624 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 11, 'TRANS': 196} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 2 Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1474 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain breaks: 1 Chain: "F" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1223 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 12, 'TRANS': 147} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 454 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1105 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 126, 'PCIS': 1} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "L" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1114 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 135, 'PCIS': 1} Chain: "M" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1080 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 960 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "O" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 771 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 2 Chain: "P" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1142 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 958 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 115} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain breaks: 1 Chain: "S" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 896 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 776 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 93, 'PCIS': 1} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 766 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1184 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "6" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "f" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 307 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "H" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 650 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'TRANS': 129} Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 130 Planarities with less than four sites: {'UNK:plan-1': 130} Unresolved non-hydrogen planarities: 130 Chain: "I" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 701 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'TRANS': 139} Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 418 Unresolved non-hydrogen dihedrals: 140 Planarities with less than four sites: {'UNK:plan-1': 139} Unresolved non-hydrogen planarities: 139 Chain: "4" Number of atoms: 6834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 6834 Classifications: {'RNA': 319} Modifications used: {'rna3p_pyr': 125, 'rna2p_pur': 33, 'rna3p_pur': 136, 'rna2p_pyr': 25} Link IDs: {'rna3p': 261, 'rna2p': 57} Chain breaks: 1 Chain: "2" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 189 Unusual residues: {' MG': 189} Classifications: {'undetermined': 189} Link IDs: {None: 188} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "8" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' MG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "9" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "1" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 397 Unusual residues: {' MG': 397} Classifications: {'undetermined': 397} Link IDs: {None: 396} Chain: "3" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' MG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" 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 35902 SG CYS i 9 180.766 218.769 170.206 1.00 55.64 S ATOM 35927 SG CYS i 12 177.118 218.167 171.409 1.00 55.55 S ATOM 36045 SG CYS i 26 179.372 220.270 173.172 1.00 59.98 S ATOM 36085 SG CYS i 31 178.331 222.242 170.373 1.00 63.17 S ATOM 46717 SG CYS s 24 170.655 222.248 107.020 1.00 51.01 S ATOM 46741 SG CYS s 27 170.738 219.393 109.208 1.00 46.73 S ATOM 46848 SG CYS s 40 167.426 219.524 107.192 1.00 51.20 S ATOM 46873 SG CYS s 43 168.624 222.089 110.299 1.00 48.76 S ATOM A0ZA9 SG CYS f 14 219.883 128.778 111.647 1.00 59.35 S ATOM A0ZDC SG CYS f 27 221.985 129.865 114.359 1.00 59.80 S Residues with excluded nonbonded symmetry interactions: 77 residue: pdb="MG MG 21626 " occ=0.98 residue: pdb="MG MG 21629 " occ=0.98 residue: pdb="MG MG 21656 " occ=0.90 residue: pdb="MG MG 21665 " occ=0.95 residue: pdb="MG MG 21670 " occ=0.87 residue: pdb="MG MG 21686 " occ=0.96 residue: pdb="MG MG 21689 " occ=0.89 residue: pdb="MG MG 21703 " occ=0.94 residue: pdb="MG MG 21709 " occ=0.98 residue: pdb="MG MG 21712 " occ=0.90 residue: pdb="MG MG 21747 " occ=0.96 residue: pdb="MG MG 21749 " occ=0.85 ... (remaining 65 not shown) Time building chain proxies: 64.17, per 1000 atoms: 0.41 Number of scatterers: 154751 At special positions: 0 Unit cell: (286.76, 294.8, 259.96, 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 3 29.99 S 118 16.00 P 4929 15.00 Mg 637 11.99 O 42508 8.00 N 29100 7.00 C 77456 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 61.31 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN f1001 " pdb="ZN ZN f1001 " - pdb=" ND1 HIS f 32 " pdb="ZN ZN f1001 " - pdb=" SG CYS f 14 " pdb="ZN ZN f1001 " - pdb=" SG CYS f 27 " pdb=" ZN i 301 " pdb="ZN ZN i 301 " - pdb=" SG CYS i 12 " pdb="ZN ZN i 301 " - pdb=" SG CYS i 26 " pdb="ZN ZN i 301 " - pdb=" SG CYS i 9 " pdb="ZN ZN i 301 " - pdb=" SG CYS i 31 " pdb=" ZN s 101 " pdb="ZN ZN s 101 " - pdb=" SG CYS s 24 " pdb="ZN ZN s 101 " - pdb=" SG CYS s 43 " pdb="ZN ZN s 101 " - pdb=" SG CYS s 27 " pdb="ZN ZN s 101 " - pdb=" SG CYS s 40 " Number of angles added : 12 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11316 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 168 helices and 65 sheets defined 35.0% alpha, 16.8% beta 1442 base pairs and 2428 stacking pairs defined. Time for finding SS restraints: 63.91 Creating SS restraints... Processing helix chain 'g' and resid 7 through 16 removed outlier: 4.539A pdb=" N LEU g 11 " --> pdb=" O VAL g 7 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLY g 14 " --> pdb=" O LEU g 10 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL g 15 " --> pdb=" O LEU g 11 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS g 16 " --> pdb=" O GLU g 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 25 through 33 removed outlier: 4.512A pdb=" N ALA g 29 " --> pdb=" O ASN g 25 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ARG g 30 " --> pdb=" O PRO g 26 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR g 31 " --> pdb=" O LYS g 27 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE g 32 " --> pdb=" O PHE g 28 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR g 33 " --> pdb=" O ALA g 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 25 through 33' Processing helix chain 'g' and resid 44 through 62 removed outlier: 3.903A pdb=" N PHE g 57 " --> pdb=" O ARG g 53 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 89 removed outlier: 3.774A pdb=" N VAL g 81 " --> pdb=" O ALA g 77 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU g 84 " --> pdb=" O ILE g 80 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU g 86 " --> pdb=" O ARG g 82 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG g 87 " --> pdb=" O MET g 83 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA g 88 " --> pdb=" O GLU g 84 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY g 89 " --> pdb=" O ALA g 85 " (cutoff:3.500A) Processing helix chain 'g' and resid 104 through 124 removed outlier: 4.318A pdb=" N GLN g 110 " --> pdb=" O LYS g 106 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG g 111 " --> pdb=" O THR g 107 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU g 121 " --> pdb=" O GLU g 117 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA g 123 " --> pdb=" O GLU g 119 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER g 124 " --> pdb=" O ALA g 120 " (cutoff:3.500A) Processing helix chain 'g' and resid 125 through 130 removed outlier: 3.846A pdb=" N GLU g 129 " --> pdb=" O PRO g 125 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ARG g 130 " --> pdb=" O GLU g 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 125 through 130' Processing helix chain 'g' and resid 131 through 149 removed outlier: 3.605A pdb=" N ARG g 137 " --> pdb=" O LYS g 133 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG g 144 " --> pdb=" O HIS g 140 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR g 148 " --> pdb=" O ARG g 144 " (cutoff:3.500A) Processing helix chain 'g' and resid 166 through 171 Processing helix chain 'g' and resid 172 through 181 removed outlier: 3.553A pdb=" N GLU g 176 " --> pdb=" O ILE g 172 " (cutoff:3.500A) Processing helix chain 'g' and resid 193 through 198 removed outlier: 4.799A pdb=" N VAL g 197 " --> pdb=" O ASP g 193 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ASP g 198 " --> pdb=" O PRO g 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 193 through 198' Processing helix chain 'g' and resid 207 through 227 removed outlier: 4.014A pdb=" N ILE g 214 " --> pdb=" O SER g 210 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 4.287A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 46 removed outlier: 4.503A pdb=" N LEU h 32 " --> pdb=" O GLN h 28 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU h 35 " --> pdb=" O HIS h 31 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG h 40 " --> pdb=" O ASP h 36 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS h 45 " --> pdb=" O GLY h 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 73 through 78 removed outlier: 4.272A pdb=" N GLY h 78 " --> pdb=" O GLY h 74 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 95 removed outlier: 5.237A pdb=" N ARG h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS h 93 " --> pdb=" O GLU h 89 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU h 94 " --> pdb=" O GLU h 90 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR h 95 " --> pdb=" O LEU h 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 3.895A pdb=" N SER h 112 " --> pdb=" O ASN h 108 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 removed outlier: 3.852A pdb=" N GLN h 118 " --> pdb=" O PRO h 114 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 145 removed outlier: 3.660A pdb=" N GLN h 139 " --> pdb=" O LYS h 135 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.706A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG i 14 " --> pdb=" O ARG i 10 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU i 15 " --> pdb=" O LEU i 11 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY i 16 " --> pdb=" O CYS i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 23 through 29 Proline residue: i 29 - end of helix Processing helix chain 'i' and resid 31 through 36 removed outlier: 6.194A pdb=" N ARG i 35 " --> pdb=" O CYS i 31 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG i 36 " --> pdb=" O ALA i 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 31 through 36' Processing helix chain 'i' and resid 52 through 69 removed outlier: 3.687A pdb=" N ARG i 57 " --> pdb=" O ASP i 53 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE i 67 " --> pdb=" O LYS i 63 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR i 68 " --> pdb=" O LEU i 64 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 86 removed outlier: 4.275A pdb=" N LYS i 84 " --> pdb=" O GLU i 80 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LYS i 86 " --> pdb=" O ALA i 82 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 100 removed outlier: 4.763A pdb=" N GLY i 95 " --> pdb=" O SER i 91 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG i 100 " --> pdb=" O LEU i 96 " (cutoff:3.500A) Processing helix chain 'i' and resid 101 through 109 Processing helix chain 'i' and resid 113 through 124 removed outlier: 3.689A pdb=" N GLY i 124 " --> pdb=" O LEU i 120 " (cutoff:3.500A) Processing helix chain 'i' and resid 150 through 156 removed outlier: 4.426A pdb=" N ASN i 154 " --> pdb=" O GLU i 150 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LEU i 155 " --> pdb=" O LYS i 151 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLU i 156 " --> pdb=" O SER i 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 150 through 156' Processing helix chain 'i' and resid 157 through 166 Processing helix chain 'i' and resid 190 through 195 removed outlier: 5.020A pdb=" N ALA i 195 " --> pdb=" O ARG i 191 " (cutoff:3.500A) Processing helix chain 'i' and resid 199 through 209 removed outlier: 3.979A pdb=" N VAL i 203 " --> pdb=" O ASN i 199 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR i 207 " --> pdb=" O VAL i 203 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER i 208 " --> pdb=" O ILE i 204 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG i 209 " --> pdb=" O GLU i 205 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 66 removed outlier: 4.072A pdb=" N MET j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 104 through 114 removed outlier: 4.099A pdb=" N ALA j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE j 109 " --> pdb=" O VAL j 105 " (cutoff:3.500A) Processing helix chain 'j' and resid 127 through 142 removed outlier: 3.695A pdb=" N ALA j 132 " --> pdb=" O PRO j 128 " (cutoff:3.500A) Processing helix chain 'j' and resid 144 through 154 removed outlier: 4.810A pdb=" N LEU j 151 " --> pdb=" O ASP j 147 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY j 154 " --> pdb=" O ARG j 150 " (cutoff:3.500A) Processing helix chain 'k' and resid 15 through 34 removed outlier: 4.166A pdb=" N LEU k 21 " --> pdb=" O SER k 17 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE k 26 " --> pdb=" O GLU k 22 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY k 34 " --> pdb=" O LEU k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 71 through 82 removed outlier: 4.237A pdb=" N ARG k 80 " --> pdb=" O ALA k 76 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG k 82 " --> pdb=" O GLU k 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 removed outlier: 4.126A pdb=" N THR l 24 " --> pdb=" O ASP l 20 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA l 25 " --> pdb=" O VAL l 21 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 54 removed outlier: 3.852A pdb=" N ARG l 41 " --> pdb=" O ASN l 37 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 4.264A pdb=" N VAL l 61 " --> pdb=" O GLU l 57 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE l 62 " --> pdb=" O PRO l 58 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 4.898A pdb=" N SER l 98 " --> pdb=" O ARG l 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 3.525A pdb=" N ILE l 120 " --> pdb=" O ALA l 116 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP l 126 " --> pdb=" O HIS l 122 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 153 removed outlier: 4.551A pdb=" N GLU l 146 " --> pdb=" O GLU l 142 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA l 147 " --> pdb=" O ARG l 143 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG l 149 " --> pdb=" O ALA l 145 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA l 150 " --> pdb=" O GLU l 146 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR l 151 " --> pdb=" O ALA l 147 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ALA l 152 " --> pdb=" O ASN l 148 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N HIS l 153 " --> pdb=" O ARG l 149 " (cutoff:3.500A) Processing helix chain 'm' and resid 4 through 20 removed outlier: 3.778A pdb=" N THR m 11 " --> pdb=" O ALA m 7 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL m 19 " --> pdb=" O ASN m 15 " (cutoff:3.500A) Processing helix chain 'm' and resid 29 through 43 Processing helix chain 'm' and resid 120 through 128 Processing helix chain 'n' and resid 32 through 38 removed outlier: 3.894A pdb=" N GLN n 38 " --> pdb=" O ASN n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 44 through 54 removed outlier: 4.229A pdb=" N GLU n 48 " --> pdb=" O VAL n 44 " (cutoff:3.500A) Proline residue: n 49 - end of helix removed outlier: 3.663A pdb=" N ALA n 52 " --> pdb=" O GLU n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 60 removed outlier: 4.190A pdb=" N PHE n 59 " --> pdb=" O ALA n 55 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASP n 60 " --> pdb=" O LEU n 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 55 through 60' Processing helix chain 'n' and resid 69 through 90 removed outlier: 3.746A pdb=" N ASP n 75 " --> pdb=" O SER n 71 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA n 82 " --> pdb=" O LYS n 78 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN n 87 " --> pdb=" O ARG n 83 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR n 88 " --> pdb=" O ALA n 84 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASN n 89 " --> pdb=" O LEU n 85 " (cutoff:3.500A) Proline residue: n 90 - end of helix Processing helix chain 'n' and resid 91 through 100 removed outlier: 5.612A pdb=" N LYS n 95 " --> pdb=" O ASP n 91 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU n 96 " --> pdb=" O TYR n 92 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYS n 97 " --> pdb=" O ARG n 93 " (cutoff:3.500A) Proline residue: n 98 - end of helix No H-bonds generated for 'chain 'n' and resid 91 through 100' Processing helix chain 'o' and resid 12 through 31 removed outlier: 4.076A pdb=" N ALA o 18 " --> pdb=" O LYS o 14 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS o 22 " --> pdb=" O ALA o 18 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE o 23 " --> pdb=" O SER o 19 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY o 31 " --> pdb=" O ALA o 27 " (cutoff:3.500A) Processing helix chain 'o' and resid 78 through 86 removed outlier: 3.619A pdb=" N GLN o 84 " --> pdb=" O LYS o 80 " (cutoff:3.500A) Processing helix chain 'p' and resid 44 through 49 removed outlier: 4.842A pdb=" N ILE p 48 " --> pdb=" O SER p 44 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N GLY p 49 " --> pdb=" O GLY p 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 44 through 49' Processing helix chain 'p' and resid 52 through 58 removed outlier: 4.577A pdb=" N GLY p 56 " --> pdb=" O GLY p 52 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR p 57 " --> pdb=" O SER p 53 " (cutoff:3.500A) Proline residue: p 58 - end of helix No H-bonds generated for 'chain 'p' and resid 52 through 58' Processing helix chain 'p' and resid 59 through 76 removed outlier: 4.017A pdb=" N ALA p 65 " --> pdb=" O ALA p 61 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS p 71 " --> pdb=" O ASP p 67 " (cutoff:3.500A) Processing helix chain 'p' and resid 90 through 101 removed outlier: 3.643A pdb=" N LEU p 98 " --> pdb=" O ALA p 94 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA p 100 " --> pdb=" O ARG p 96 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER p 101 " --> pdb=" O ALA p 97 " (cutoff:3.500A) Processing helix chain 'p' and resid 122 through 127 removed outlier: 4.943A pdb=" N LYS p 127 " --> pdb=" O LYS p 123 " (cutoff:3.500A) Processing helix chain 'q' and resid 6 through 13 removed outlier: 3.861A pdb=" N LEU q 10 " --> pdb=" O THR q 6 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 23 removed outlier: 5.463A pdb=" N THR r 20 " --> pdb=" O ASP r 16 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR r 21 " --> pdb=" O VAL r 17 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TYR r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 4.147A pdb=" N LEU r 34 " --> pdb=" O ALA r 30 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU r 35 " --> pdb=" O LYS r 31 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR r 37 " --> pdb=" O ALA r 33 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 61 removed outlier: 4.162A pdb=" N TYR r 59 " --> pdb=" O ARG r 55 " (cutoff:3.500A) Processing helix chain 'r' and resid 68 through 83 removed outlier: 6.361A pdb=" N GLU r 73 " --> pdb=" O GLU r 69 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP r 83 " --> pdb=" O LYS r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 86 through 95 removed outlier: 4.726A pdb=" N ARG r 91 " --> pdb=" O TYR r 87 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS r 92 " --> pdb=" O ARG r 88 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG r 94 " --> pdb=" O LEU r 90 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 13 removed outlier: 5.162A pdb=" N LEU s 6 " --> pdb=" O ALA s 2 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU s 8 " --> pdb=" O LYS s 4 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS s 11 " --> pdb=" O ILE s 7 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N THR s 13 " --> pdb=" O LYS s 9 " (cutoff:3.500A) Processing helix chain 's' and resid 40 through 51 removed outlier: 3.813A pdb=" N LYS s 50 " --> pdb=" O GLU s 46 " (cutoff:3.500A) Processing helix chain 's' and resid 16 through 21 removed outlier: 3.615A pdb=" N ARG s 19 " --> pdb=" O PHE s 16 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA s 20 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR s 21 " --> pdb=" O VAL s 18 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 16 through 21' Processing helix chain 't' and resid 4 through 16 removed outlier: 4.284A pdb=" N VAL t 11 " --> pdb=" O GLU t 7 " (cutoff:3.500A) Processing helix chain 't' and resid 24 through 47 removed outlier: 4.421A pdb=" N VAL t 29 " --> pdb=" O THR t 25 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS t 42 " --> pdb=" O ARG t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 3.635A pdb=" N ARG t 65 " --> pdb=" O GLY t 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU t 66 " --> pdb=" O GLN t 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR t 69 " --> pdb=" O ARG t 65 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 removed outlier: 3.679A pdb=" N LEU t 81 " --> pdb=" O ARG t 77 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS t 84 " --> pdb=" O ALA t 80 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 63 removed outlier: 3.571A pdb=" N GLY u 63 " --> pdb=" O TRP u 59 " (cutoff:3.500A) Processing helix chain 'u' and resid 67 through 78 removed outlier: 4.572A pdb=" N ARG u 72 " --> pdb=" O ASP u 68 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA u 77 " --> pdb=" O LEU u 73 " (cutoff:3.500A) Processing helix chain 'v' and resid 81 through 99 removed outlier: 4.008A pdb=" N LYS v 87 " --> pdb=" O ASP v 83 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR v 88 " --> pdb=" O LEU v 84 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN v 93 " --> pdb=" O LEU v 89 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR v 95 " --> pdb=" O ARG v 91 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU v 96 " --> pdb=" O ARG v 92 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER v 97 " --> pdb=" O GLN v 93 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU v 98 " --> pdb=" O ASN v 94 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER v 99 " --> pdb=" O TYR v 95 " (cutoff:3.500A) Processing helix chain 'w' and resid 21 through 27 removed outlier: 3.910A pdb=" N THR w 25 " --> pdb=" O LYS w 21 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY w 27 " --> pdb=" O LYS w 23 " (cutoff:3.500A) Processing helix chain 'w' and resid 36 through 45 removed outlier: 5.255A pdb=" N ARG w 42 " --> pdb=" O GLU w 38 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE w 43 " --> pdb=" O VAL w 39 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU w 44 " --> pdb=" O LEU w 40 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N SER w 45 " --> pdb=" O LYS w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 52 through 57 Processing helix chain 'w' and resid 59 through 77 removed outlier: 3.578A pdb=" N ILE w 65 " --> pdb=" O LYS w 61 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS w 68 " --> pdb=" O ARG w 64 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA w 73 " --> pdb=" O THR w 69 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE w 75 " --> pdb=" O LYS w 71 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU w 76 " --> pdb=" O ARG w 72 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 24 removed outlier: 4.909A pdb=" N GLU x 17 " --> pdb=" O ASP x 13 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA x 24 " --> pdb=" O LEU x 20 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.712A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'y' and resid 11 through 47 removed outlier: 4.831A pdb=" N ARG y 15 " --> pdb=" O SER y 11 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS y 21 " --> pdb=" O ARG y 17 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA y 28 " --> pdb=" O LEU y 24 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS y 29 " --> pdb=" O ARG y 25 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA y 32 " --> pdb=" O ALA y 28 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE y 33 " --> pdb=" O LYS y 29 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS y 34 " --> pdb=" O LYS y 30 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY y 47 " --> pdb=" O LEU y 43 " (cutoff:3.500A) Processing helix chain 'y' and resid 49 through 70 removed outlier: 4.132A pdb=" N ILE y 55 " --> pdb=" O GLU y 51 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET y 56 " --> pdb=" O ALA y 52 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS y 68 " --> pdb=" O ASP y 64 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLY y 69 " --> pdb=" O LYS y 65 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER y 70 " --> pdb=" O ALA y 66 " (cutoff:3.500A) Processing helix chain 'y' and resid 73 through 96 removed outlier: 4.294A pdb=" N ARG y 86 " --> pdb=" O SER y 82 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS y 87 " --> pdb=" O ARG y 83 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA y 94 " --> pdb=" O GLN y 90 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ALA y 95 " --> pdb=" O LEU y 91 " (cutoff:3.500A) Processing helix chain 'z' and resid 8 through 16 removed outlier: 3.582A pdb=" N LYS z 12 " --> pdb=" O THR z 8 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG z 15 " --> pdb=" O GLY z 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 76 removed outlier: 6.117A pdb=" N ILE X 67 " --> pdb=" O ALA X 63 " (cutoff:3.500A) Proline residue: X 68 - end of helix removed outlier: 4.846A pdb=" N ARG X 76 " --> pdb=" O GLU X 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 94 removed outlier: 4.585A pdb=" N ILE X 90 " --> pdb=" O SER X 86 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU X 93 " --> pdb=" O GLU X 89 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU X 94 " --> pdb=" O ILE X 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 14 through 35 Proline residue: Y 18 - end of helix removed outlier: 4.543A pdb=" N ARG Y 30 " --> pdb=" O ARG Y 26 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU Y 34 " --> pdb=" O ARG Y 30 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N LEU Y 35 " --> pdb=" O GLU Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 56 removed outlier: 5.346A pdb=" N ASP Y 52 " --> pdb=" O HIS Y 48 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS Y 54 " --> pdb=" O ILE Y 50 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG Y 55 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLN Y 56 " --> pdb=" O ASP Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 45 removed outlier: 4.000A pdb=" N SER Y 45 " --> pdb=" O SER Y 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 40 through 45' Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.752A pdb=" N LYS Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 Processing helix chain 'a' and resid 48 through 57 removed outlier: 4.334A pdb=" N GLU a 57 " --> pdb=" O GLU a 53 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 22 removed outlier: 4.213A pdb=" N SER b 21 " --> pdb=" O ASP b 17 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N HIS b 22 " --> pdb=" O ALA b 18 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 25 removed outlier: 3.840A pdb=" N ARG d 23 " --> pdb=" O ARG d 19 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) Proline residue: d 25 - end of helix Processing helix chain 'd' and resid 26 through 38 removed outlier: 3.941A pdb=" N VAL d 30 " --> pdb=" O GLY d 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS d 37 " --> pdb=" O ARG d 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 38 through 45 removed outlier: 6.224A pdb=" N ARG e 42 " --> pdb=" O GLY e 38 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLY e 45 " --> pdb=" O ILE e 41 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 61 removed outlier: 4.341A pdb=" N ALA e 55 " --> pdb=" O ALA e 51 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE e 58 " --> pdb=" O GLU e 54 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS e 59 " --> pdb=" O ALA e 55 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU e 60 " --> pdb=" O GLU e 56 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU e 61 " --> pdb=" O ARG e 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 27 removed outlier: 4.845A pdb=" N ALA A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ARG A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 22 through 27' Processing helix chain 'A' and resid 83 through 90 removed outlier: 3.865A pdb=" N ALA A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 removed outlier: 3.512A pdb=" N GLN A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 102' Processing helix chain 'A' and resid 184 through 194 removed outlier: 4.179A pdb=" N ASN A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ALA A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 202 Proline residue: A 201 - end of helix No H-bonds generated for 'chain 'A' and resid 197 through 202' Processing helix chain 'B' and resid 10 through 16 removed outlier: 6.934A pdb=" N PHE B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N MET B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 73 removed outlier: 4.194A pdb=" N LYS B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 68 through 73' Processing helix chain 'B' and resid 132 through 137 Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 208 through 216 removed outlier: 5.007A pdb=" N SER B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N TRP B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 227 removed outlier: 4.764A pdb=" N MET B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASN B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 227' Processing helix chain 'B' and resid 266 through 271 removed outlier: 4.285A pdb=" N ILE B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ILE B 271 " --> pdb=" O SER B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 271' Processing helix chain 'C' and resid 115 through 121 removed outlier: 5.526A pdb=" N TRP C 120 " --> pdb=" O GLY C 115 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN C 121 " --> pdb=" O VAL C 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 115 through 121' Processing helix chain 'D' and resid 29 through 46 removed outlier: 5.381A pdb=" N ARG D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 121 removed outlier: 3.775A pdb=" N VAL D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.660A pdb=" N GLU D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 168 removed outlier: 4.703A pdb=" N ALA D 166 " --> pdb=" O LEU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 190 removed outlier: 4.237A pdb=" N THR D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLU D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 207 removed outlier: 4.679A pdb=" N VAL D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLY D 207 " --> pdb=" O GLN D 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 24 removed outlier: 5.716A pdb=" N ARG E 16 " --> pdb=" O TYR E 12 " (cutoff:3.500A) Proline residue: E 17 - end of helix Processing helix chain 'E' and resid 53 through 65 removed outlier: 5.238A pdb=" N ALA E 57 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN E 58 " --> pdb=" O GLU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 114 removed outlier: 3.924A pdb=" N ASN E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Proline residue: E 112 - end of helix Processing helix chain 'E' and resid 145 through 150 removed outlier: 4.716A pdb=" N VAL E 149 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASP E 150 " --> pdb=" O TYR E 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 145 through 150' Processing helix chain 'E' and resid 165 through 177 removed outlier: 3.907A pdb=" N ALA E 169 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU E 175 " --> pdb=" O ALA E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 126 removed outlier: 6.035A pdb=" N PHE E 125 " --> pdb=" O PRO E 122 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP E 126 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 81 removed outlier: 3.868A pdb=" N SER F 63 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU F 64 " --> pdb=" O ARG F 60 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLY F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ARG F 69 " --> pdb=" O HIS F 65 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 5.262A pdb=" N VAL F 141 " --> pdb=" O ASP F 137 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE F 148 " --> pdb=" O VAL F 144 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG F 152 " --> pdb=" O ILE F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 40 through 59 removed outlier: 3.721A pdb=" N ARG G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA G 53 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS G 56 " --> pdb=" O ARG G 52 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 36 removed outlier: 5.248A pdb=" N ALA J 27 " --> pdb=" O LEU J 23 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS J 29 " --> pdb=" O ARG J 25 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLY J 36 " --> pdb=" O THR J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 94 removed outlier: 4.617A pdb=" N HIS J 94 " --> pdb=" O MET J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 108 removed outlier: 4.704A pdb=" N GLU J 100 " --> pdb=" O GLU J 96 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY J 105 " --> pdb=" O HIS J 101 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET J 106 " --> pdb=" O ALA J 102 " (cutoff:3.500A) Proline residue: J 108 - end of helix Processing helix chain 'J' and resid 110 through 121 removed outlier: 3.522A pdb=" N LYS J 118 " --> pdb=" O ARG J 114 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG J 119 " --> pdb=" O ARG J 115 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU J 120 " --> pdb=" O LEU J 116 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS J 121 " --> pdb=" O PHE J 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 4.861A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 6 through 11 Proline residue: L 10 - end of helix No H-bonds generated for 'chain 'L' and resid 6 through 11' Processing helix chain 'L' and resid 84 through 90 removed outlier: 3.584A pdb=" N ALA L 89 " --> pdb=" O LEU L 85 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG L 90 " --> pdb=" O LYS L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 102 removed outlier: 6.461A pdb=" N VAL L 101 " --> pdb=" O PRO L 97 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ARG L 102 " --> pdb=" O GLU L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 142 removed outlier: 3.764A pdb=" N ALA L 140 " --> pdb=" O GLU L 136 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA L 141 " --> pdb=" O LYS L 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 25 removed outlier: 5.656A pdb=" N GLY M 24 " --> pdb=" O ALA M 20 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP M 25 " --> pdb=" O THR M 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 20 through 25' Processing helix chain 'M' and resid 43 through 59 removed outlier: 3.764A pdb=" N ARG M 56 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG M 59 " --> pdb=" O VAL M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 126 removed outlier: 3.671A pdb=" N GLU M 116 " --> pdb=" O GLU M 112 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG M 119 " --> pdb=" O MET M 115 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE M 120 " --> pdb=" O GLU M 116 " (cutoff:3.500A) Proline residue: M 126 - end of helix Processing helix chain 'N' and resid 13 through 31 removed outlier: 3.879A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER N 27 " --> pdb=" O ASN N 23 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR N 30 " --> pdb=" O LYS N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 58 removed outlier: 4.142A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLY N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N PHE N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG N 57 " --> pdb=" O HIS N 53 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLY N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 3.986A pdb=" N ASP N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN N 71 " --> pdb=" O LEU N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.251A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS N 78 " --> pdb=" O LYS N 74 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALA N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 3.822A pdb=" N ARG N 88 " --> pdb=" O ALA N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 20 removed outlier: 4.357A pdb=" N LYS O 19 " --> pdb=" O ARG O 15 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG O 20 " --> pdb=" O ASN O 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 15 through 20' Processing helix chain 'O' and resid 62 through 81 removed outlier: 3.593A pdb=" N GLY O 70 " --> pdb=" O ALA O 66 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU O 80 " --> pdb=" O LYS O 76 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 13 removed outlier: 4.660A pdb=" N LYS P 8 " --> pdb=" O GLY P 4 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER P 12 " --> pdb=" O LYS P 8 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG P 13 " --> pdb=" O LEU P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 106 removed outlier: 4.739A pdb=" N ASN P 104 " --> pdb=" O TYR P 100 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU P 105 " --> pdb=" O PHE P 101 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N SER P 106 " --> pdb=" O ILE P 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 100 through 106' Processing helix chain 'P' and resid 107 through 115 removed outlier: 4.131A pdb=" N ARG P 111 " --> pdb=" O ASP P 107 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG P 115 " --> pdb=" O ARG P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 117 through 128 removed outlier: 3.957A pdb=" N ARG P 125 " --> pdb=" O ILE P 121 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU P 128 " --> pdb=" O ASP P 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 22 removed outlier: 4.172A pdb=" N ARG Q 11 " --> pdb=" O GLY Q 7 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.987A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG Q 55 " --> pdb=" O LYS Q 51 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL Q 63 " --> pdb=" O ARG Q 59 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG Q 70 " --> pdb=" O ASN Q 66 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.734A pdb=" N HIS Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 101 removed outlier: 4.828A pdb=" N ALA Q 96 " --> pdb=" O ARG Q 92 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASP Q 97 " --> pdb=" O LYS Q 93 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU Q 98 " --> pdb=" O ASN Q 94 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ALA Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 118 removed outlier: 4.276A pdb=" N PHE Q 106 " --> pdb=" O GLU Q 102 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU Q 111 " --> pdb=" O ALA Q 107 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA Q 116 " --> pdb=" O ARG Q 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.541A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 4.038A pdb=" N ASN S 34 " --> pdb=" O GLU S 30 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR S 38 " --> pdb=" O ASN S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.528A pdb=" N TYR S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE S 46 " --> pdb=" O ARG S 42 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN S 61 " --> pdb=" O ASN S 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 9 removed outlier: 5.626A pdb=" N VAL T 7 " --> pdb=" O THR T 3 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE T 8 " --> pdb=" O ALA T 4 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU T 9 " --> pdb=" O TYR T 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 3 through 9' Processing helix chain 'T' and resid 14 through 24 removed outlier: 4.195A pdb=" N ALA T 19 " --> pdb=" O GLU T 15 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY T 20 " --> pdb=" O LYS T 16 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE T 21 " --> pdb=" O ALA T 17 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALA T 22 " --> pdb=" O TYR T 18 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU T 23 " --> pdb=" O ALA T 19 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 48 removed outlier: 5.123A pdb=" N ALA T 42 " --> pdb=" O GLU T 38 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N THR T 45 " --> pdb=" O ASN T 41 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA T 46 " --> pdb=" O ALA T 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 22 Processing helix chain 'V' and resid 41 through 51 removed outlier: 4.781A pdb=" N LYS V 46 " --> pdb=" O VAL V 42 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 14 Processing helix chain '5' and resid 30 through 37 removed outlier: 4.946A pdb=" N LEU 5 34 " --> pdb=" O GLU 5 30 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 96 removed outlier: 4.263A pdb=" N GLU 5 94 " --> pdb=" O LEU 5 90 " (cutoff:3.500A) Processing helix chain '5' and resid 132 through 144 removed outlier: 4.227A pdb=" N ARG 5 138 " --> pdb=" O LYS 5 134 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'g' and resid 90 through 93 removed outlier: 3.665A pdb=" N ILE g 162 " --> pdb=" O PRO g 183 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'h' and resid 19 through 22 removed outlier: 6.129A pdb=" N GLU h 19 " --> pdb=" O VAL h 55 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG h 59 " --> pdb=" O ARG h 21 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG h 54 " --> pdb=" O HIS h 69 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN h 102 " --> pdb=" O VAL h 66 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'h' and resid 163 through 170 removed outlier: 3.502A pdb=" N GLY h 148 " --> pdb=" O PHE h 203 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLY h 197 " --> pdb=" O SER h 154 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY h 194 " --> pdb=" O THR h 191 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR h 191 " --> pdb=" O GLY h 194 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ASN h 181 " --> pdb=" O LEU h 204 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'i' and resid 144 through 148 removed outlier: 3.721A pdb=" N ASP i 144 " --> pdb=" O PHE i 185 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET i 181 " --> pdb=" O VAL i 148 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS i 184 " --> pdb=" O SER i 175 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'j' and resid 6 through 11 removed outlier: 6.333A pdb=" N GLY j 35 " --> pdb=" O GLU j 7 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU j 31 " --> pdb=" O ILE j 11 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU j 12 " --> pdb=" O LEU j 31 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'j' and resid 79 through 83 removed outlier: 3.799A pdb=" N LYS j 88 " --> pdb=" O LEU j 123 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP j 117 " --> pdb=" O ALA j 94 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'j' and resid 28 through 35 Processing sheet with id= 8, first strand: chain 'k' and resid 38 through 41 removed outlier: 4.213A pdb=" N TRP k 62 " --> pdb=" O GLU k 41 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG k 3 " --> pdb=" O SER k 93 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'k' and resid 44 through 47 removed outlier: 3.736A pdb=" N GLY k 44 " --> pdb=" O PHE k 60 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'l' and resid 72 through 79 removed outlier: 6.418A pdb=" N ARG l 72 " --> pdb=" O VAL l 91 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'm' and resid 22 through 27 removed outlier: 7.037A pdb=" N GLU m 22 " --> pdb=" O LEU m 63 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'm' and resid 82 through 85 removed outlier: 6.761A pdb=" N ILE m 111 " --> pdb=" O ILE m 134 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'n' and resid 4 through 9 Processing sheet with id= 14, first strand: chain 'o' and resid 42 through 50 removed outlier: 3.541A pdb=" N GLY o 10 " --> pdb=" O HIS o 68 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU o 95 " --> pdb=" O ARG o 9 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'p' and resid 40 through 43 Processing sheet with id= 16, first strand: chain 'q' and resid 32 through 36 removed outlier: 4.767A pdb=" N LEU q 84 " --> pdb=" O VAL q 101 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N HIS q 99 " --> pdb=" O ARG q 86 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'q' and resid 39 through 44 removed outlier: 5.102A pdb=" N LYS q 54 " --> pdb=" O ILE q 70 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR q 64 " --> pdb=" O LEU q 60 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'u' and resid 4 through 10 removed outlier: 6.260A pdb=" N TRP u 48 " --> pdb=" O ASP u 40 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'v' and resid 4 through 9 removed outlier: 5.243A pdb=" N LYS v 4 " --> pdb=" O GLU v 61 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU v 58 " --> pdb=" O LEU v 74 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'v' and resid 17 through 24 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'x' and resid 29 through 34 Processing sheet with id= 22, first strand: chain 'W' and resid 51 through 54 removed outlier: 4.795A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'W' and resid 65 through 71 Processing sheet with id= 24, first strand: chain 'X' and resid 16 through 23 removed outlier: 4.186A pdb=" N SER X 17 " --> pdb=" O PRO X 44 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN X 42 " --> pdb=" O GLN X 19 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG X 40 " --> pdb=" O ARG X 21 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER X 38 " --> pdb=" O LYS X 23 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'X' and resid 50 through 53 Processing sheet with id= 26, first strand: chain 'Z' and resid 34 through 38 removed outlier: 7.764A pdb=" N LEU Z 53 " --> pdb=" O VAL Z 9 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'a' and resid 11 through 16 removed outlier: 5.113A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'c' and resid 10 through 14 removed outlier: 5.333A pdb=" N CYS c 13 " --> pdb=" O ALA c 22 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'c' and resid 35 through 39 removed outlier: 6.045A pdb=" N GLU c 35 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG c 37 " --> pdb=" O HIS c 49 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS c 49 " --> pdb=" O ARG c 37 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR c 39 " --> pdb=" O THR c 47 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'A' and resid 41 through 46 removed outlier: 5.505A pdb=" N GLU A 42 " --> pdb=" O TYR A 213 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR A 213 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER A 211 " --> pdb=" O HIS A 44 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU A 209 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'B' and resid 35 through 38 No H-bonds generated for sheet with id= 31 Processing sheet with id= 32, first strand: chain 'B' and resid 101 through 107 removed outlier: 4.482A pdb=" N GLU B 101 " --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ARG B 91 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 94 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE B 75 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA B 119 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN B 115 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 139 through 143 removed outlier: 5.131A pdb=" N THR B 140 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE B 174 " --> pdb=" O GLN B 166 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ASP B 171 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 187 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'C' and resid 2 through 6 removed outlier: 7.489A pdb=" N LYS C 2 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP C 103 " --> pdb=" O ARG C 199 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'C' and resid 10 through 15 removed outlier: 3.913A pdb=" N GLY C 10 " --> pdb=" O VAL C 25 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 176 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP C 174 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'C' and resid 31 through 34 removed outlier: 6.804A pdb=" N GLN C 48 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN C 35 " --> pdb=" O GLN C 48 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 46 through 50 removed outlier: 3.581A pdb=" N ARG C 79 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 99 through 103 removed outlier: 4.193A pdb=" N GLU C 100 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 3 through 8 removed outlier: 5.173A pdb=" N GLU D 3 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 20 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA D 5 " --> pdb=" O ARG D 18 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG D 18 " --> pdb=" O ALA D 5 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 122 through 125 Processing sheet with id= 41, first strand: chain 'E' and resid 68 through 72 removed outlier: 3.666A pdb=" N LYS E 36 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N GLY E 42 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N GLY E 154 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET E 155 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N THR E 161 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLY E 129 " --> pdb=" O THR E 161 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'F' and resid 16 through 19 removed outlier: 3.787A pdb=" N LYS F 27 " --> pdb=" O SER F 16 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'F' and resid 83 through 89 removed outlier: 4.742A pdb=" N TYR F 83 " --> pdb=" O GLY F 135 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY F 135 " --> pdb=" O TYR F 83 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS F 85 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THR F 129 " --> pdb=" O ILE F 89 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'F' and resid 94 through 98 removed outlier: 4.007A pdb=" N ARG F 95 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'G' and resid 2 through 6 removed outlier: 6.087A pdb=" N LYS G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU G 35 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'J' and resid 13 through 17 removed outlier: 3.775A pdb=" N VAL J 14 " --> pdb=" O PHE J 51 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'K' and resid 56 through 60 removed outlier: 4.774A pdb=" N ASP K 56 " --> pdb=" O VAL K 43 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL K 43 " --> pdb=" O ASP K 56 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASN K 82 " --> pdb=" O TYR K 7 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA K 84 " --> pdb=" O GLU K 9 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'K' and resid 66 through 71 removed outlier: 5.925A pdb=" N LYS K 67 " --> pdb=" O PHE K 79 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N PHE K 79 " --> pdb=" O LYS K 67 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'L' and resid 79 through 83 removed outlier: 4.630A pdb=" N ARG L 111 " --> pdb=" O ARG L 79 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN L 81 " --> pdb=" O ARG L 111 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'M' and resid 63 through 67 removed outlier: 3.889A pdb=" N LYS M 63 " --> pdb=" O ALA M 107 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N MET M 103 " --> pdb=" O ARG M 67 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE M 104 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N ASP M 31 " --> pdb=" O ARG M 134 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG M 134 " --> pdb=" O ASP M 31 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LYS M 128 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'N' and resid 32 through 37 removed outlier: 9.262A pdb=" N GLY N 32 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU N 111 " --> pdb=" O LEU N 100 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'O' and resid 48 through 53 removed outlier: 3.690A pdb=" N VAL O 49 " --> pdb=" O ILE O 39 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE O 35 " --> pdb=" O SER O 53 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N VAL O 28 " --> pdb=" O ASP O 88 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'P' and resid 28 through 33 removed outlier: 4.255A pdb=" N GLN P 43 " --> pdb=" O SER P 31 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS P 33 " --> pdb=" O ARG P 41 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ARG P 41 " --> pdb=" O LYS P 33 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'P' and resid 51 through 54 removed outlier: 3.591A pdb=" N ARG P 51 " --> pdb=" O THR P 62 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG P 53 " --> pdb=" O THR P 60 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'R' and resid 3 through 6 Processing sheet with id= 56, first strand: chain 'R' and resid 33 through 37 removed outlier: 3.975A pdb=" N GLU R 34 " --> pdb=" O LEU R 62 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU R 60 " --> pdb=" O PRO R 36 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL R 61 " --> pdb=" O ILE R 99 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU R 95 " --> pdb=" O GLY R 65 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.196A pdb=" N ALA S 5 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL S 105 " --> pdb=" O ALA S 5 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA S 73 " --> pdb=" O ILE S 106 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'S' and resid 81 through 88 removed outlier: 5.958A pdb=" N ARG S 88 " --> pdb=" O ARG S 92 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'T' and resid 25 through 30 removed outlier: 4.740A pdb=" N TYR T 26 " --> pdb=" O ALA T 79 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA T 79 " --> pdb=" O TYR T 26 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP T 75 " --> pdb=" O VAL T 30 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG T 76 " --> pdb=" O LEU T 57 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU T 57 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS T 78 " --> pdb=" O ASN T 55 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN T 55 " --> pdb=" O LYS T 78 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS T 53 " --> pdb=" O ILE T 80 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'U' and resid 21 through 26 removed outlier: 5.569A pdb=" N LYS U 21 " --> pdb=" O SER U 17 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N SER U 17 " --> pdb=" O LYS U 21 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 62, first strand: chain 'V' and resid 66 through 70 removed outlier: 3.872A pdb=" N TYR V 3 " --> pdb=" O VAL V 56 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LYS V 6 " --> pdb=" O ASP V 40 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP V 40 " --> pdb=" O LYS V 6 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR V 38 " --> pdb=" O TYR V 8 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS V 36 " --> pdb=" O ARG V 10 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLU V 84 " --> pdb=" O LYS V 23 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain '5' and resid 78 through 81 removed outlier: 4.205A pdb=" N LYS 5 78 " --> pdb=" O ALA 5 25 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU 5 18 " --> pdb=" O LEU 5 119 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL 5 115 " --> pdb=" O ALA 5 22 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR 5 99 " --> pdb=" O ALA 5 120 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '5' and resid 103 through 108 removed outlier: 3.985A pdb=" N LYS 5 104 " --> pdb=" O LEU 5 116 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR 5 112 " --> pdb=" O ASN 5 108 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'f' and resid 2 through 5 removed outlier: 4.361A pdb=" N LYS f 2 " --> pdb=" O LYS f 33 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG f 4 " --> pdb=" O ARG f 35 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN f 36 " --> pdb=" O VAL f 23 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL f 23 " --> pdb=" O GLN f 36 " (cutoff:3.500A) 1495 hydrogen bonds defined for protein. 4440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3844 hydrogen bonds 6442 hydrogen bond angles 0 basepair planarities 1442 basepair parallelities 2428 stacking parallelities Total time for adding SS restraints: 298.24 Time building geometry restraints manager: 67.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.38: 58736 1.38 - 1.57: 98744 1.57 - 1.76: 9827 1.76 - 1.95: 203 1.95 - 2.14: 3 Bond restraints: 167513 Sorted by residual: bond pdb=" C6 A 1 271 " pdb=" N1 A 1 271 " ideal model delta sigma weight residual 1.351 2.138 -0.787 2.00e-02 2.50e+03 1.55e+03 bond pdb=" C4 U 11142 " pdb=" C5 U 11142 " ideal model delta sigma weight residual 1.431 2.109 -0.678 2.00e-02 2.50e+03 1.15e+03 bond pdb=" C6 A 1 271 " pdb=" N6 A 1 271 " ideal model delta sigma weight residual 1.335 1.945 -0.610 2.00e-02 2.50e+03 9.30e+02 bond pdb=" N9 A 1 271 " pdb=" C8 A 1 271 " ideal model delta sigma weight residual 1.373 1.961 -0.588 2.00e-02 2.50e+03 8.65e+02 bond pdb=" N1 U 11142 " pdb=" C2 U 11142 " ideal model delta sigma weight residual 1.381 1.871 -0.490 2.00e-02 2.50e+03 6.00e+02 ... (remaining 167508 not shown) Histogram of bond angle deviations from ideal: 30.78 - 57.55: 7 57.55 - 84.33: 5 84.33 - 111.11: 99502 111.11 - 137.88: 151259 137.88 - 164.66: 16 Bond angle restraints: 250789 Sorted by residual: angle pdb=" C2 U 11142 " pdb=" N3 U 11142 " pdb=" C4 U 11142 " ideal model delta sigma weight residual 127.00 32.90 94.10 3.00e+00 1.11e-01 9.84e+02 angle pdb=" N7 G 1 363 " pdb=" C5 G 1 363 " pdb=" C4 G 1 363 " ideal model delta sigma weight residual 110.80 34.00 76.80 3.00e+00 1.11e-01 6.55e+02 angle pdb=" C8 A 1 271 " pdb=" N9 A 1 271 " pdb=" C4 A 1 271 " ideal model delta sigma weight residual 105.80 30.78 75.02 3.00e+00 1.11e-01 6.25e+02 angle pdb=" N9 G 1 363 " pdb=" C8 G 1 363 " pdb=" N7 G 1 363 " ideal model delta sigma weight residual 113.10 40.33 72.77 3.00e+00 1.11e-01 5.88e+02 angle pdb=" N3 U 11142 " pdb=" C4 U 11142 " pdb=" O4 U 11142 " ideal model delta sigma weight residual 119.40 53.88 65.52 3.00e+00 1.11e-01 4.77e+02 ... (remaining 250784 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 83533 35.99 - 71.99: 5194 71.99 - 107.98: 478 107.98 - 143.98: 48 143.98 - 179.97: 87 Dihedral angle restraints: 89340 sinusoidal: 71735 harmonic: 17605 Sorted by residual: dihedral pdb=" CA GLY L 34 " pdb=" C GLY L 34 " pdb=" N HIS L 35 " pdb=" CA HIS L 35 " ideal model delta harmonic sigma weight residual -180.00 -105.09 -74.91 0 5.00e+00 4.00e-02 2.24e+02 dihedral pdb=" CA HIS e 31 " pdb=" C HIS e 31 " pdb=" N LEU e 32 " pdb=" CA LEU e 32 " ideal model delta harmonic sigma weight residual 180.00 -113.31 -66.69 0 5.00e+00 4.00e-02 1.78e+02 dihedral pdb=" CA THR L 57 " pdb=" C THR L 57 " pdb=" N THR L 58 " pdb=" CA THR L 58 " ideal model delta harmonic sigma weight residual 180.00 121.35 58.65 0 5.00e+00 4.00e-02 1.38e+02 ... (remaining 89337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 29177 0.108 - 0.215: 2434 0.215 - 0.323: 221 0.323 - 0.430: 44 0.430 - 0.538: 6 Chirality restraints: 31882 Sorted by residual: chirality pdb=" C3' G 11541 " pdb=" C4' G 11541 " pdb=" O3' G 11541 " pdb=" C2' G 11541 " both_signs ideal model delta sigma weight residual False -2.48 -1.94 -0.54 2.00e-01 2.50e+01 7.23e+00 chirality pdb=" C1' C 21006 " pdb=" O4' C 21006 " pdb=" C2' C 21006 " pdb=" N1 C 21006 " both_signs ideal model delta sigma weight residual False 2.47 1.97 0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" C3' A 1 752 " pdb=" C4' A 1 752 " pdb=" O3' A 1 752 " pdb=" C2' A 1 752 " both_signs ideal model delta sigma weight residual False -2.74 -2.26 -0.48 2.00e-01 2.50e+01 5.84e+00 ... (remaining 31879 not shown) Planarity restraints: 13445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 1 271 " 0.181 2.00e-02 2.50e+03 4.81e-01 6.37e+03 pdb=" N9 A 1 271 " 0.648 2.00e-02 2.50e+03 pdb=" C8 A 1 271 " 0.888 2.00e-02 2.50e+03 pdb=" N7 A 1 271 " 0.093 2.00e-02 2.50e+03 pdb=" C5 A 1 271 " -0.097 2.00e-02 2.50e+03 pdb=" C6 A 1 271 " -0.850 2.00e-02 2.50e+03 pdb=" N6 A 1 271 " -0.533 2.00e-02 2.50e+03 pdb=" N1 A 1 271 " -0.499 2.00e-02 2.50e+03 pdb=" C2 A 1 271 " -0.025 2.00e-02 2.50e+03 pdb=" N3 A 1 271 " 0.019 2.00e-02 2.50e+03 pdb=" C4 A 1 271 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU 7 54 " 0.003 2.00e-02 2.50e+03 4.85e-01 5.29e+03 pdb=" C4' 5MU 7 54 " -0.373 2.00e-02 2.50e+03 pdb=" O4' 5MU 7 54 " -0.470 2.00e-02 2.50e+03 pdb=" C3' 5MU 7 54 " 0.617 2.00e-02 2.50e+03 pdb=" O3' 5MU 7 54 " 0.367 2.00e-02 2.50e+03 pdb=" C2' 5MU 7 54 " 0.250 2.00e-02 2.50e+03 pdb=" O2' 5MU 7 54 " -0.789 2.00e-02 2.50e+03 pdb=" C1' 5MU 7 54 " -0.292 2.00e-02 2.50e+03 pdb=" N1 5MU 7 54 " 0.685 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 11142 " -0.030 2.00e-02 2.50e+03 2.02e-01 9.21e+02 pdb=" N1 U 11142 " -0.140 2.00e-02 2.50e+03 pdb=" C2 U 11142 " -0.332 2.00e-02 2.50e+03 pdb=" O2 U 11142 " -0.143 2.00e-02 2.50e+03 pdb=" N3 U 11142 " -0.082 2.00e-02 2.50e+03 pdb=" C4 U 11142 " 0.365 2.00e-02 2.50e+03 pdb=" O4 U 11142 " 0.127 2.00e-02 2.50e+03 pdb=" C5 U 11142 " 0.247 2.00e-02 2.50e+03 pdb=" C6 U 11142 " -0.012 2.00e-02 2.50e+03 ... (remaining 13442 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 17 1.98 - 2.71: 19484 2.71 - 3.44: 208876 3.44 - 4.17: 514553 4.17 - 4.90: 706113 Nonbonded interactions: 1449043 Sorted by model distance: nonbonded pdb="MG MG 13035 " pdb="MG MG 13373 " model vdw 1.247 1.300 nonbonded pdb="MG MG 21777 " pdb="MG MG 21785 " model vdw 1.262 1.300 nonbonded pdb="MG MG 13197 " pdb="MG MG 13363 " model vdw 1.275 1.300 nonbonded pdb="MG MG 13156 " pdb="MG MG 13315 " model vdw 1.294 1.300 nonbonded pdb="MG MG 13165 " pdb="MG MG 13167 " model vdw 1.301 1.300 ... (remaining 1449038 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'H' selection = (chain 'I' and (resid 144 through 273 and (name N or name CA or name C or name O \ or name CB ))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 4929 5.49 5 Mg 637 5.21 5 S 118 5.16 5 C 77456 2.51 5 N 29100 2.21 5 O 42508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.54 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 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: 0.180 Extract box with map and model: 20.330 Check model and map are aligned: 1.720 Convert atoms to be neutral: 0.990 Process input model: 626.610 Find NCS groups from input model: 3.460 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 659.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.012 0.787 167513 Z= 0.752 Angle : 1.384 94.103 250789 Z= 0.649 Chirality : 0.064 0.538 31882 Planarity : 0.011 0.485 13445 Dihedral : 19.078 179.969 78024 Min Nonbonded Distance : 1.247 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.85 % Allowed : 16.58 % Favored : 82.57 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % Cis-general : 0.00 % Twisted Proline : 2.46 % Twisted General : 1.44 % 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: -5.45 (0.08), residues: 5779 helix: -3.58 (0.08), residues: 1654 sheet: -3.50 (0.14), residues: 925 loop : -3.78 (0.09), residues: 3200 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1955 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1901 time to evaluate : 6.673 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 outliers start: 54 outliers final: 27 residues processed: 1935 average time/residue: 1.5573 time to fit residues: 5041.2905 Evaluate side-chains 1498 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1471 time to evaluate : 8.574 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 1.2625 time to fit residues: 72.9627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 915 optimal weight: 0.0980 chunk 821 optimal weight: 7.9990 chunk 455 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 554 optimal weight: 20.0000 chunk 438 optimal weight: 1.9990 chunk 849 optimal weight: 8.9990 chunk 328 optimal weight: 2.9990 chunk 516 optimal weight: 6.9990 chunk 632 optimal weight: 2.9990 chunk 984 optimal weight: 0.8980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 110 ASN h 118 GLN i 45 GLN j 20 GLN ** j 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 GLN ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 ASN l 148 ASN n 124 GLN ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 22 HIS p 38 ASN ** p 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 75 HIS r 12 ASN u 76 GLN v 94 ASN w 63 GLN W 80 HIS ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 66 HIS ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 46 GLN b 23 HIS b 43 HIS c 20 ASN A 56 GLN A 71 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 137 HIS ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN F 74 ASN F 143 GLN K 3 GLN K 82 ASN K 88 ASN L 9 ASN M 12 GLN M 113 GLN M 123 HIS N 61 HIS Q 66 ASN Q 81 HIS Q 117 GLN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 ASN V 73 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.624 167513 Z= 0.253 Angle : 0.860 101.944 250789 Z= 0.399 Chirality : 0.038 0.320 31882 Planarity : 0.007 0.194 13445 Dihedral : 18.425 179.598 66051 Min Nonbonded Distance : 1.050 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.54 % Allowed : 13.24 % Favored : 86.23 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 1.76 % Twisted General : 0.63 % 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: -4.37 (0.10), residues: 5779 helix: -2.10 (0.11), residues: 1649 sheet: -3.12 (0.15), residues: 917 loop : -3.38 (0.10), residues: 3213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1855 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1683 time to evaluate : 6.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 92 residues processed: 1760 average time/residue: 1.4906 time to fit residues: 4474.8225 Evaluate side-chains 1541 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1449 time to evaluate : 6.767 Switching outliers to nearest non-outliers outliers start: 92 outliers final: 0 residues processed: 92 average time/residue: 1.2675 time to fit residues: 230.0515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 547 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 chunk 819 optimal weight: 0.8980 chunk 670 optimal weight: 8.9990 chunk 271 optimal weight: 6.9990 chunk 986 optimal weight: 5.9990 chunk 1065 optimal weight: 30.0000 chunk 878 optimal weight: 2.9990 chunk 977 optimal weight: 1.9990 chunk 336 optimal weight: 7.9990 chunk 791 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 28 GLN h 170 GLN ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 124 GLN ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 69 ASN p 117 ASN r 77 ASN u 76 GLN v 94 ASN w 63 GLN y 42 GLN ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 HIS A 56 GLN B 44 ASN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 ASN ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN V 50 GLN ** 5 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 36 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.572 167513 Z= 0.299 Angle : 0.868 103.439 250789 Z= 0.401 Chirality : 0.038 0.354 31882 Planarity : 0.007 0.205 13445 Dihedral : 18.336 179.776 66051 Min Nonbonded Distance : 1.045 Molprobity Statistics. All-atom Clashscore : 19.40 Ramachandran Plot: Outliers : 0.54 % Allowed : 14.73 % Favored : 84.74 % Rotamer Outliers : 3.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % Cis-general : 0.00 % Twisted Proline : 2.11 % Twisted General : 0.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.10), residues: 5779 helix: -1.48 (0.12), residues: 1659 sheet: -2.93 (0.15), residues: 935 loop : -3.24 (0.10), residues: 3185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1747 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1559 time to evaluate : 6.783 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 outliers start: 188 outliers final: 116 residues processed: 1647 average time/residue: 1.5444 time to fit residues: 4382.9081 Evaluate side-chains 1551 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1435 time to evaluate : 6.764 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 0 residues processed: 116 average time/residue: 1.3068 time to fit residues: 295.3784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 974 optimal weight: 0.5980 chunk 741 optimal weight: 0.0970 chunk 511 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 470 optimal weight: 20.0000 chunk 662 optimal weight: 6.9990 chunk 989 optimal weight: 3.9990 chunk 1047 optimal weight: 30.0000 chunk 517 optimal weight: 7.9990 chunk 937 optimal weight: 8.9990 chunk 282 optimal weight: 5.9990 overall best weight: 3.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 136 GLN h 170 GLN h 181 ASN ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 124 GLN o 13 HIS ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 77 ASN u 76 GLN v 94 ASN w 63 GLN y 42 GLN ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 47 GLN ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 180 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.575 167513 Z= 0.359 Angle : 0.896 103.328 250789 Z= 0.416 Chirality : 0.040 0.363 31882 Planarity : 0.007 0.204 13445 Dihedral : 18.403 179.957 66051 Min Nonbonded Distance : 1.021 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.52 % Allowed : 15.52 % Favored : 83.96 % Rotamer Outliers : 4.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 2.11 % Twisted General : 0.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.10), residues: 5779 helix: -1.23 (0.12), residues: 1648 sheet: -2.78 (0.15), residues: 910 loop : -3.17 (0.10), residues: 3221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1695 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1495 time to evaluate : 6.607 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 outliers start: 200 outliers final: 124 residues processed: 1595 average time/residue: 1.4369 time to fit residues: 3930.9602 Evaluate side-chains 1527 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1403 time to evaluate : 6.554 Switching outliers to nearest non-outliers outliers start: 124 outliers final: 0 residues processed: 124 average time/residue: 1.1279 time to fit residues: 269.2005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 872 optimal weight: 5.9990 chunk 594 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 780 optimal weight: 7.9990 chunk 432 optimal weight: 8.9990 chunk 894 optimal weight: 7.9990 chunk 724 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 535 optimal weight: 7.9990 chunk 940 optimal weight: 5.9990 chunk 264 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 45 GLN ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 89 ASN n 124 GLN ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 76 GLN v 94 ASN ** w 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 42 GLN ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 HIS d 36 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 180 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 5 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 36 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.573 167513 Z= 0.498 Angle : 1.002 103.366 250789 Z= 0.469 Chirality : 0.045 0.394 31882 Planarity : 0.008 0.204 13445 Dihedral : 18.671 179.496 66051 Min Nonbonded Distance : 0.974 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.59 % Allowed : 17.13 % Favored : 82.28 % Rotamer Outliers : 4.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % Cis-general : 0.00 % Twisted Proline : 2.46 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.10), residues: 5779 helix: -1.32 (0.12), residues: 1652 sheet: -2.70 (0.16), residues: 917 loop : -3.28 (0.10), residues: 3210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1688 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1477 time to evaluate : 6.636 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 outliers start: 211 outliers final: 134 residues processed: 1578 average time/residue: 1.4341 time to fit residues: 3870.6193 Evaluate side-chains 1521 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1387 time to evaluate : 6.733 Switching outliers to nearest non-outliers outliers start: 134 outliers final: 0 residues processed: 134 average time/residue: 1.1983 time to fit residues: 306.0271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 352 optimal weight: 1.9990 chunk 943 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 615 optimal weight: 9.9990 chunk 258 optimal weight: 5.9990 chunk 1048 optimal weight: 30.0000 chunk 870 optimal weight: 2.9990 chunk 485 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 346 optimal weight: 9.9990 chunk 550 optimal weight: 30.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 110 ASN h 170 GLN ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 38 GLN ** j 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 37 ASN u 76 GLN w 63 GLN y 42 GLN ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN J 38 HIS J 130 HIS ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 GLN ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 HIS U 43 ASN ** 5 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.576 167513 Z= 0.366 Angle : 0.912 103.307 250789 Z= 0.425 Chirality : 0.041 0.369 31882 Planarity : 0.007 0.204 13445 Dihedral : 18.540 179.647 66051 Min Nonbonded Distance : 1.007 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.52 % Allowed : 16.02 % Favored : 83.46 % Rotamer Outliers : 3.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 2.11 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.10), residues: 5779 helix: -1.15 (0.12), residues: 1650 sheet: -2.59 (0.16), residues: 877 loop : -3.15 (0.10), residues: 3252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1657 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1486 time to evaluate : 9.075 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 outliers start: 171 outliers final: 116 residues processed: 1572 average time/residue: 1.5267 time to fit residues: 4128.5744 Evaluate side-chains 1538 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1422 time to evaluate : 6.693 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 0 residues processed: 116 average time/residue: 1.2810 time to fit residues: 284.2079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 1011 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 597 optimal weight: 10.0000 chunk 765 optimal weight: 0.8980 chunk 593 optimal weight: 10.0000 chunk 882 optimal weight: 10.0000 chunk 585 optimal weight: 10.0000 chunk 1044 optimal weight: 30.0000 chunk 653 optimal weight: 20.0000 chunk 636 optimal weight: 6.9990 chunk 482 optimal weight: 5.9990 overall best weight: 6.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 110 ASN h 170 GLN ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 38 GLN ** j 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 84 ASN ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 124 GLN ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 37 ASN u 76 GLN ** w 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 65 ASN y 42 GLN ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.574 167513 Z= 0.582 Angle : 1.059 103.388 250789 Z= 0.496 Chirality : 0.047 0.407 31882 Planarity : 0.008 0.203 13445 Dihedral : 18.742 179.824 66051 Min Nonbonded Distance : 0.959 Molprobity Statistics. All-atom Clashscore : 25.91 Ramachandran Plot: Outliers : 0.62 % Allowed : 17.89 % Favored : 81.48 % Rotamer Outliers : 3.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % Cis-general : 0.00 % Twisted Proline : 2.46 % Twisted General : 0.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.10), residues: 5779 helix: -1.36 (0.12), residues: 1646 sheet: -2.68 (0.16), residues: 893 loop : -3.31 (0.10), residues: 3240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1621 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1453 time to evaluate : 6.697 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 outliers start: 168 outliers final: 115 residues processed: 1525 average time/residue: 1.5244 time to fit residues: 4012.9679 Evaluate side-chains 1511 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1396 time to evaluate : 6.693 Switching outliers to nearest non-outliers outliers start: 115 outliers final: 0 residues processed: 115 average time/residue: 1.1620 time to fit residues: 261.3667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 646 optimal weight: 0.6980 chunk 417 optimal weight: 1.9990 chunk 624 optimal weight: 0.9990 chunk 314 optimal weight: 20.0000 chunk 205 optimal weight: 0.5980 chunk 202 optimal weight: 0.9990 chunk 664 optimal weight: 4.9990 chunk 711 optimal weight: 6.9990 chunk 516 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 821 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 212 GLN h 110 ASN ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 38 GLN ** j 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 78 GLN o 62 HIS p 116 HIS t 37 ASN u 76 GLN w 63 GLN y 42 GLN ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 56 GLN ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 HIS ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN E 121 ASN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 ASN T 58 HIS U 43 ASN V 34 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.607 167513 Z= 0.270 Angle : 0.868 103.242 250789 Z= 0.400 Chirality : 0.037 0.433 31882 Planarity : 0.007 0.202 13445 Dihedral : 18.350 179.634 66051 Min Nonbonded Distance : 1.076 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.54 % Allowed : 13.60 % Favored : 85.86 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 1.76 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.10), residues: 5779 helix: -0.92 (0.13), residues: 1631 sheet: -2.49 (0.16), residues: 923 loop : -3.00 (0.10), residues: 3225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1611 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1541 time to evaluate : 6.614 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 outliers start: 70 outliers final: 38 residues processed: 1564 average time/residue: 1.4998 time to fit residues: 4028.6848 Evaluate side-chains 1458 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1420 time to evaluate : 6.679 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 1.1464 time to fit residues: 90.6256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 950 optimal weight: 5.9990 chunk 1000 optimal weight: 10.0000 chunk 913 optimal weight: 6.9990 chunk 973 optimal weight: 0.9990 chunk 586 optimal weight: 9.9990 chunk 424 optimal weight: 0.0970 chunk 764 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 879 optimal weight: 0.4980 chunk 920 optimal weight: 3.9990 chunk 970 optimal weight: 9.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 110 ASN h 170 GLN h 181 ASN ** i 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 38 GLN ** j 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 HIS u 65 GLN u 76 GLN w 63 GLN ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 42 GLN ** y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN E 121 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 ASN T 55 ASN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.576 167513 Z= 0.369 Angle : 0.913 103.270 250789 Z= 0.426 Chirality : 0.038 0.406 31882 Planarity : 0.008 0.243 13445 Dihedral : 18.339 179.618 66051 Min Nonbonded Distance : 1.071 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.52 % Allowed : 13.98 % Favored : 85.50 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 2.82 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.10), residues: 5779 helix: -0.92 (0.12), residues: 1632 sheet: -2.46 (0.16), residues: 921 loop : -2.99 (0.10), residues: 3226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1473 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1408 time to evaluate : 6.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 47 residues processed: 1427 average time/residue: 1.4570 time to fit residues: 3579.0899 Evaluate side-chains 1437 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1390 time to evaluate : 6.421 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 1.2620 time to fit residues: 115.6791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 639 optimal weight: 7.9990 chunk 1029 optimal weight: 30.0000 chunk 628 optimal weight: 10.0000 chunk 488 optimal weight: 10.0000 chunk 715 optimal weight: 7.9990 chunk 1079 optimal weight: 30.0000 chunk 993 optimal weight: 4.9990 chunk 859 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 664 optimal weight: 7.9990 chunk 527 optimal weight: 6.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 110 ASN h 170 GLN ** i 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 127 ASN ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 HIS w 63 GLN ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 42 GLN ** y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN E 132 ASN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.576 167513 Z= 0.379 Angle : 0.920 103.270 250789 Z= 0.432 Chirality : 0.038 0.405 31882 Planarity : 0.008 0.278 13445 Dihedral : 18.339 179.618 66051 Min Nonbonded Distance : 1.071 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.52 % Allowed : 13.98 % Favored : 85.50 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 2.82 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.10), residues: 5779 helix: -0.92 (0.12), residues: 1632 sheet: -2.46 (0.16), residues: 921 loop : -2.99 (0.10), residues: 3226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11558 Ramachandran restraints generated. 5779 Oldfield, 0 Emsley, 5779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1392 time to evaluate : 6.575 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 outliers start: 3 outliers final: 0 residues processed: 1392 average time/residue: 1.4833 time to fit residues: 3543.4691 Evaluate side-chains 1387 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1387 time to evaluate : 6.721 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 683 optimal weight: 6.9990 chunk 916 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 792 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 861 optimal weight: 0.8980 chunk 360 optimal weight: 0.0050 chunk 884 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 158 optimal weight: 0.8980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 110 ASN ** i 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 HIS w 63 GLN ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN ** C 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.129386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108666 restraints weight = 345959.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.110712 restraints weight = 182931.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111037 restraints weight = 99406.253| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.580 167513 Z= 0.385 Angle : 0.917 103.270 250789 Z= 0.429 Chirality : 0.038 0.405 31882 Planarity : 0.008 0.278 13445 Dihedral : 18.339 179.618 66051 Min Nonbonded Distance : 1.071 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.52 % Allowed : 13.98 % Favored : 85.50 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 2.82 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.10), residues: 5779 helix: -0.92 (0.12), residues: 1632 sheet: -2.46 (0.16), residues: 921 loop : -2.99 (0.10), residues: 3226 =============================================================================== Job complete usr+sys time: 51548.95 seconds wall clock time: 884 minutes 10.90 seconds (53050.90 seconds total)