Starting phenix.real_space_refine on Sat Mar 2 20:48:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/03_2024/6q95_4475_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/03_2024/6q95_4475.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/03_2024/6q95_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_4475/03_2024/6q95_4475_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/03_2024/6q95_4475_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/03_2024/6q95_4475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/03_2024/6q95_4475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/03_2024/6q95_4475_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q95_4475/03_2024/6q95_4475_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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, 'rna2p_pyr': 79, 'rna3p_pur': 743, 'rna3p_pyr': 571} Link IDs: {'rna2p': 190, 'rna3p': 1313} 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: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p': 1, 'rna3p_pur': 31, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 65} 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: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 30, 'rna3p_pyr': 37} Link IDs: {'rna2p': 9, 'rna3p': 66} Chain: "9" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 125 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 4} 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, 'rna2p_pyr': 129, 'rna3p_pur': 1387, 'rna3p_pyr': 1042} Link IDs: {'rna2p': 402, 'rna3p': 2428} 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: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 62, 'rna3p_pyr': 51} Link IDs: {'rna2p': 6, 'rna3p': 112} 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: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 250} 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: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 188} 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: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 126} 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: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 135} 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: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 93} 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: {'rna2p_pur': 33, 'rna2p_pyr': 25, 'rna3p_pur': 136, 'rna3p_pyr': 125} Link IDs: {'rna2p': 57, 'rna3p': 261} 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: 58.72, per 1000 atoms: 0.38 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: 69.18 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal 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 for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 168 helices and 65 sheets defined 35.0% alpha, 16.8% beta 1442 base pairs and 2428 stacking pairs defined. Time for finding SS restraints: 76.40 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: 240.96 Time building geometry restraints manager: 74.36 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: 92750 35.99 - 71.99: 13996 71.99 - 107.98: 1637 107.98 - 143.98: 48 143.98 - 179.97: 87 Dihedral angle restraints: 108518 sinusoidal: 90913 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 108515 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 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: 2.480 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: 0.100 Extract box with map and model: 14.870 Check model and map are aligned: 1.700 Set scattering table: 1.000 Process input model: 573.410 Find NCS groups from input model: 3.210 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 599.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 25.819 179.969 97202 Min Nonbonded Distance : 1.247 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.85 % Allowed : 16.58 % Favored : 82.57 % Rotamer: Outliers : 1.13 % Allowed : 9.90 % Favored : 88.97 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP g 24 HIS 0.019 0.003 HIS o 56 PHE 0.048 0.004 PHE x 10 TYR 0.050 0.004 TYR T 26 ARG 0.020 0.001 ARG O 97 *********************** 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 : 6.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: g 28 PHE cc_start: 0.8659 (t80) cc_final: 0.8410 (t80) REVERT: g 63 MET cc_start: 0.7635 (ppp) cc_final: 0.7380 (tmm) REVERT: g 92 TYR cc_start: 0.8804 (p90) cc_final: 0.8542 (p90) REVERT: g 135 GLN cc_start: 0.7698 (tt0) cc_final: 0.7461 (mm-40) REVERT: g 148 TYR cc_start: 0.7586 (m-80) cc_final: 0.7335 (m-10) REVERT: g 169 LYS cc_start: 0.8046 (tppt) cc_final: 0.7540 (mmtm) REVERT: g 221 LEU cc_start: 0.7954 (mt) cc_final: 0.7426 (mt) REVERT: h 19 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6842 (mm-30) REVERT: h 85 ARG cc_start: 0.7516 (mtt-85) cc_final: 0.7138 (mtt-85) REVERT: h 123 GLN cc_start: 0.8285 (mm110) cc_final: 0.8051 (mm110) REVERT: i 42 GLN cc_start: 0.7976 (tt0) cc_final: 0.7482 (tt0) REVERT: i 93 PHE cc_start: 0.8904 (t80) cc_final: 0.8682 (t80) REVERT: i 101 LEU cc_start: 0.9011 (tp) cc_final: 0.8788 (tp) REVERT: i 160 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8133 (tm-30) REVERT: i 161 ASN cc_start: 0.8241 (m110) cc_final: 0.7974 (m110) REVERT: i 199 ASN cc_start: 0.7653 (t0) cc_final: 0.6644 (t0) REVERT: i 205 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6911 (mt-10) REVERT: j 13 ILE cc_start: 0.9423 (mm) cc_final: 0.9217 (mm) REVERT: j 19 MET cc_start: 0.7846 (mmm) cc_final: 0.7551 (mtp) REVERT: j 79 GLU cc_start: 0.7485 (mp0) cc_final: 0.6780 (mt-10) REVERT: j 142 LEU cc_start: 0.8876 (tp) cc_final: 0.8457 (tp) REVERT: k 5 GLU cc_start: 0.8294 (mp0) cc_final: 0.7655 (tp30) REVERT: k 33 TYR cc_start: 0.8104 (m-80) cc_final: 0.7572 (m-10) REVERT: l 37 ASN cc_start: 0.8970 (t0) cc_final: 0.8451 (t0) REVERT: l 86 GLN cc_start: 0.7712 (tt0) cc_final: 0.7321 (tt0) REVERT: l 109 ASN cc_start: 0.8372 (m-40) cc_final: 0.8114 (m110) REVERT: l 120 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8839 (mp) REVERT: l 131 LYS cc_start: 0.7992 (mtmm) cc_final: 0.7707 (tmtt) REVERT: m 48 TYR cc_start: 0.8642 (p90) cc_final: 0.7423 (p90) REVERT: n 78 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8487 (ttmt) REVERT: n 110 GLU cc_start: 0.7808 (pt0) cc_final: 0.7605 (pt0) REVERT: o 64 GLU cc_start: 0.7985 (pt0) cc_final: 0.7718 (pt0) REVERT: p 20 TYR cc_start: 0.8436 (m-80) cc_final: 0.8216 (m-80) REVERT: p 116 HIS cc_start: 0.8227 (m-70) cc_final: 0.7716 (m-70) REVERT: q 9 GLN cc_start: 0.8443 (mt0) cc_final: 0.8107 (mt0) REVERT: r 12 ASN cc_start: 0.6939 (m-40) cc_final: 0.6702 (m-40) REVERT: r 82 MET cc_start: 0.5859 (ttt) cc_final: 0.5462 (ttt) REVERT: s 3 ARG cc_start: 0.6001 (ptt-90) cc_final: 0.5739 (ptt-90) REVERT: s 52 GLN cc_start: 0.7978 (mt0) cc_final: 0.7735 (mt0) REVERT: t 14 GLU cc_start: 0.7394 (pt0) cc_final: 0.7138 (pt0) REVERT: t 68 ARG cc_start: 0.7761 (ptm160) cc_final: 0.7524 (ttp-110) REVERT: t 71 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7558 (tm-30) REVERT: t 79 ARG cc_start: 0.8058 (ptt90) cc_final: 0.7809 (tmm160) REVERT: u 1 MET cc_start: 0.7747 (ptp) cc_final: 0.7391 (ptp) REVERT: u 12 LYS cc_start: 0.8859 (mtmt) cc_final: 0.8287 (mtpt) REVERT: u 22 THR cc_start: 0.8468 (p) cc_final: 0.8249 (p) REVERT: u 38 TYR cc_start: 0.8685 (p90) cc_final: 0.8373 (p90) REVERT: w 37 VAL cc_start: 0.8789 (t) cc_final: 0.8359 (p) REVERT: w 61 LYS cc_start: 0.8798 (ttmm) cc_final: 0.8405 (ttmt) REVERT: x 64 GLU cc_start: 0.8399 (tt0) cc_final: 0.8128 (tp30) REVERT: x 71 LEU cc_start: 0.9032 (mm) cc_final: 0.8781 (mm) REVERT: y 18 GLN cc_start: 0.8662 (mt0) cc_final: 0.8298 (mt0) REVERT: y 37 SER cc_start: 0.8806 (m) cc_final: 0.8583 (m) REVERT: z 15 ARG cc_start: 0.8790 (mmt90) cc_final: 0.8579 (mtt-85) REVERT: z 20 LYS cc_start: 0.8761 (tttt) cc_final: 0.8559 (ttmt) REVERT: z 22 ARG cc_start: 0.8068 (ttt-90) cc_final: 0.7041 (ttt-90) REVERT: W 15 ASP cc_start: 0.6943 (t0) cc_final: 0.6736 (t0) REVERT: X 26 ARG cc_start: 0.6846 (ptt180) cc_final: 0.6582 (ptt180) REVERT: X 39 LYS cc_start: 0.7303 (mmtt) cc_final: 0.7093 (mmtt) REVERT: X 71 TYR cc_start: 0.7546 (m-80) cc_final: 0.7316 (m-80) REVERT: Z 5 LYS cc_start: 0.8145 (tttt) cc_final: 0.7492 (tttm) REVERT: Z 24 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8378 (mtpp) REVERT: a 28 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7956 (ttpt) REVERT: b 37 LYS cc_start: 0.8865 (pttp) cc_final: 0.8496 (mmpt) REVERT: b 39 MET cc_start: 0.7232 (mmm) cc_final: 0.6695 (mtm) REVERT: c 45 LYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5674 (mmmm) REVERT: c 46 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.7148 (m90) REVERT: c 50 ARG cc_start: 0.7696 (mmt90) cc_final: 0.7356 (ptp-170) REVERT: d 22 MET cc_start: 0.8377 (mmm) cc_final: 0.7936 (mmt) REVERT: d 29 LYS cc_start: 0.8432 (mmmt) cc_final: 0.7876 (mmtt) REVERT: e 29 LYS cc_start: 0.7158 (tttt) cc_final: 0.6665 (ttpt) REVERT: A 85 GLU cc_start: 0.4168 (tt0) cc_final: 0.3758 (tt0) REVERT: B 7 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7854 (mmmt) REVERT: B 24 ILE cc_start: 0.8290 (mm) cc_final: 0.8085 (mm) REVERT: B 71 ASP cc_start: 0.7331 (t70) cc_final: 0.7052 (t0) REVERT: B 99 ASP cc_start: 0.8383 (t0) cc_final: 0.7660 (t0) REVERT: B 115 GLN cc_start: 0.7236 (tt0) cc_final: 0.6824 (tp40) REVERT: B 171 ASP cc_start: 0.8245 (t0) cc_final: 0.7939 (t0) REVERT: B 181 GLU cc_start: 0.7764 (tt0) cc_final: 0.7499 (tt0) REVERT: C 41 LYS cc_start: 0.7910 (mttt) cc_final: 0.7670 (mtpt) REVERT: C 94 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7531 (mm-30) REVERT: D 1 MET cc_start: 0.5166 (mtp) cc_final: 0.4563 (mtt) REVERT: D 205 ARG cc_start: 0.8170 (tmt170) cc_final: 0.7610 (tpt-90) REVERT: E 36 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8128 (ttmm) REVERT: E 71 THR cc_start: 0.7794 (p) cc_final: 0.7549 (p) REVERT: E 93 THR cc_start: 0.8847 (m) cc_final: 0.8245 (p) REVERT: E 136 ARG cc_start: 0.7983 (mpt180) cc_final: 0.7765 (mtt90) REVERT: E 164 GLU cc_start: 0.7622 (mm-30) cc_final: 0.6480 (pt0) REVERT: F 51 ARG cc_start: 0.6529 (mpp-170) cc_final: 0.4972 (mmp-170) REVERT: F 86 GLU cc_start: 0.7570 (mm-30) cc_final: 0.6587 (pm20) REVERT: G 12 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6959 (pp) REVERT: G 28 ASN cc_start: 0.7724 (m-40) cc_final: 0.7196 (m-40) REVERT: G 31 LEU cc_start: 0.8833 (tp) cc_final: 0.8345 (tp) REVERT: G 35 LEU cc_start: 0.7991 (mt) cc_final: 0.7781 (mp) REVERT: J 7 LYS cc_start: 0.8091 (mttm) cc_final: 0.7123 (tptt) REVERT: J 16 ILE cc_start: 0.8545 (mt) cc_final: 0.8303 (mt) REVERT: J 89 LYS cc_start: 0.8384 (tppp) cc_final: 0.8097 (ttmm) REVERT: J 104 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8039 (tptm) REVERT: K 13 ASN cc_start: 0.6428 (p0) cc_final: 0.5944 (p0) REVERT: K 48 PRO cc_start: 0.8333 (Cg_exo) cc_final: 0.8080 (Cg_endo) REVERT: K 104 ARG cc_start: 0.8119 (ptp-110) cc_final: 0.7506 (ptp-110) REVERT: L 7 ARG cc_start: 0.7414 (mmp-170) cc_final: 0.6791 (mmp-170) REVERT: L 27 HIS cc_start: 0.6673 (t-170) cc_final: 0.6379 (t70) REVERT: L 33 ARG cc_start: 0.6824 (mmm160) cc_final: 0.6469 (mmm160) REVERT: L 61 ARG cc_start: 0.6644 (ptt180) cc_final: 0.6387 (ptt180) REVERT: L 70 GLN cc_start: 0.8664 (mp-120) cc_final: 0.8276 (mp10) REVERT: L 115 LEU cc_start: 0.9115 (pp) cc_final: 0.8892 (pp) REVERT: L 126 VAL cc_start: 0.8595 (m) cc_final: 0.8251 (p) REVERT: M 29 PHE cc_start: 0.7811 (m-80) cc_final: 0.7499 (m-80) REVERT: M 101 ARG cc_start: 0.8312 (tpt170) cc_final: 0.7208 (tpm170) REVERT: M 105 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7208 (mt-10) REVERT: N 40 LYS cc_start: 0.9162 (mttt) cc_final: 0.8943 (mttp) REVERT: O 84 GLN cc_start: 0.7760 (tp40) cc_final: 0.6602 (tm-30) REVERT: O 94 TYR cc_start: 0.8424 (t80) cc_final: 0.7759 (t80) REVERT: P 7 ILE cc_start: 0.9312 (mm) cc_final: 0.9077 (mt) REVERT: P 33 LYS cc_start: 0.7573 (mptt) cc_final: 0.7159 (tptt) REVERT: P 44 ASP cc_start: 0.8266 (m-30) cc_final: 0.7591 (m-30) REVERT: P 99 LEU cc_start: 0.9528 (pp) cc_final: 0.9310 (pp) REVERT: Q 62 ILE cc_start: 0.9491 (mm) cc_final: 0.9280 (mm) REVERT: Q 71 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8222 (mm-40) REVERT: R 76 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7788 (ptmm) REVERT: R 98 GLU cc_start: 0.8007 (pp20) cc_final: 0.7537 (pp20) REVERT: S 65 LEU cc_start: 0.7793 (tp) cc_final: 0.7517 (tt) REVERT: S 72 LYS cc_start: 0.8934 (tptm) cc_final: 0.8663 (tppt) REVERT: S 110 LYS cc_start: 0.8241 (tptt) cc_final: 0.7727 (mttt) REVERT: T 29 TRP cc_start: 0.8313 (m100) cc_final: 0.7733 (m100) REVERT: U 38 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.6668 (mm) REVERT: U 46 LYS cc_start: 0.7380 (mttt) cc_final: 0.6897 (ttmt) REVERT: U 101 LYS cc_start: 0.6636 (ttmt) cc_final: 0.6004 (tmtt) REVERT: V 6 LYS cc_start: 0.8489 (tptt) cc_final: 0.8232 (tptt) REVERT: V 40 ASP cc_start: 0.7643 (m-30) cc_final: 0.7359 (m-30) REVERT: V 56 VAL cc_start: 0.9318 (t) cc_final: 0.8847 (p) REVERT: V 63 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6479 (p0) REVERT: 5 1 MET cc_start: 0.4443 (ptm) cc_final: 0.4157 (ttp) REVERT: 5 47 ARG cc_start: 0.6888 (tpp-160) cc_final: 0.6364 (tmm-80) REVERT: 5 96 LYS cc_start: 0.8089 (mttt) cc_final: 0.7881 (mttp) REVERT: 5 108 ASN cc_start: 0.7541 (p0) cc_final: 0.6968 (p0) REVERT: 5 109 GLU cc_start: 0.6691 (pm20) cc_final: 0.6429 (mp0) REVERT: 5 128 LYS cc_start: 0.7246 (pttm) cc_final: 0.6997 (pttp) REVERT: f 1 MET cc_start: 0.7404 (mtp) cc_final: 0.7126 (mtp) REVERT: f 4 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7490 (mtt180) REVERT: f 36 GLN cc_start: 0.8564 (tt0) cc_final: 0.8362 (tt0) outliers start: 54 outliers final: 27 residues processed: 1935 average time/residue: 1.5524 time to fit residues: 5008.0038 Evaluate side-chains 1535 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1502 time to evaluate : 6.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain l residue 120 ILE Chi-restraints excluded: chain n residue 53 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain v residue 35 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain c residue 45 LYS Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain T residue 26 TYR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain 5 residue 72 ASP Chi-restraints excluded: chain f residue 16 VAL 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: 0.7980 chunk 280 optimal weight: 4.9990 chunk 554 optimal weight: 20.0000 chunk 438 optimal weight: 1.9990 chunk 849 optimal weight: 6.9990 chunk 328 optimal weight: 5.9990 chunk 516 optimal weight: 6.9990 chunk 632 optimal weight: 2.9990 chunk 984 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: g 135 GLN h 37 GLN h 110 ASN h 118 GLN i 45 GLN ** i 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 161 ASN j 20 GLN j 78 HIS k 27 GLN ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 GLN l 109 ASN l 148 ASN n 124 GLN ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 22 HIS p 116 HIS p 117 ASN q 75 HIS q 99 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 L 9 ASN M 12 GLN ** M 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 GLN M 123 HIS N 61 HIS ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.622 167513 Z= 0.244 Angle : 0.852 102.880 250789 Z= 0.394 Chirality : 0.038 0.313 31882 Planarity : 0.006 0.192 13445 Dihedral : 26.186 179.113 85276 Min Nonbonded Distance : 1.054 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.54 % Allowed : 13.17 % Favored : 86.30 % Rotamer: Outliers : 3.95 % Allowed : 20.40 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 2.11 % Twisted General : 0.65 % 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: -2.11 (0.11), residues: 1650 sheet: -3.09 (0.14), residues: 941 loop : -3.39 (0.10), residues: 3188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 42 HIS 0.013 0.001 HIS J 101 PHE 0.028 0.002 PHE i 110 TYR 0.025 0.002 TYR n 4 ARG 0.012 0.001 ARG o 60 *********************** 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 1879 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1690 time to evaluate : 8.448 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: g 28 PHE cc_start: 0.8581 (t80) cc_final: 0.8301 (t80) REVERT: g 76 GLN cc_start: 0.7053 (mp10) cc_final: 0.6690 (mt0) REVERT: g 92 TYR cc_start: 0.8767 (p90) cc_final: 0.8099 (p90) REVERT: g 169 LYS cc_start: 0.7912 (tppt) cc_final: 0.7445 (mmtm) REVERT: h 27 LYS cc_start: 0.8340 (tptp) cc_final: 0.8110 (tptt) REVERT: h 45 LYS cc_start: 0.7209 (ptpt) cc_final: 0.6720 (ptpt) REVERT: h 122 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6855 (mt-10) REVERT: h 136 GLN cc_start: 0.7612 (tm-30) cc_final: 0.6861 (tp-100) REVERT: h 181 ASN cc_start: 0.8473 (t0) cc_final: 0.8248 (t0) REVERT: i 77 ASN cc_start: 0.8333 (m-40) cc_final: 0.7654 (m110) REVERT: i 101 LEU cc_start: 0.8795 (tp) cc_final: 0.8468 (tp) REVERT: i 134 ASP cc_start: 0.7289 (p0) cc_final: 0.6808 (p0) REVERT: i 161 ASN cc_start: 0.8261 (m-40) cc_final: 0.8027 (m110) REVERT: i 181 MET cc_start: 0.7247 (mtm) cc_final: 0.7003 (mtm) REVERT: j 76 ILE cc_start: 0.9242 (mt) cc_final: 0.9024 (mt) REVERT: j 112 LEU cc_start: 0.8584 (mt) cc_final: 0.8350 (mt) REVERT: j 118 ILE cc_start: 0.9174 (tp) cc_final: 0.8715 (tp) REVERT: k 5 GLU cc_start: 0.7923 (mp0) cc_final: 0.7655 (tp30) REVERT: k 7 ASN cc_start: 0.7694 (m-40) cc_final: 0.7410 (m110) REVERT: k 33 TYR cc_start: 0.8388 (m-80) cc_final: 0.7760 (m-10) REVERT: k 86 ARG cc_start: 0.7072 (mtt90) cc_final: 0.6702 (mtt90) REVERT: l 86 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7055 (mt0) REVERT: l 144 MET cc_start: 0.7731 (tpp) cc_final: 0.7353 (tpp) REVERT: m 6 ILE cc_start: 0.8940 (mm) cc_final: 0.8677 (mm) REVERT: m 48 TYR cc_start: 0.8638 (p90) cc_final: 0.7453 (p90) REVERT: m 105 ARG cc_start: 0.7132 (mmt-90) cc_final: 0.6705 (mmt-90) REVERT: m 126 LYS cc_start: 0.8967 (ttmm) cc_final: 0.8557 (mttp) REVERT: n 121 ARG cc_start: 0.7585 (tpt-90) cc_final: 0.7208 (tpt90) REVERT: o 29 ARG cc_start: 0.6028 (mtp-110) cc_final: 0.5504 (mtt-85) REVERT: o 38 ILE cc_start: 0.8232 (mp) cc_final: 0.7924 (mt) REVERT: o 64 GLU cc_start: 0.7952 (pt0) cc_final: 0.7647 (pt0) REVERT: o 66 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8244 (mtp85) REVERT: p 116 HIS cc_start: 0.7904 (m170) cc_final: 0.7337 (m-70) REVERT: q 9 GLN cc_start: 0.8221 (mt0) cc_final: 0.7855 (mt0) REVERT: q 21 LYS cc_start: 0.8436 (pttt) cc_final: 0.8197 (pttt) REVERT: q 47 LYS cc_start: 0.8400 (tppt) cc_final: 0.8068 (tppt) REVERT: r 27 LYS cc_start: 0.9007 (ptpt) cc_final: 0.8761 (ptpt) REVERT: r 90 LEU cc_start: 0.7961 (mp) cc_final: 0.7592 (mp) REVERT: s 3 ARG cc_start: 0.5799 (ptt-90) cc_final: 0.5555 (ptt-90) REVERT: s 31 ARG cc_start: 0.8298 (mmt180) cc_final: 0.8025 (mtp85) REVERT: t 46 HIS cc_start: 0.8286 (m90) cc_final: 0.7966 (m90) REVERT: t 68 ARG cc_start: 0.7662 (ptm160) cc_final: 0.7421 (ttp-110) REVERT: t 85 LEU cc_start: 0.8353 (mt) cc_final: 0.8101 (mp) REVERT: u 12 LYS cc_start: 0.8641 (mtmt) cc_final: 0.8028 (mtpt) REVERT: u 39 TYR cc_start: 0.8803 (t80) cc_final: 0.8525 (t80) REVERT: v 25 ARG cc_start: 0.8414 (ptt90) cc_final: 0.8152 (ptm-80) REVERT: v 93 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6814 (mp10) REVERT: v 94 ASN cc_start: 0.8024 (OUTLIER) cc_final: 0.7776 (t0) REVERT: w 34 TYR cc_start: 0.7850 (p90) cc_final: 0.7617 (p90) REVERT: x 66 MET cc_start: 0.6994 (ptp) cc_final: 0.6651 (pmm) REVERT: x 71 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8670 (mm) REVERT: z 22 ARG cc_start: 0.8034 (ttt-90) cc_final: 0.7372 (ttt-90) REVERT: W 26 TYR cc_start: 0.8691 (m-80) cc_final: 0.8275 (m-80) REVERT: Y 26 ARG cc_start: 0.7085 (mmt-90) cc_final: 0.6487 (mmt-90) REVERT: Z 5 LYS cc_start: 0.7972 (tttt) cc_final: 0.7373 (tttm) REVERT: Z 24 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8399 (mtpp) REVERT: Z 43 ILE cc_start: 0.9329 (mm) cc_final: 0.9002 (mm) REVERT: a 28 LYS cc_start: 0.8268 (ttpt) cc_final: 0.8050 (ttpt) REVERT: c 25 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8114 (ttpt) REVERT: c 39 TYR cc_start: 0.6784 (t80) cc_final: 0.5961 (t80) REVERT: c 46 HIS cc_start: 0.6630 (OUTLIER) cc_final: 0.6087 (m90) REVERT: c 51 GLU cc_start: 0.7834 (pm20) cc_final: 0.7252 (pm20) REVERT: e 21 LYS cc_start: 0.8053 (mttp) cc_final: 0.7842 (mttt) REVERT: e 29 LYS cc_start: 0.5886 (tttt) cc_final: 0.5674 (tmmt) REVERT: A 85 GLU cc_start: 0.4388 (tt0) cc_final: 0.3611 (tt0) REVERT: B 7 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7851 (mmmt) REVERT: B 43 ARG cc_start: 0.6953 (pmt-80) cc_final: 0.4555 (pmt-80) REVERT: B 95 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8678 (pp) REVERT: B 148 GLU cc_start: 0.7969 (tt0) cc_final: 0.7732 (tt0) REVERT: B 171 ASP cc_start: 0.8125 (t0) cc_final: 0.7920 (t0) REVERT: B 252 TRP cc_start: 0.9043 (p-90) cc_final: 0.8650 (p-90) REVERT: C 40 GLU cc_start: 0.7084 (mp0) cc_final: 0.6719 (mp0) REVERT: D 1 MET cc_start: 0.5153 (mtp) cc_final: 0.4947 (mtp) REVERT: D 29 ASN cc_start: 0.8923 (t0) cc_final: 0.8533 (t0) REVERT: D 97 TYR cc_start: 0.8205 (m-80) cc_final: 0.7866 (m-10) REVERT: D 161 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6942 (tm-30) REVERT: D 205 ARG cc_start: 0.8134 (tmt170) cc_final: 0.7433 (tpp80) REVERT: E 36 LYS cc_start: 0.8368 (ttmt) cc_final: 0.8042 (ttmm) REVERT: E 71 THR cc_start: 0.7448 (p) cc_final: 0.7154 (p) REVERT: E 136 ARG cc_start: 0.7840 (mpt180) cc_final: 0.7585 (mtt90) REVERT: E 164 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6447 (pt0) REVERT: F 51 ARG cc_start: 0.6633 (mpp-170) cc_final: 0.5056 (mmp-170) REVERT: F 86 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6560 (pm20) REVERT: F 140 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7880 (mttt) REVERT: G 12 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6274 (pp) REVERT: G 22 LYS cc_start: 0.8839 (ttmm) cc_final: 0.8262 (ttpt) REVERT: G 23 PRO cc_start: 0.9178 (Cg_exo) cc_final: 0.8961 (Cg_endo) REVERT: J 17 ASP cc_start: 0.7865 (t70) cc_final: 0.7558 (t0) REVERT: J 97 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.7906 (tpp80) REVERT: J 104 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8191 (tptm) REVERT: K 12 ASP cc_start: 0.8437 (p0) cc_final: 0.8213 (p0) REVERT: K 13 ASN cc_start: 0.6135 (p0) cc_final: 0.5756 (p0) REVERT: K 45 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7952 (mm-30) REVERT: K 73 ASP cc_start: 0.6852 (p0) cc_final: 0.6613 (p0) REVERT: L 7 ARG cc_start: 0.7499 (mmp-170) cc_final: 0.7278 (mmp-170) REVERT: L 27 HIS cc_start: 0.6115 (t-170) cc_final: 0.5906 (t70) REVERT: L 61 ARG cc_start: 0.6679 (ptt180) cc_final: 0.6096 (ptt180) REVERT: L 98 GLU cc_start: 0.6426 (mm-30) cc_final: 0.5710 (mm-30) REVERT: L 102 ARG cc_start: 0.8567 (mtp85) cc_final: 0.8259 (mtp-110) REVERT: L 115 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8936 (pp) REVERT: L 126 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8528 (p) REVERT: M 32 TYR cc_start: 0.7382 (m-80) cc_final: 0.7152 (m-80) REVERT: M 56 ARG cc_start: 0.7101 (tpt90) cc_final: 0.6545 (mmm160) REVERT: M 105 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6885 (mt-10) REVERT: N 107 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8051 (p0) REVERT: O 67 ARG cc_start: 0.7904 (mtt180) cc_final: 0.7627 (mtm-85) REVERT: O 84 GLN cc_start: 0.7589 (tp40) cc_final: 0.6539 (tm-30) REVERT: O 93 LYS cc_start: 0.8376 (tptp) cc_final: 0.7715 (tppp) REVERT: O 94 TYR cc_start: 0.8189 (t80) cc_final: 0.7499 (t80) REVERT: P 99 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9254 (pp) REVERT: Q 17 ILE cc_start: 0.9444 (mm) cc_final: 0.9126 (mt) REVERT: Q 71 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8311 (mm-40) REVERT: R 10 LYS cc_start: 0.8498 (mtmt) cc_final: 0.8150 (mtpt) REVERT: R 74 LYS cc_start: 0.8078 (pttm) cc_final: 0.7737 (pttm) REVERT: R 76 LYS cc_start: 0.8054 (ttpt) cc_final: 0.7583 (ptmm) REVERT: S 65 LEU cc_start: 0.8179 (tp) cc_final: 0.7839 (tt) REVERT: S 72 LYS cc_start: 0.8954 (tptm) cc_final: 0.8648 (tppt) REVERT: S 110 LYS cc_start: 0.8008 (tptt) cc_final: 0.7621 (mttt) REVERT: T 9 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.7939 (mp) REVERT: T 12 VAL cc_start: 0.7118 (OUTLIER) cc_final: 0.6916 (p) REVERT: T 29 TRP cc_start: 0.8178 (m100) cc_final: 0.7790 (m100) REVERT: U 38 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6592 (mm) REVERT: U 46 LYS cc_start: 0.7177 (mttt) cc_final: 0.6697 (ttmt) REVERT: U 101 LYS cc_start: 0.6548 (ttmt) cc_final: 0.6128 (tmtt) REVERT: V 56 VAL cc_start: 0.9153 (t) cc_final: 0.8793 (p) REVERT: V 63 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6700 (p0) REVERT: 5 1 MET cc_start: 0.4219 (ptm) cc_final: 0.3817 (ttp) REVERT: 5 47 ARG cc_start: 0.6737 (tpp-160) cc_final: 0.6185 (tmm-80) REVERT: 5 108 ASN cc_start: 0.7291 (p0) cc_final: 0.6836 (p0) REVERT: 5 109 GLU cc_start: 0.6644 (pm20) cc_final: 0.6321 (mp0) REVERT: f 1 MET cc_start: 0.7198 (mtp) cc_final: 0.6994 (mtp) REVERT: f 4 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7266 (mtt180) outliers start: 189 outliers final: 104 residues processed: 1776 average time/residue: 1.5096 time to fit residues: 4569.9989 Evaluate side-chains 1604 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1486 time to evaluate : 6.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain i residue 127 THR Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain i residue 158 ILE Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 120 THR Chi-restraints excluded: chain j residue 147 ASP Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain l residue 84 ASN Chi-restraints excluded: chain l residue 86 GLN Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain n residue 31 GLN Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 53 VAL Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 23 ILE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 87 THR Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 37 CYS Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 93 LEU Chi-restraints excluded: chain q residue 122 THR Chi-restraints excluded: chain r residue 17 VAL Chi-restraints excluded: chain r residue 86 CYS Chi-restraints excluded: chain r residue 103 THR Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain v residue 5 VAL Chi-restraints excluded: chain v residue 35 VAL Chi-restraints excluded: chain v residue 90 ILE Chi-restraints excluded: chain v residue 94 ASN Chi-restraints excluded: chain x residue 31 ILE Chi-restraints excluded: chain x residue 41 VAL Chi-restraints excluded: chain x residue 71 LEU Chi-restraints excluded: chain y residue 33 ILE Chi-restraints excluded: chain Y residue 47 ASN Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain c residue 46 HIS Chi-restraints excluded: chain c residue 47 THR Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 88 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 26 TYR Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 72 VAL Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain 5 residue 40 ASP Chi-restraints excluded: chain 5 residue 72 ASP Chi-restraints excluded: chain 5 residue 144 LEU Chi-restraints excluded: chain f residue 16 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 547 optimal weight: 9.9990 chunk 305 optimal weight: 9.9990 chunk 819 optimal weight: 0.9980 chunk 670 optimal weight: 8.9990 chunk 271 optimal weight: 10.0000 chunk 986 optimal weight: 0.8980 chunk 1065 optimal weight: 30.0000 chunk 878 optimal weight: 0.9980 chunk 977 optimal weight: 6.9990 chunk 336 optimal weight: 7.9990 chunk 791 optimal weight: 6.9990 overall best weight: 3.3784 ------------------------------------------------------------------------------- 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 170 GLN i 119 GLN ** i 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 ASN ** l 148 ASN ** 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 18 GLN y 42 GLN ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 HIS ** c 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN ** O 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN V 50 GLN ** 5 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.571 167513 Z= 0.350 Angle : 0.895 103.365 250789 Z= 0.414 Chirality : 0.040 0.361 31882 Planarity : 0.007 0.205 13445 Dihedral : 26.145 179.946 85266 Min Nonbonded Distance : 1.023 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.55 % Allowed : 15.35 % Favored : 84.10 % Rotamer: Outliers : 5.95 % Allowed : 23.32 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % Cis-general : 0.00 % Twisted Proline : 2.46 % 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: -3.92 (0.10), residues: 5779 helix: -1.51 (0.12), residues: 1655 sheet: -2.90 (0.15), residues: 894 loop : -3.24 (0.10), residues: 3230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP d 5 HIS 0.010 0.002 HIS o 56 PHE 0.024 0.002 PHE M 58 TYR 0.043 0.002 TYR a 25 ARG 0.011 0.001 ARG B 183 *********************** 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 1826 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1541 time to evaluate : 6.540 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: g 28 PHE cc_start: 0.8606 (t80) cc_final: 0.8322 (t80) REVERT: g 76 GLN cc_start: 0.7173 (mp10) cc_final: 0.6654 (mt0) REVERT: g 169 LYS cc_start: 0.7874 (tppt) cc_final: 0.7399 (mmtm) REVERT: h 18 TRP cc_start: 0.8839 (m-90) cc_final: 0.8607 (m-90) REVERT: h 123 GLN cc_start: 0.8313 (mm110) cc_final: 0.8108 (mm110) REVERT: h 136 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7580 (tp40) REVERT: i 77 ASN cc_start: 0.8420 (m-40) cc_final: 0.7923 (m-40) REVERT: i 101 LEU cc_start: 0.8927 (tp) cc_final: 0.8581 (tp) REVERT: i 134 ASP cc_start: 0.7404 (p0) cc_final: 0.6834 (p0) REVERT: i 138 TYR cc_start: 0.9027 (t80) cc_final: 0.8563 (t80) REVERT: i 160 GLN cc_start: 0.8333 (tm-30) cc_final: 0.8052 (tm-30) REVERT: j 76 ILE cc_start: 0.9283 (mt) cc_final: 0.9033 (mt) REVERT: j 118 ILE cc_start: 0.9155 (tp) cc_final: 0.8763 (tp) REVERT: k 5 GLU cc_start: 0.8061 (mp0) cc_final: 0.7656 (mp0) REVERT: k 33 TYR cc_start: 0.8099 (m-80) cc_final: 0.7819 (m-10) REVERT: k 54 LYS cc_start: 0.7833 (mtmm) cc_final: 0.7547 (mtpt) REVERT: k 86 ARG cc_start: 0.6802 (mtt90) cc_final: 0.6462 (mtt90) REVERT: l 144 MET cc_start: 0.7789 (tpp) cc_final: 0.7278 (tpp) REVERT: m 6 ILE cc_start: 0.8952 (mm) cc_final: 0.8674 (mm) REVERT: m 48 TYR cc_start: 0.8755 (p90) cc_final: 0.7587 (p90) REVERT: m 123 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7343 (mt-10) REVERT: n 38 GLN cc_start: 0.8110 (tt0) cc_final: 0.7630 (tt0) REVERT: n 42 ARG cc_start: 0.7136 (ttt-90) cc_final: 0.6834 (ttt-90) REVERT: n 121 ARG cc_start: 0.7699 (tpt-90) cc_final: 0.7306 (tpt90) REVERT: o 29 ARG cc_start: 0.5857 (mtp-110) cc_final: 0.5346 (mtt-85) REVERT: o 57 LYS cc_start: 0.8181 (tptm) cc_final: 0.7817 (tppt) REVERT: o 60 ARG cc_start: 0.7783 (ptp-170) cc_final: 0.7191 (ptp-170) REVERT: p 116 HIS cc_start: 0.7953 (m170) cc_final: 0.7472 (m-70) REVERT: q 9 GLN cc_start: 0.8360 (mt0) cc_final: 0.7977 (mt0) REVERT: q 21 LYS cc_start: 0.8414 (pttt) cc_final: 0.8212 (pttt) REVERT: r 27 LYS cc_start: 0.9049 (ptpt) cc_final: 0.8844 (ptpt) REVERT: s 40 CYS cc_start: 0.8221 (p) cc_final: 0.7511 (p) REVERT: t 68 ARG cc_start: 0.7675 (ptm160) cc_final: 0.7435 (ttp-110) REVERT: u 12 LYS cc_start: 0.8727 (mtmt) cc_final: 0.8132 (mtpt) REVERT: u 17 TYR cc_start: 0.8876 (m-80) cc_final: 0.8664 (m-80) REVERT: u 41 PRO cc_start: 0.9327 (Cg_exo) cc_final: 0.9111 (Cg_endo) REVERT: w 23 LYS cc_start: 0.7140 (tptm) cc_final: 0.6741 (tttt) REVERT: w 71 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8555 (mtmt) REVERT: x 66 MET cc_start: 0.7085 (ptp) cc_final: 0.6664 (pmm) REVERT: x 71 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8734 (mm) REVERT: y 45 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8282 (tm-30) REVERT: z 21 TYR cc_start: 0.7753 (m-80) cc_final: 0.7373 (m-10) REVERT: z 22 ARG cc_start: 0.8240 (ttt-90) cc_final: 0.7430 (ttt-90) REVERT: W 26 TYR cc_start: 0.8661 (m-80) cc_final: 0.8451 (m-80) REVERT: X 57 GLU cc_start: 0.7304 (tp30) cc_final: 0.7076 (pp20) REVERT: Y 26 ARG cc_start: 0.7232 (mmt-90) cc_final: 0.7014 (mmt-90) REVERT: Z 5 LYS cc_start: 0.7912 (tttt) cc_final: 0.7378 (tttm) REVERT: Z 38 GLU cc_start: 0.7478 (mp0) cc_final: 0.7244 (mp0) REVERT: Z 43 ILE cc_start: 0.9331 (mm) cc_final: 0.9001 (mm) REVERT: a 28 LYS cc_start: 0.8249 (ttpt) cc_final: 0.8035 (ttpt) REVERT: c 36 LEU cc_start: 0.7198 (pt) cc_final: 0.6521 (mt) REVERT: c 39 TYR cc_start: 0.6892 (t80) cc_final: 0.6173 (t80) REVERT: c 51 GLU cc_start: 0.7973 (pm20) cc_final: 0.7123 (pm20) REVERT: e 4 MET cc_start: 0.7812 (ttt) cc_final: 0.7477 (ttt) REVERT: e 29 LYS cc_start: 0.6332 (tttt) cc_final: 0.6127 (ttpt) REVERT: A 79 LYS cc_start: 0.3063 (mttt) cc_final: 0.1606 (mptt) REVERT: A 85 GLU cc_start: 0.4122 (tt0) cc_final: 0.3887 (tt0) REVERT: B 7 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8206 (mmtt) REVERT: B 43 ARG cc_start: 0.7004 (pmt-80) cc_final: 0.5251 (pmt-80) REVERT: B 112 GLN cc_start: 0.7042 (mp10) cc_final: 0.6407 (mp10) REVERT: B 171 ASP cc_start: 0.8119 (t0) cc_final: 0.7902 (t0) REVERT: D 7 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.5214 (t80) REVERT: D 161 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7204 (tm-30) REVERT: D 205 ARG cc_start: 0.8188 (tmt170) cc_final: 0.7769 (ttm170) REVERT: E 36 LYS cc_start: 0.8481 (ttmt) cc_final: 0.8093 (ttmm) REVERT: E 55 LYS cc_start: 0.8586 (tmmt) cc_final: 0.8385 (tmmt) REVERT: E 71 THR cc_start: 0.7476 (p) cc_final: 0.7171 (p) REVERT: E 114 ILE cc_start: 0.7545 (mm) cc_final: 0.7331 (mm) REVERT: E 116 ASP cc_start: 0.7213 (p0) cc_final: 0.6942 (p0) REVERT: E 164 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6493 (pt0) REVERT: F 86 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6614 (pm20) REVERT: F 140 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7933 (mttt) REVERT: G 22 LYS cc_start: 0.8369 (ttmm) cc_final: 0.7948 (ttpt) REVERT: G 23 PRO cc_start: 0.9238 (Cg_exo) cc_final: 0.9008 (Cg_endo) REVERT: J 17 ASP cc_start: 0.7998 (t70) cc_final: 0.7752 (t0) REVERT: J 97 ARG cc_start: 0.8250 (tpp-160) cc_final: 0.7965 (tpp80) REVERT: J 104 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8206 (tptm) REVERT: K 13 ASN cc_start: 0.6328 (p0) cc_final: 0.5956 (p0) REVERT: L 7 ARG cc_start: 0.7588 (mmp-170) cc_final: 0.7167 (mmp-170) REVERT: L 115 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8877 (pp) REVERT: M 101 ARG cc_start: 0.8325 (tpt170) cc_final: 0.7066 (tpm170) REVERT: M 115 MET cc_start: 0.8071 (mmp) cc_final: 0.7743 (mmp) REVERT: N 4 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6759 (tm) REVERT: N 107 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8291 (p0) REVERT: O 67 ARG cc_start: 0.7841 (mtt180) cc_final: 0.7581 (mtm-85) REVERT: O 84 GLN cc_start: 0.7657 (tp40) cc_final: 0.6632 (tm-30) REVERT: O 94 TYR cc_start: 0.8303 (t80) cc_final: 0.7625 (t80) REVERT: P 99 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9303 (pp) REVERT: Q 17 ILE cc_start: 0.9520 (mm) cc_final: 0.9226 (mt) REVERT: Q 59 ARG cc_start: 0.7823 (ttm170) cc_final: 0.6948 (ttm170) REVERT: Q 71 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8276 (mm-40) REVERT: R 23 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7422 (mt-10) REVERT: R 74 LYS cc_start: 0.8185 (pttm) cc_final: 0.7862 (pttm) REVERT: R 76 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7851 (ptmm) REVERT: R 98 GLU cc_start: 0.7961 (pp20) cc_final: 0.7441 (pp20) REVERT: S 65 LEU cc_start: 0.8173 (tp) cc_final: 0.7894 (tt) REVERT: T 29 TRP cc_start: 0.8184 (m100) cc_final: 0.7665 (m100) REVERT: T 73 ARG cc_start: 0.8280 (mmm160) cc_final: 0.6885 (mmm160) REVERT: U 38 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.6656 (mm) REVERT: U 46 LYS cc_start: 0.7294 (mttt) cc_final: 0.6631 (ttmt) REVERT: U 101 LYS cc_start: 0.6570 (ttmt) cc_final: 0.6278 (tmtt) REVERT: V 56 VAL cc_start: 0.9199 (t) cc_final: 0.8862 (p) REVERT: V 61 LEU cc_start: 0.7742 (mm) cc_final: 0.7413 (mt) REVERT: 5 47 ARG cc_start: 0.6838 (tpp-160) cc_final: 0.5911 (tmm-80) REVERT: 5 108 ASN cc_start: 0.7696 (p0) cc_final: 0.7049 (p0) REVERT: 5 109 GLU cc_start: 0.6758 (pm20) cc_final: 0.6262 (mp0) REVERT: f 1 MET cc_start: 0.7119 (mtp) cc_final: 0.6917 (mtp) REVERT: f 4 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7106 (mtt180) outliers start: 285 outliers final: 210 residues processed: 1676 average time/residue: 1.3904 time to fit residues: 3959.5912 Evaluate side-chains 1670 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1452 time to evaluate : 6.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 185 ILE Chi-restraints excluded: chain g residue 187 LEU Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 222 ILE Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 62 ASP Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain i residue 127 THR Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain i residue 158 ILE Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 36 ASP Chi-restraints excluded: chain j residue 67 VAL Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain j residue 120 THR Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain j residue 147 ASP Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain l residue 84 ASN Chi-restraints excluded: chain l residue 141 VAL Chi-restraints excluded: chain m residue 35 ILE Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 100 ILE Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 123 GLU Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 53 VAL Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 24 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 87 THR Chi-restraints excluded: chain p residue 114 VAL Chi-restraints excluded: chain q residue 7 ILE Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 37 CYS Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 93 LEU Chi-restraints excluded: chain q residue 122 THR Chi-restraints excluded: chain r residue 12 ASN Chi-restraints excluded: chain r residue 86 CYS Chi-restraints excluded: chain r residue 103 THR Chi-restraints excluded: chain s residue 60 SER Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain u residue 45 THR Chi-restraints excluded: chain u residue 67 THR Chi-restraints excluded: chain u residue 69 THR Chi-restraints excluded: chain v residue 5 VAL Chi-restraints excluded: chain v residue 35 VAL Chi-restraints excluded: chain v residue 46 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 90 ILE Chi-restraints excluded: chain w residue 39 VAL Chi-restraints excluded: chain w residue 68 LYS Chi-restraints excluded: chain x residue 41 VAL Chi-restraints excluded: chain x residue 71 LEU Chi-restraints excluded: chain y residue 86 ARG Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 47 ASN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 42 PHE Chi-restraints excluded: chain b residue 13 LYS Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 47 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 78 TYR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 26 TYR Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain V residue 23 LYS Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain 5 residue 8 ARG Chi-restraints excluded: chain 5 residue 40 ASP Chi-restraints excluded: chain 5 residue 72 ASP Chi-restraints excluded: chain 5 residue 101 VAL Chi-restraints excluded: chain 5 residue 119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 974 optimal weight: 0.1980 chunk 741 optimal weight: 0.0010 chunk 511 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 470 optimal weight: 20.0000 chunk 662 optimal weight: 6.9990 chunk 989 optimal weight: 0.0370 chunk 1047 optimal weight: 30.0000 chunk 517 optimal weight: 6.9990 chunk 937 optimal weight: 7.9990 chunk 282 optimal weight: 5.9990 overall best weight: 2.6468 ------------------------------------------------------------------------------- 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 i 45 GLN i 119 GLN i 123 HIS ** i 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 73 ASN ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 GLN ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 124 GLN o 13 HIS ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 77 ASN u 76 GLN v 94 ASN w 63 GLN y 18 GLN y 42 GLN ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 HIS ** d 6 GLN ** 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 ** 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** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 87 GLN ** 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.576 167513 Z= 0.297 Angle : 0.852 103.302 250789 Z= 0.392 Chirality : 0.038 0.350 31882 Planarity : 0.006 0.204 13445 Dihedral : 26.075 179.706 85260 Min Nonbonded Distance : 1.037 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.54 % Allowed : 14.78 % Favored : 84.69 % Rotamer: Outliers : 6.83 % Allowed : 24.56 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 1.76 % 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: -3.66 (0.10), residues: 5779 helix: -1.18 (0.12), residues: 1655 sheet: -2.72 (0.16), residues: 923 loop : -3.14 (0.10), residues: 3201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP m 138 HIS 0.010 0.001 HIS L 27 PHE 0.034 0.002 PHE i 93 TYR 0.020 0.002 TYR u 32 ARG 0.011 0.001 ARG V 35 *********************** 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 1852 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 1525 time to evaluate : 6.583 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: g 28 PHE cc_start: 0.8614 (t80) cc_final: 0.8324 (t80) REVERT: g 76 GLN cc_start: 0.7128 (mp10) cc_final: 0.6620 (mt0) REVERT: g 169 LYS cc_start: 0.7878 (tppt) cc_final: 0.7416 (mmtm) REVERT: g 212 GLN cc_start: 0.7673 (tp40) cc_final: 0.7344 (tp-100) REVERT: h 54 ARG cc_start: 0.7383 (ptp90) cc_final: 0.6924 (ptp90) REVERT: h 122 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6805 (mt-10) REVERT: h 136 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7266 (tp40) REVERT: i 42 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8021 (tm-30) REVERT: i 62 GLN cc_start: 0.8067 (mm110) cc_final: 0.6585 (mm110) REVERT: i 77 ASN cc_start: 0.8293 (m-40) cc_final: 0.7735 (m110) REVERT: i 101 LEU cc_start: 0.8907 (tp) cc_final: 0.8564 (tp) REVERT: i 134 ASP cc_start: 0.7595 (p0) cc_final: 0.7195 (p0) REVERT: i 160 GLN cc_start: 0.8334 (tm-30) cc_final: 0.8094 (tm-30) REVERT: i 161 ASN cc_start: 0.8305 (m-40) cc_final: 0.8009 (m110) REVERT: k 5 GLU cc_start: 0.8077 (mp0) cc_final: 0.7784 (mp0) REVERT: k 86 ARG cc_start: 0.6648 (mtt90) cc_final: 0.6316 (mtt90) REVERT: k 92 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8464 (mtpp) REVERT: l 12 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7852 (mm) REVERT: l 30 ILE cc_start: 0.8694 (tp) cc_final: 0.8490 (tp) REVERT: l 86 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.6884 (mt0) REVERT: l 120 ILE cc_start: 0.8720 (mp) cc_final: 0.8517 (mp) REVERT: m 6 ILE cc_start: 0.9061 (mm) cc_final: 0.8784 (mm) REVERT: m 48 TYR cc_start: 0.8793 (p90) cc_final: 0.7625 (p90) REVERT: m 123 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: m 126 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8614 (mttp) REVERT: n 38 GLN cc_start: 0.8111 (tt0) cc_final: 0.7696 (tt0) REVERT: n 121 ARG cc_start: 0.7670 (tpt-90) cc_final: 0.7299 (tpt90) REVERT: o 29 ARG cc_start: 0.5753 (mtp-110) cc_final: 0.5351 (mtt-85) REVERT: o 60 ARG cc_start: 0.7728 (ptp-170) cc_final: 0.7384 (ptp-170) REVERT: p 20 TYR cc_start: 0.8188 (m-80) cc_final: 0.7982 (m-80) REVERT: p 59 TYR cc_start: 0.8595 (t80) cc_final: 0.8249 (t80) REVERT: p 116 HIS cc_start: 0.7774 (m170) cc_final: 0.7324 (m-70) REVERT: q 9 GLN cc_start: 0.8330 (mt0) cc_final: 0.7957 (mt0) REVERT: q 21 LYS cc_start: 0.8375 (pttt) cc_final: 0.8158 (pttt) REVERT: q 47 LYS cc_start: 0.8462 (tppt) cc_final: 0.8235 (tppt) REVERT: r 27 LYS cc_start: 0.9055 (ptpt) cc_final: 0.8844 (ptpt) REVERT: r 82 MET cc_start: 0.4805 (ttt) cc_final: 0.4392 (ttt) REVERT: r 106 ASN cc_start: 0.7777 (m110) cc_final: 0.7517 (m110) REVERT: s 36 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7598 (t80) REVERT: s 37 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: s 40 CYS cc_start: 0.8135 (p) cc_final: 0.7437 (p) REVERT: s 46 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: t 21 ASP cc_start: 0.7177 (t0) cc_final: 0.6818 (t70) REVERT: u 12 LYS cc_start: 0.8693 (mtmt) cc_final: 0.8058 (mtpt) REVERT: u 17 TYR cc_start: 0.8826 (m-80) cc_final: 0.8622 (m-80) REVERT: w 23 LYS cc_start: 0.7140 (tptm) cc_final: 0.6688 (tttt) REVERT: w 71 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8779 (mtmt) REVERT: x 71 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8746 (mm) REVERT: x 80 TYR cc_start: 0.4124 (OUTLIER) cc_final: 0.1782 (t80) REVERT: y 18 GLN cc_start: 0.8534 (mt0) cc_final: 0.8183 (mt0) REVERT: y 45 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8271 (tm-30) REVERT: z 22 ARG cc_start: 0.8180 (ttt-90) cc_final: 0.7374 (ttt-90) REVERT: Y 22 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8721 (mt-10) REVERT: Y 26 ARG cc_start: 0.7081 (mmt-90) cc_final: 0.6400 (mmt-90) REVERT: Z 5 LYS cc_start: 0.7812 (tttt) cc_final: 0.7459 (tttm) REVERT: Z 15 TYR cc_start: 0.8232 (m-80) cc_final: 0.8030 (m-80) REVERT: Z 43 ILE cc_start: 0.9344 (mm) cc_final: 0.9023 (mm) REVERT: a 28 LYS cc_start: 0.8336 (ttpt) cc_final: 0.8124 (ttpt) REVERT: b 39 MET cc_start: 0.7414 (mmm) cc_final: 0.7012 (mtm) REVERT: c 36 LEU cc_start: 0.7471 (pt) cc_final: 0.6718 (mt) REVERT: c 37 ARG cc_start: 0.7179 (mmt180) cc_final: 0.6873 (mmt180) REVERT: c 51 GLU cc_start: 0.8024 (pm20) cc_final: 0.7176 (pm20) REVERT: e 29 LYS cc_start: 0.6101 (tttt) cc_final: 0.5846 (tmmt) REVERT: A 79 LYS cc_start: 0.3031 (mttt) cc_final: 0.1591 (mptt) REVERT: B 7 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8236 (mmtt) REVERT: B 43 ARG cc_start: 0.6716 (pmt-80) cc_final: 0.6345 (pmt-80) REVERT: B 97 TYR cc_start: 0.8608 (m-10) cc_final: 0.8353 (m-10) REVERT: B 112 GLN cc_start: 0.6957 (mp10) cc_final: 0.6364 (mp10) REVERT: B 171 ASP cc_start: 0.8135 (t0) cc_final: 0.7783 (t0) REVERT: C 40 GLU cc_start: 0.7208 (mp0) cc_final: 0.6933 (mp0) REVERT: D 7 TYR cc_start: 0.6724 (OUTLIER) cc_final: 0.5289 (t80) REVERT: D 161 GLU cc_start: 0.7561 (tm-30) cc_final: 0.7175 (tm-30) REVERT: D 205 ARG cc_start: 0.8186 (tmt170) cc_final: 0.7435 (mmm160) REVERT: E 29 TRP cc_start: 0.8282 (m100) cc_final: 0.7775 (m100) REVERT: E 71 THR cc_start: 0.7500 (p) cc_final: 0.7205 (p) REVERT: E 74 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6781 (mttt) REVERT: E 80 PHE cc_start: 0.6951 (OUTLIER) cc_final: 0.6265 (m-80) REVERT: E 114 ILE cc_start: 0.7700 (mm) cc_final: 0.7473 (mm) REVERT: E 116 ASP cc_start: 0.7176 (p0) cc_final: 0.6898 (p0) REVERT: E 164 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6253 (pt0) REVERT: F 86 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6599 (pm20) REVERT: F 140 LYS cc_start: 0.8184 (mtmt) cc_final: 0.7688 (mtpt) REVERT: G 22 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8001 (ttpt) REVERT: G 23 PRO cc_start: 0.9255 (Cg_exo) cc_final: 0.9019 (Cg_endo) REVERT: G 33 ARG cc_start: 0.7590 (mtm-85) cc_final: 0.7203 (mtt-85) REVERT: J 17 ASP cc_start: 0.7996 (t70) cc_final: 0.7749 (t0) REVERT: J 114 ARG cc_start: 0.7678 (mtm110) cc_final: 0.6931 (mtm110) REVERT: K 13 ASN cc_start: 0.6257 (p0) cc_final: 0.5849 (p0) REVERT: L 7 ARG cc_start: 0.7599 (mmp-170) cc_final: 0.7103 (mmp-170) REVERT: L 50 ARG cc_start: 0.8410 (ptp-110) cc_final: 0.8125 (ptp90) REVERT: L 102 ARG cc_start: 0.8627 (mtp-110) cc_final: 0.8352 (mtp-110) REVERT: L 115 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8861 (pp) REVERT: M 32 TYR cc_start: 0.7643 (m-80) cc_final: 0.6808 (m-80) REVERT: M 101 ARG cc_start: 0.8317 (tpt170) cc_final: 0.7055 (tpm170) REVERT: N 4 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6860 (tm) REVERT: O 17 ARG cc_start: 0.5995 (mpp-170) cc_final: 0.4045 (mtm180) REVERT: O 44 LYS cc_start: 0.6806 (ptpp) cc_final: 0.6399 (ptpt) REVERT: O 67 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7592 (mtm-85) REVERT: O 84 GLN cc_start: 0.7633 (tp40) cc_final: 0.6727 (tm-30) REVERT: O 93 LYS cc_start: 0.8528 (tptp) cc_final: 0.7688 (tppp) REVERT: O 94 TYR cc_start: 0.8328 (t80) cc_final: 0.7589 (t80) REVERT: Q 17 ILE cc_start: 0.9488 (mm) cc_final: 0.9247 (mt) REVERT: Q 108 GLU cc_start: 0.7399 (tp30) cc_final: 0.7126 (tp30) REVERT: R 10 LYS cc_start: 0.8233 (mtmt) cc_final: 0.8010 (mtpt) REVERT: R 74 LYS cc_start: 0.8251 (pttm) cc_final: 0.8010 (pttm) REVERT: R 76 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7817 (ptmm) REVERT: R 98 GLU cc_start: 0.7885 (pp20) cc_final: 0.7543 (pp20) REVERT: S 65 LEU cc_start: 0.8228 (tp) cc_final: 0.7955 (tt) REVERT: S 92 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7743 (mtp-110) REVERT: T 29 TRP cc_start: 0.8187 (m100) cc_final: 0.7754 (m100) REVERT: U 38 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.6671 (mm) REVERT: U 46 LYS cc_start: 0.7439 (mttt) cc_final: 0.6613 (ttmt) REVERT: V 56 VAL cc_start: 0.9187 (t) cc_final: 0.8846 (p) REVERT: 5 47 ARG cc_start: 0.6987 (tpp-160) cc_final: 0.5989 (tmm-80) REVERT: 5 108 ASN cc_start: 0.7597 (p0) cc_final: 0.7025 (p0) REVERT: 5 109 GLU cc_start: 0.6737 (pm20) cc_final: 0.6224 (mp0) REVERT: f 1 MET cc_start: 0.7237 (mtp) cc_final: 0.6975 (mtp) REVERT: f 4 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7107 (mtt180) outliers start: 327 outliers final: 247 residues processed: 1685 average time/residue: 1.3890 time to fit residues: 3997.3295 Evaluate side-chains 1715 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1454 time to evaluate : 6.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain g residue 165 VAL Chi-restraints excluded: chain g residue 187 LEU Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain i residue 4 TYR Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 71 SER Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain i residue 127 THR Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain i residue 137 SER Chi-restraints excluded: chain i residue 158 ILE Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 36 ASP Chi-restraints excluded: chain j residue 67 VAL Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain j residue 120 THR Chi-restraints excluded: chain j residue 147 ASP Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain k residue 98 LEU Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 42 ILE Chi-restraints excluded: chain l residue 84 ASN Chi-restraints excluded: chain l residue 86 GLN Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 141 VAL Chi-restraints excluded: chain l residue 151 TYR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 35 ILE Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 100 ILE Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 123 GLU Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 23 ILE Chi-restraints excluded: chain o residue 24 VAL Chi-restraints excluded: chain o residue 47 PHE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 71 LEU Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 87 THR Chi-restraints excluded: chain p residue 114 VAL Chi-restraints excluded: chain q residue 7 ILE Chi-restraints excluded: chain q residue 22 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 37 CYS Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 93 LEU Chi-restraints excluded: chain q residue 122 THR Chi-restraints excluded: chain r residue 12 ASN Chi-restraints excluded: chain r residue 17 VAL Chi-restraints excluded: chain r residue 32 GLU Chi-restraints excluded: chain r residue 86 CYS Chi-restraints excluded: chain r residue 103 THR Chi-restraints excluded: chain s residue 36 PHE Chi-restraints excluded: chain s residue 37 PHE Chi-restraints excluded: chain s residue 46 GLU Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain u residue 29 ASP Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 45 THR Chi-restraints excluded: chain u residue 69 THR Chi-restraints excluded: chain v residue 5 VAL Chi-restraints excluded: chain v residue 35 VAL Chi-restraints excluded: chain v residue 46 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 90 ILE Chi-restraints excluded: chain w residue 39 VAL Chi-restraints excluded: chain x residue 38 SER Chi-restraints excluded: chain x residue 41 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 71 LEU Chi-restraints excluded: chain x residue 80 TYR Chi-restraints excluded: chain y residue 26 ASN Chi-restraints excluded: chain y residue 36 LEU Chi-restraints excluded: chain y residue 86 ARG Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 18 ILE Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 47 ASN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 42 PHE Chi-restraints excluded: chain b residue 13 LYS Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 47 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 78 TYR Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 55 ARG Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain M residue 12 GLN Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 91 GLN Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain Q residue 105 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 26 TYR Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 72 VAL Chi-restraints excluded: chain V residue 23 LYS Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain 5 residue 8 ARG Chi-restraints excluded: chain 5 residue 40 ASP Chi-restraints excluded: chain 5 residue 72 ASP Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 101 VAL Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 133 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 872 optimal weight: 7.9990 chunk 594 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 780 optimal weight: 2.9990 chunk 432 optimal weight: 10.0000 chunk 894 optimal weight: 6.9990 chunk 724 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 535 optimal weight: 7.9990 chunk 940 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** h 170 GLN h 181 ASN i 45 GLN ** i 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 38 GLN j 73 ASN ** j 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 94 GLN ** l 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 GLN ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 89 ASN n 124 GLN ** o 56 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** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 55 ASN ** 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** ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 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 55 ASN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.574 167513 Z= 0.427 Angle : 0.939 103.370 250789 Z= 0.436 Chirality : 0.042 0.374 31882 Planarity : 0.007 0.204 13445 Dihedral : 26.131 179.718 85259 Min Nonbonded Distance : 1.000 Molprobity Statistics. All-atom Clashscore : 22.83 Ramachandran Plot: Outliers : 0.57 % Allowed : 16.82 % Favored : 82.61 % Rotamer: Outliers : 7.68 % Allowed : 25.31 % Favored : 67.01 % 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: -3.66 (0.10), residues: 5779 helix: -1.19 (0.12), residues: 1647 sheet: -2.64 (0.16), residues: 905 loop : -3.17 (0.10), residues: 3227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP m 138 HIS 0.015 0.002 HIS L 128 PHE 0.035 0.002 PHE j 26 TYR 0.031 0.002 TYR D 97 ARG 0.009 0.001 ARG K 107 *********************** 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 1848 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 1480 time to evaluate : 6.793 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: g 28 PHE cc_start: 0.8717 (t80) cc_final: 0.8408 (t80) REVERT: g 76 GLN cc_start: 0.7126 (mp10) cc_final: 0.6581 (mt0) REVERT: g 95 GLN cc_start: 0.8481 (mm-40) cc_final: 0.7926 (tm-30) REVERT: g 113 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.7430 (m-70) REVERT: g 169 LYS cc_start: 0.7935 (tppt) cc_final: 0.7465 (mmtm) REVERT: h 54 ARG cc_start: 0.7513 (ptp90) cc_final: 0.6965 (ptp90) REVERT: h 104 GLN cc_start: 0.7437 (tt0) cc_final: 0.7204 (tt0) REVERT: h 136 GLN cc_start: 0.7960 (tm-30) cc_final: 0.7557 (tp-100) REVERT: i 42 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8125 (tm-30) REVERT: i 62 GLN cc_start: 0.8389 (mm110) cc_final: 0.7108 (mm110) REVERT: i 77 ASN cc_start: 0.8425 (m-40) cc_final: 0.7985 (m-40) REVERT: i 101 LEU cc_start: 0.8939 (tp) cc_final: 0.8585 (tp) REVERT: i 103 ASN cc_start: 0.8735 (t0) cc_final: 0.8444 (t0) REVERT: i 134 ASP cc_start: 0.7627 (p0) cc_final: 0.7242 (p0) REVERT: i 161 ASN cc_start: 0.8384 (m-40) cc_final: 0.8077 (m110) REVERT: j 79 GLU cc_start: 0.7698 (mp0) cc_final: 0.7090 (mt-10) REVERT: j 118 ILE cc_start: 0.9075 (tp) cc_final: 0.8729 (tp) REVERT: j 127 ASN cc_start: 0.8690 (t0) cc_final: 0.8012 (t0) REVERT: k 24 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6318 (tp30) REVERT: k 69 GLU cc_start: 0.7273 (pp20) cc_final: 0.6484 (pp20) REVERT: k 86 ARG cc_start: 0.6869 (mtt90) cc_final: 0.6450 (mtt90) REVERT: l 12 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7939 (mm) REVERT: l 85 TYR cc_start: 0.7516 (m-10) cc_final: 0.7111 (m-10) REVERT: m 18 ARG cc_start: 0.8426 (mmp-170) cc_final: 0.7653 (mmp-170) REVERT: m 48 TYR cc_start: 0.8823 (p90) cc_final: 0.7945 (p90) REVERT: m 78 GLN cc_start: 0.7452 (mt0) cc_final: 0.6985 (mt0) REVERT: m 123 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7328 (mt-10) REVERT: n 4 TYR cc_start: 0.6950 (OUTLIER) cc_final: 0.5825 (m-80) REVERT: n 38 GLN cc_start: 0.8167 (tt0) cc_final: 0.7837 (tt0) REVERT: o 29 ARG cc_start: 0.6073 (mtp-110) cc_final: 0.5341 (mtt-85) REVERT: o 84 GLN cc_start: 0.6557 (OUTLIER) cc_final: 0.5405 (mp10) REVERT: p 20 TYR cc_start: 0.8209 (m-80) cc_final: 0.8003 (m-80) REVERT: p 59 TYR cc_start: 0.8608 (t80) cc_final: 0.8368 (t80) REVERT: p 75 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7764 (m-10) REVERT: p 116 HIS cc_start: 0.7829 (m170) cc_final: 0.7232 (m-70) REVERT: r 27 LYS cc_start: 0.9070 (ptpt) cc_final: 0.8836 (ptpt) REVERT: r 91 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6456 (ptp-110) REVERT: s 36 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7602 (t80) REVERT: s 37 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8422 (m-80) REVERT: s 40 CYS cc_start: 0.8150 (p) cc_final: 0.7427 (p) REVERT: s 46 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7418 (mp0) REVERT: t 37 ASN cc_start: 0.7919 (m110) cc_final: 0.7128 (t0) REVERT: u 73 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9006 (mm) REVERT: v 96 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: w 23 LYS cc_start: 0.7209 (tptm) cc_final: 0.6734 (tttt) REVERT: w 36 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7785 (p0) REVERT: w 68 LYS cc_start: 0.7887 (tttm) cc_final: 0.7637 (tttp) REVERT: w 71 LYS cc_start: 0.9080 (mtpt) cc_final: 0.8745 (mtmt) REVERT: x 66 MET cc_start: 0.7377 (ptp) cc_final: 0.7012 (pmm) REVERT: x 80 TYR cc_start: 0.4059 (OUTLIER) cc_final: 0.1655 (t80) REVERT: y 18 GLN cc_start: 0.8611 (mt0) cc_final: 0.8404 (mt0) REVERT: y 25 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8000 (ttp-110) REVERT: z 22 ARG cc_start: 0.8289 (ttt-90) cc_final: 0.7489 (ttt-90) REVERT: W 15 ASP cc_start: 0.7108 (t0) cc_final: 0.6865 (t0) REVERT: Y 31 GLU cc_start: 0.8620 (tp30) cc_final: 0.8405 (tp30) REVERT: Z 1 MET cc_start: 0.5343 (tmm) cc_final: 0.4909 (tmm) REVERT: Z 5 LYS cc_start: 0.7903 (tttt) cc_final: 0.7503 (tttm) REVERT: Z 38 GLU cc_start: 0.7578 (mp0) cc_final: 0.7158 (mp0) REVERT: Z 43 ILE cc_start: 0.9338 (mm) cc_final: 0.9003 (mm) REVERT: a 25 TYR cc_start: 0.8596 (m-80) cc_final: 0.8347 (m-80) REVERT: a 28 LYS cc_start: 0.8340 (ttpt) cc_final: 0.8131 (ttpt) REVERT: b 37 LYS cc_start: 0.8856 (pttp) cc_final: 0.8495 (mmtm) REVERT: b 39 MET cc_start: 0.7394 (mmm) cc_final: 0.6766 (mtm) REVERT: b 52 TYR cc_start: 0.6983 (t80) cc_final: 0.6725 (t80) REVERT: c 36 LEU cc_start: 0.7339 (pt) cc_final: 0.6508 (mt) REVERT: c 37 ARG cc_start: 0.7163 (mmt180) cc_final: 0.6887 (mmt180) REVERT: c 51 GLU cc_start: 0.8025 (pm20) cc_final: 0.7111 (pm20) REVERT: e 29 LYS cc_start: 0.6737 (tttt) cc_final: 0.6402 (ttpt) REVERT: A 47 LEU cc_start: 0.4444 (OUTLIER) cc_final: 0.4110 (mt) REVERT: A 79 LYS cc_start: 0.3104 (mttt) cc_final: 0.1605 (mptt) REVERT: B 7 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8246 (mmtt) REVERT: B 97 TYR cc_start: 0.8683 (m-10) cc_final: 0.8104 (m-10) REVERT: B 112 GLN cc_start: 0.7019 (mp10) cc_final: 0.6439 (mp10) REVERT: B 171 ASP cc_start: 0.8136 (t0) cc_final: 0.7744 (t0) REVERT: D 7 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.5221 (t80) REVERT: D 161 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7249 (tm-30) REVERT: D 205 ARG cc_start: 0.8255 (tmt170) cc_final: 0.7691 (ttt180) REVERT: E 71 THR cc_start: 0.7561 (p) cc_final: 0.7197 (p) REVERT: E 74 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6800 (mttt) REVERT: E 80 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6508 (m-80) REVERT: E 114 ILE cc_start: 0.7814 (mm) cc_final: 0.7572 (mm) REVERT: E 164 GLU cc_start: 0.7513 (mm-30) cc_final: 0.6619 (pt0) REVERT: F 121 ILE cc_start: 0.8771 (mp) cc_final: 0.8474 (mt) REVERT: F 139 GLN cc_start: 0.8063 (tp40) cc_final: 0.7827 (tp40) REVERT: F 140 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7768 (mtpt) REVERT: G 22 LYS cc_start: 0.8376 (ttmm) cc_final: 0.7987 (ttpt) REVERT: G 23 PRO cc_start: 0.9277 (Cg_exo) cc_final: 0.9022 (Cg_endo) REVERT: G 33 ARG cc_start: 0.7627 (mtm-85) cc_final: 0.7270 (mtt-85) REVERT: J 17 ASP cc_start: 0.8100 (t70) cc_final: 0.7870 (t0) REVERT: K 13 ASN cc_start: 0.6472 (p0) cc_final: 0.6045 (p0) REVERT: L 7 ARG cc_start: 0.7569 (mmp-170) cc_final: 0.7109 (mmp-170) REVERT: L 50 ARG cc_start: 0.8485 (ptp-110) cc_final: 0.8270 (ptp90) REVERT: L 102 ARG cc_start: 0.8737 (mtp-110) cc_final: 0.8419 (mtp-110) REVERT: L 115 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8878 (pp) REVERT: M 32 TYR cc_start: 0.7814 (m-80) cc_final: 0.7207 (m-80) REVERT: M 115 MET cc_start: 0.8002 (mmp) cc_final: 0.7797 (mmp) REVERT: N 4 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6813 (tm) REVERT: N 102 GLU cc_start: 0.6884 (tt0) cc_final: 0.6667 (tt0) REVERT: N 107 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8314 (p0) REVERT: O 44 LYS cc_start: 0.6487 (ptpp) cc_final: 0.6012 (ptpt) REVERT: O 84 GLN cc_start: 0.7654 (tp40) cc_final: 0.6666 (tm-30) REVERT: O 93 LYS cc_start: 0.8567 (tptp) cc_final: 0.7722 (tppp) REVERT: O 94 TYR cc_start: 0.8456 (t80) cc_final: 0.7557 (t80) REVERT: Q 17 ILE cc_start: 0.9533 (mm) cc_final: 0.9307 (mt) REVERT: Q 71 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8107 (mm-40) REVERT: R 76 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7905 (ptmm) REVERT: R 81 TYR cc_start: 0.6492 (OUTLIER) cc_final: 0.4731 (t80) REVERT: S 1 MET cc_start: 0.7477 (tpt) cc_final: 0.7170 (tpt) REVERT: S 65 LEU cc_start: 0.8285 (tp) cc_final: 0.8048 (tt) REVERT: S 66 GLU cc_start: 0.7968 (tt0) cc_final: 0.7759 (tt0) REVERT: S 92 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7786 (mtp-110) REVERT: T 29 TRP cc_start: 0.8363 (m100) cc_final: 0.7738 (m100) REVERT: U 38 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.6742 (mm) REVERT: U 46 LYS cc_start: 0.7509 (mttt) cc_final: 0.6621 (ttmt) REVERT: V 56 VAL cc_start: 0.9256 (t) cc_final: 0.8920 (p) REVERT: V 61 LEU cc_start: 0.8140 (mm) cc_final: 0.7808 (mt) REVERT: 5 108 ASN cc_start: 0.7743 (p0) cc_final: 0.7191 (p0) REVERT: 5 109 GLU cc_start: 0.6644 (pm20) cc_final: 0.6227 (mp0) REVERT: f 1 MET cc_start: 0.7370 (mtp) cc_final: 0.6966 (mtp) REVERT: f 4 ARG cc_start: 0.8120 (mtt180) cc_final: 0.6866 (mtt180) REVERT: f 31 LYS cc_start: 0.9110 (mtpt) cc_final: 0.8910 (mtpt) outliers start: 368 outliers final: 288 residues processed: 1673 average time/residue: 1.5116 time to fit residues: 4334.5079 Evaluate side-chains 1737 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1425 time to evaluate : 5.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 81 VAL Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain g residue 113 HIS Chi-restraints excluded: chain g residue 162 ILE Chi-restraints excluded: chain g residue 165 VAL Chi-restraints excluded: chain g residue 185 ILE Chi-restraints excluded: chain g residue 187 LEU Chi-restraints excluded: chain g residue 193 ASP Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 222 ILE Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 62 ASP Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 4 TYR Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain i residue 127 THR Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain i residue 137 SER Chi-restraints excluded: chain i residue 158 ILE Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 36 ASP Chi-restraints excluded: chain j residue 67 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 115 VAL Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain j residue 120 THR Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain j residue 147 ASP Chi-restraints excluded: chain k residue 15 ASP Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain k residue 98 LEU Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 42 ILE Chi-restraints excluded: chain l residue 84 ASN Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 141 VAL Chi-restraints excluded: chain l residue 151 TYR Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 35 ILE Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 100 ILE Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 120 THR Chi-restraints excluded: chain m residue 123 GLU Chi-restraints excluded: chain n residue 4 TYR Chi-restraints excluded: chain n residue 16 ARG Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 23 ILE Chi-restraints excluded: chain o residue 24 VAL Chi-restraints excluded: chain o residue 47 PHE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 71 LEU Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 GLN Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 75 TYR Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 87 THR Chi-restraints excluded: chain p residue 114 VAL Chi-restraints excluded: chain q residue 7 ILE Chi-restraints excluded: chain q residue 22 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 37 CYS Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 93 LEU Chi-restraints excluded: chain q residue 122 THR Chi-restraints excluded: chain r residue 12 ASN Chi-restraints excluded: chain r residue 17 VAL Chi-restraints excluded: chain r residue 32 GLU Chi-restraints excluded: chain r residue 70 LEU Chi-restraints excluded: chain r residue 86 CYS Chi-restraints excluded: chain r residue 91 ARG Chi-restraints excluded: chain r residue 103 THR Chi-restraints excluded: chain s residue 36 PHE Chi-restraints excluded: chain s residue 37 PHE Chi-restraints excluded: chain s residue 46 GLU Chi-restraints excluded: chain s residue 60 SER Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain u residue 29 ASP Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 45 THR Chi-restraints excluded: chain u residue 68 ASP Chi-restraints excluded: chain u residue 69 THR Chi-restraints excluded: chain u residue 73 LEU Chi-restraints excluded: chain v residue 5 VAL Chi-restraints excluded: chain v residue 35 VAL Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 46 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 90 ILE Chi-restraints excluded: chain v residue 96 GLU Chi-restraints excluded: chain w residue 36 ASN Chi-restraints excluded: chain w residue 39 VAL Chi-restraints excluded: chain w residue 59 SER Chi-restraints excluded: chain x residue 38 SER Chi-restraints excluded: chain x residue 41 VAL Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 80 TYR Chi-restraints excluded: chain y residue 25 ARG Chi-restraints excluded: chain y residue 26 ASN Chi-restraints excluded: chain y residue 31 SER Chi-restraints excluded: chain y residue 36 LEU Chi-restraints excluded: chain y residue 73 HIS Chi-restraints excluded: chain y residue 86 ARG Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 18 ILE Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 47 ASN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 42 PHE Chi-restraints excluded: chain b residue 13 LYS Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 78 TYR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain M residue 12 GLN Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 91 GLN Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 69 CYS Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 60 GLU Chi-restraints excluded: chain R residue 81 TYR Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 26 TYR Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 52 VAL Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain V residue 23 LYS Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain 5 residue 8 ARG Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 5 residue 40 ASP Chi-restraints excluded: chain 5 residue 53 LEU Chi-restraints excluded: chain 5 residue 72 ASP Chi-restraints excluded: chain 5 residue 81 LEU Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 133 LYS 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: 0.7980 chunk 207 optimal weight: 5.9990 chunk 615 optimal weight: 10.0000 chunk 258 optimal weight: 5.9990 chunk 1048 optimal weight: 30.0000 chunk 870 optimal weight: 0.8980 chunk 485 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 346 optimal weight: 4.9990 chunk 550 optimal weight: 30.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 45 GLN ** i 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 38 GLN j 73 ASN ** j 127 ASN ** 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** ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 76 GLN v 94 ASN w 63 GLN y 42 GLN ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 HIS ** B 87 ASN ** 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 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 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** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 HIS ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7981 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.576 167513 Z= 0.315 Angle : 0.864 103.305 250789 Z= 0.399 Chirality : 0.038 0.355 31882 Planarity : 0.006 0.204 13445 Dihedral : 26.062 179.746 85259 Min Nonbonded Distance : 1.027 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.54 % Allowed : 15.16 % Favored : 84.31 % Rotamer: Outliers : 7.48 % Allowed : 27.17 % Favored : 65.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 2.11 % 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: -3.47 (0.10), residues: 5779 helix: -0.95 (0.13), residues: 1637 sheet: -2.57 (0.16), residues: 912 loop : -3.07 (0.10), residues: 3230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP g 97 HIS 0.012 0.001 HIS L 128 PHE 0.036 0.002 PHE i 93 TYR 0.020 0.002 TYR D 97 ARG 0.010 0.001 ARG i 115 *********************** 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 1846 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 358 poor density : 1488 time to evaluate : 6.592 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: g 28 PHE cc_start: 0.8681 (t80) cc_final: 0.8343 (t80) REVERT: g 49 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7422 (mm-30) REVERT: g 76 GLN cc_start: 0.7092 (mp10) cc_final: 0.6491 (mt0) REVERT: g 95 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7949 (tm-30) REVERT: g 113 HIS cc_start: 0.8526 (OUTLIER) cc_final: 0.7373 (m-70) REVERT: g 169 LYS cc_start: 0.7903 (tppt) cc_final: 0.7428 (mmtm) REVERT: h 5 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8235 (pt) REVERT: h 17 ASP cc_start: 0.7681 (p0) cc_final: 0.7476 (p0) REVERT: h 36 ASP cc_start: 0.7539 (t0) cc_final: 0.7172 (m-30) REVERT: h 54 ARG cc_start: 0.7512 (ptp90) cc_final: 0.6893 (ptp90) REVERT: h 123 GLN cc_start: 0.8524 (mm110) cc_final: 0.8137 (mp10) REVERT: h 125 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7368 (mt-10) REVERT: h 136 GLN cc_start: 0.7846 (tm-30) cc_final: 0.7629 (tp40) REVERT: h 142 MET cc_start: 0.7672 (mmp) cc_final: 0.7419 (mmp) REVERT: i 42 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8112 (tm-30) REVERT: i 76 ARG cc_start: 0.8584 (ttt-90) cc_final: 0.8292 (ttt90) REVERT: i 77 ASN cc_start: 0.8309 (m-40) cc_final: 0.7847 (m-40) REVERT: i 101 LEU cc_start: 0.8889 (tp) cc_final: 0.8512 (tp) REVERT: i 134 ASP cc_start: 0.7699 (p0) cc_final: 0.7367 (p0) REVERT: i 160 GLN cc_start: 0.8317 (tm-30) cc_final: 0.8110 (tm-30) REVERT: i 161 ASN cc_start: 0.8345 (m-40) cc_final: 0.8063 (m110) REVERT: j 79 GLU cc_start: 0.7657 (mp0) cc_final: 0.7061 (mt-10) REVERT: j 118 ILE cc_start: 0.9012 (tp) cc_final: 0.8677 (tp) REVERT: j 127 ASN cc_start: 0.8680 (t0) cc_final: 0.8346 (t0) REVERT: k 33 TYR cc_start: 0.8269 (m-80) cc_final: 0.8033 (m-10) REVERT: k 69 GLU cc_start: 0.7112 (pp20) cc_final: 0.6291 (pp20) REVERT: k 86 ARG cc_start: 0.6787 (mtt90) cc_final: 0.6397 (mtt90) REVERT: l 12 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7895 (mm) REVERT: l 86 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7300 (mt0) REVERT: l 144 MET cc_start: 0.7957 (tpp) cc_final: 0.7449 (tpp) REVERT: m 18 ARG cc_start: 0.8375 (mmp-170) cc_final: 0.8136 (mmp-170) REVERT: m 48 TYR cc_start: 0.8685 (p90) cc_final: 0.7605 (p90) REVERT: m 49 GLU cc_start: 0.7910 (mp0) cc_final: 0.7592 (mp0) REVERT: m 123 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: n 4 TYR cc_start: 0.6797 (OUTLIER) cc_final: 0.5685 (m-80) REVERT: n 121 ARG cc_start: 0.7699 (tpt-90) cc_final: 0.7465 (tpt90) REVERT: o 29 ARG cc_start: 0.5983 (mtp-110) cc_final: 0.5351 (mtt-85) REVERT: o 84 GLN cc_start: 0.6359 (OUTLIER) cc_final: 0.5148 (mp10) REVERT: p 25 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6934 (m-80) REVERT: p 59 TYR cc_start: 0.8660 (t80) cc_final: 0.8365 (t80) REVERT: p 75 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7612 (m-10) REVERT: p 116 HIS cc_start: 0.7799 (m170) cc_final: 0.7197 (m-70) REVERT: q 47 LYS cc_start: 0.8573 (tppt) cc_final: 0.8339 (tppt) REVERT: r 27 LYS cc_start: 0.9057 (ptpt) cc_final: 0.8851 (ptpt) REVERT: r 91 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6475 (ptp-110) REVERT: s 36 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7656 (t80) REVERT: s 37 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8306 (m-80) REVERT: s 40 CYS cc_start: 0.8129 (p) cc_final: 0.7404 (p) REVERT: s 46 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: t 37 ASN cc_start: 0.8120 (m110) cc_final: 0.7135 (t0) REVERT: t 83 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7939 (mm-30) REVERT: u 17 TYR cc_start: 0.8904 (m-80) cc_final: 0.8698 (m-80) REVERT: u 73 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8964 (mm) REVERT: v 96 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: w 36 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7847 (p0) REVERT: w 71 LYS cc_start: 0.9086 (mtpt) cc_final: 0.8733 (mtmt) REVERT: x 38 SER cc_start: 0.8078 (t) cc_final: 0.7596 (p) REVERT: x 66 MET cc_start: 0.7278 (ptp) cc_final: 0.6914 (pmm) REVERT: x 80 TYR cc_start: 0.3886 (OUTLIER) cc_final: 0.1792 (t80) REVERT: y 18 GLN cc_start: 0.8577 (mt0) cc_final: 0.8377 (mt0) REVERT: y 25 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7943 (ttp-110) REVERT: z 3 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8179 (mtmm) REVERT: z 9 ARG cc_start: 0.7201 (ttp80) cc_final: 0.6901 (ttp-110) REVERT: z 14 TRP cc_start: 0.9057 (t60) cc_final: 0.8796 (t60) REVERT: z 22 ARG cc_start: 0.8269 (ttt-90) cc_final: 0.7449 (ttt-90) REVERT: W 15 ASP cc_start: 0.7116 (t0) cc_final: 0.6890 (t0) REVERT: Y 26 ARG cc_start: 0.7667 (tmm160) cc_final: 0.7077 (tmm160) REVERT: Y 31 GLU cc_start: 0.8613 (tp30) cc_final: 0.8411 (tp30) REVERT: Z 1 MET cc_start: 0.5428 (tmm) cc_final: 0.5003 (tmm) REVERT: Z 5 LYS cc_start: 0.7849 (tttt) cc_final: 0.7476 (tttm) REVERT: Z 33 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7751 (mt0) REVERT: Z 38 GLU cc_start: 0.7536 (mp0) cc_final: 0.7081 (mp0) REVERT: Z 43 ILE cc_start: 0.9331 (mm) cc_final: 0.9010 (mm) REVERT: a 25 TYR cc_start: 0.8490 (m-80) cc_final: 0.8129 (m-80) REVERT: a 28 LYS cc_start: 0.8305 (ttpt) cc_final: 0.8095 (ttpt) REVERT: b 37 LYS cc_start: 0.8901 (pttp) cc_final: 0.8486 (mmtm) REVERT: b 39 MET cc_start: 0.7267 (mmm) cc_final: 0.6828 (mtm) REVERT: b 52 TYR cc_start: 0.6844 (t80) cc_final: 0.6632 (t80) REVERT: c 36 LEU cc_start: 0.7244 (pt) cc_final: 0.6470 (mt) REVERT: c 37 ARG cc_start: 0.7127 (mmt180) cc_final: 0.6835 (mmt180) REVERT: c 51 GLU cc_start: 0.7996 (pm20) cc_final: 0.7034 (pm20) REVERT: e 12 LYS cc_start: 0.8290 (mtmm) cc_final: 0.7986 (mtmm) REVERT: e 29 LYS cc_start: 0.6351 (tttt) cc_final: 0.6004 (tmmt) REVERT: A 47 LEU cc_start: 0.4682 (OUTLIER) cc_final: 0.4319 (mt) REVERT: A 79 LYS cc_start: 0.2823 (mttt) cc_final: 0.1456 (mptt) REVERT: A 85 GLU cc_start: 0.3538 (tt0) cc_final: 0.3269 (tt0) REVERT: B 7 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8285 (mmtt) REVERT: B 112 GLN cc_start: 0.7011 (mp10) cc_final: 0.6438 (mp10) REVERT: B 171 ASP cc_start: 0.8143 (t0) cc_final: 0.7773 (t0) REVERT: B 237 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7169 (pp20) REVERT: C 103 ASP cc_start: 0.7606 (m-30) cc_final: 0.6887 (m-30) REVERT: C 168 MET cc_start: 0.7257 (mmt) cc_final: 0.6625 (mmp) REVERT: D 7 TYR cc_start: 0.6586 (OUTLIER) cc_final: 0.5110 (t80) REVERT: D 161 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7133 (tm-30) REVERT: D 181 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8112 (mt) REVERT: D 205 ARG cc_start: 0.8238 (tmt170) cc_final: 0.7616 (ttt180) REVERT: E 71 THR cc_start: 0.7522 (p) cc_final: 0.7179 (p) REVERT: E 74 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6749 (mttt) REVERT: E 80 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6479 (m-80) REVERT: E 95 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7487 (mtt-85) REVERT: F 86 GLU cc_start: 0.7496 (mm-30) cc_final: 0.6624 (pm20) REVERT: F 121 ILE cc_start: 0.8717 (mp) cc_final: 0.8448 (mt) REVERT: F 139 GLN cc_start: 0.8014 (tp40) cc_final: 0.7682 (tp40) REVERT: F 140 LYS cc_start: 0.8201 (mtmt) cc_final: 0.7841 (mtpt) REVERT: G 23 PRO cc_start: 0.9283 (Cg_exo) cc_final: 0.9052 (Cg_endo) REVERT: G 33 ARG cc_start: 0.7594 (mtm-85) cc_final: 0.7299 (mtt-85) REVERT: J 17 ASP cc_start: 0.8090 (t70) cc_final: 0.7829 (t0) REVERT: K 13 ASN cc_start: 0.6430 (p0) cc_final: 0.6091 (p0) REVERT: K 14 THR cc_start: 0.7895 (p) cc_final: 0.7584 (p) REVERT: L 7 ARG cc_start: 0.7549 (mmp-170) cc_final: 0.7040 (mmp-170) REVERT: L 61 ARG cc_start: 0.6266 (ptt180) cc_final: 0.6032 (ptt180) REVERT: L 102 ARG cc_start: 0.8733 (mtp-110) cc_final: 0.8379 (mtp-110) REVERT: M 32 TYR cc_start: 0.7736 (m-80) cc_final: 0.7417 (m-80) REVERT: M 115 MET cc_start: 0.8079 (mmp) cc_final: 0.7807 (mmp) REVERT: N 4 LEU cc_start: 0.7110 (OUTLIER) cc_final: 0.6882 (tm) REVERT: N 43 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7947 (mm-30) REVERT: O 44 LYS cc_start: 0.6381 (ptpp) cc_final: 0.5935 (ptpt) REVERT: O 84 GLN cc_start: 0.7605 (tp40) cc_final: 0.6725 (tm-30) REVERT: O 93 LYS cc_start: 0.8560 (tptp) cc_final: 0.7682 (tppp) REVERT: O 94 TYR cc_start: 0.8407 (t80) cc_final: 0.7585 (t80) REVERT: Q 17 ILE cc_start: 0.9488 (mm) cc_final: 0.9268 (mt) REVERT: Q 71 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8069 (mm-40) REVERT: R 23 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7420 (mt-10) REVERT: R 74 LYS cc_start: 0.8198 (pttm) cc_final: 0.7994 (pttm) REVERT: R 76 LYS cc_start: 0.8232 (ttpt) cc_final: 0.7857 (ptmm) REVERT: R 81 TYR cc_start: 0.6374 (OUTLIER) cc_final: 0.4793 (t80) REVERT: R 98 GLU cc_start: 0.7870 (pp20) cc_final: 0.7574 (pp20) REVERT: S 1 MET cc_start: 0.7338 (tpt) cc_final: 0.7090 (tpt) REVERT: S 65 LEU cc_start: 0.8246 (tp) cc_final: 0.8035 (tt) REVERT: T 29 TRP cc_start: 0.8283 (m100) cc_final: 0.7685 (m100) REVERT: U 35 TYR cc_start: 0.6987 (OUTLIER) cc_final: 0.6772 (t80) REVERT: U 38 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.6511 (mm) REVERT: U 46 LYS cc_start: 0.7475 (mttt) cc_final: 0.6615 (ttmt) REVERT: V 9 TYR cc_start: 0.7779 (m-80) cc_final: 0.7503 (m-80) REVERT: V 56 VAL cc_start: 0.9220 (t) cc_final: 0.8890 (p) REVERT: V 77 ASP cc_start: 0.6869 (t0) cc_final: 0.6357 (p0) REVERT: V 87 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7250 (p0) REVERT: 5 47 ARG cc_start: 0.6628 (tpp-160) cc_final: 0.5790 (tmm-80) REVERT: 5 108 ASN cc_start: 0.7698 (p0) cc_final: 0.7221 (p0) REVERT: 5 109 GLU cc_start: 0.6283 (pm20) cc_final: 0.5873 (mp0) REVERT: f 4 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7046 (mtt180) REVERT: f 31 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8903 (mtpt) outliers start: 358 outliers final: 274 residues processed: 1680 average time/residue: 1.3986 time to fit residues: 4001.8373 Evaluate side-chains 1745 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1440 time to evaluate : 6.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 113 HIS Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 165 VAL Chi-restraints excluded: chain g residue 185 ILE Chi-restraints excluded: chain g residue 187 LEU Chi-restraints excluded: chain g residue 193 ASP Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 4 TYR Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 71 SER Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain i residue 127 THR Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain i residue 137 SER Chi-restraints excluded: chain i residue 158 ILE Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 36 ASP Chi-restraints excluded: chain j residue 67 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 115 VAL Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain j residue 120 THR Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain j residue 147 ASP Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain k residue 98 LEU Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 42 ILE Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 84 ASN Chi-restraints excluded: chain l residue 86 GLN Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 141 VAL Chi-restraints excluded: chain l residue 151 TYR Chi-restraints excluded: chain m residue 35 ILE Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 100 ILE Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 120 THR Chi-restraints excluded: chain m residue 123 GLU Chi-restraints excluded: chain n residue 4 TYR Chi-restraints excluded: chain n residue 16 ARG Chi-restraints excluded: chain n residue 40 LEU Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 53 VAL Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 47 PHE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 GLN Chi-restraints excluded: chain p residue 25 TYR Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 75 TYR Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 87 THR Chi-restraints excluded: chain p residue 114 VAL Chi-restraints excluded: chain q residue 7 ILE Chi-restraints excluded: chain q residue 22 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 37 CYS Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 93 LEU Chi-restraints excluded: chain q residue 122 THR Chi-restraints excluded: chain r residue 12 ASN Chi-restraints excluded: chain r residue 17 VAL Chi-restraints excluded: chain r residue 32 GLU Chi-restraints excluded: chain r residue 86 CYS Chi-restraints excluded: chain r residue 91 ARG Chi-restraints excluded: chain r residue 103 THR Chi-restraints excluded: chain s residue 16 PHE Chi-restraints excluded: chain s residue 36 PHE Chi-restraints excluded: chain s residue 37 PHE Chi-restraints excluded: chain s residue 46 GLU Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain u residue 29 ASP Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 45 THR Chi-restraints excluded: chain u residue 68 ASP Chi-restraints excluded: chain u residue 69 THR Chi-restraints excluded: chain u residue 73 LEU Chi-restraints excluded: chain v residue 5 VAL Chi-restraints excluded: chain v residue 35 VAL Chi-restraints excluded: chain v residue 46 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 90 ILE Chi-restraints excluded: chain v residue 96 GLU Chi-restraints excluded: chain w residue 36 ASN Chi-restraints excluded: chain w residue 39 VAL Chi-restraints excluded: chain w residue 59 SER Chi-restraints excluded: chain x residue 41 VAL Chi-restraints excluded: chain x residue 80 TYR Chi-restraints excluded: chain y residue 25 ARG Chi-restraints excluded: chain y residue 26 ASN Chi-restraints excluded: chain y residue 31 SER Chi-restraints excluded: chain y residue 36 LEU Chi-restraints excluded: chain y residue 86 ARG Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 18 ILE Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 72 GLU Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 47 ASN Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 42 PHE Chi-restraints excluded: chain b residue 13 LYS Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 78 TYR Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 GLU Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain M residue 12 GLN Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 91 GLN Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 32 TYR Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 81 TYR Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 26 TYR Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain V residue 23 LYS Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 54 HIS Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain 5 residue 8 ARG Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 5 residue 40 ASP Chi-restraints excluded: chain 5 residue 72 ASP Chi-restraints excluded: chain 5 residue 81 LEU Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 133 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 1011 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 597 optimal weight: 10.0000 chunk 765 optimal weight: 0.6980 chunk 593 optimal weight: 10.0000 chunk 882 optimal weight: 7.9990 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: 5.9388 ------------------------------------------------------------------------------- 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 h 181 ASN ** i 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 38 GLN j 73 ASN ** j 127 ASN ** 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** ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 65 GLN u 76 GLN v 94 ASN ** w 63 GLN ** 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** X 56 GLN ** Z 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** 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 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN ** L 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 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** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS Q 104 GLN T 41 ASN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.574 167513 Z= 0.524 Angle : 1.012 103.383 250789 Z= 0.471 Chirality : 0.045 0.389 31882 Planarity : 0.007 0.203 13445 Dihedral : 26.177 179.748 85259 Min Nonbonded Distance : 0.968 Molprobity Statistics. All-atom Clashscore : 24.93 Ramachandran Plot: Outliers : 0.61 % Allowed : 17.58 % Favored : 81.81 % Rotamer: Outliers : 8.27 % Allowed : 27.27 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % Cis-general : 0.00 % Twisted Proline : 2.46 % 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: -3.66 (0.10), residues: 5779 helix: -1.21 (0.12), residues: 1651 sheet: -2.58 (0.16), residues: 890 loop : -3.18 (0.10), residues: 3238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP m 138 HIS 0.022 0.002 HIS L 128 PHE 0.037 0.003 PHE g 57 TYR 0.036 0.003 TYR D 97 ARG 0.011 0.001 ARG i 115 *********************** 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 1853 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 396 poor density : 1457 time to evaluate : 6.581 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: g 28 PHE cc_start: 0.8787 (t80) cc_final: 0.8463 (t80) REVERT: g 49 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7531 (mm-30) REVERT: g 76 GLN cc_start: 0.7114 (mp10) cc_final: 0.6551 (mt0) REVERT: g 95 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8219 (tm-30) REVERT: g 113 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.7415 (m-70) REVERT: g 169 LYS cc_start: 0.7804 (tppt) cc_final: 0.7384 (mmtm) REVERT: h 5 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8503 (pt) REVERT: h 17 ASP cc_start: 0.7728 (p0) cc_final: 0.7528 (p0) REVERT: h 54 ARG cc_start: 0.7566 (ptp90) cc_final: 0.7018 (ptp90) REVERT: h 123 GLN cc_start: 0.8575 (mm110) cc_final: 0.8106 (mp10) REVERT: h 136 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7753 (tp40) REVERT: i 42 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8157 (tm-30) REVERT: i 77 ASN cc_start: 0.8468 (m-40) cc_final: 0.8062 (m-40) REVERT: i 101 LEU cc_start: 0.8986 (tp) cc_final: 0.8617 (tp) REVERT: i 103 ASN cc_start: 0.8918 (t0) cc_final: 0.8637 (t0) REVERT: i 134 ASP cc_start: 0.7692 (p0) cc_final: 0.7429 (p0) REVERT: i 138 TYR cc_start: 0.9071 (t80) cc_final: 0.8524 (t80) REVERT: i 160 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8163 (tm-30) REVERT: i 161 ASN cc_start: 0.8440 (m-40) cc_final: 0.8119 (m110) REVERT: j 101 ILE cc_start: 0.9364 (mm) cc_final: 0.9160 (mm) REVERT: j 118 ILE cc_start: 0.9079 (tp) cc_final: 0.8768 (tp) REVERT: j 127 ASN cc_start: 0.8974 (t0) cc_final: 0.8549 (t0) REVERT: k 33 TYR cc_start: 0.8370 (m-80) cc_final: 0.8128 (m-10) REVERT: k 54 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7549 (mtpt) REVERT: l 12 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7978 (mm) REVERT: l 86 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7429 (mt0) REVERT: m 18 ARG cc_start: 0.8366 (mmp-170) cc_final: 0.7910 (mmp-170) REVERT: m 48 TYR cc_start: 0.8839 (p90) cc_final: 0.7712 (p90) REVERT: m 123 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7420 (mt-10) REVERT: n 4 TYR cc_start: 0.6898 (OUTLIER) cc_final: 0.5769 (m-80) REVERT: o 84 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.5413 (mp10) REVERT: p 20 TYR cc_start: 0.8471 (m-80) cc_final: 0.8195 (m-80) REVERT: p 25 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: p 75 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.7714 (m-10) REVERT: p 116 HIS cc_start: 0.8035 (m170) cc_final: 0.7558 (m-70) REVERT: r 58 GLU cc_start: 0.7707 (pp20) cc_final: 0.7135 (pp20) REVERT: r 82 MET cc_start: 0.5563 (ttt) cc_final: 0.5154 (ttt) REVERT: r 91 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6720 (ptp-110) REVERT: r 94 ARG cc_start: 0.6581 (ttm-80) cc_final: 0.6339 (ttm110) REVERT: s 36 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7826 (t80) REVERT: s 37 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8493 (m-80) REVERT: s 40 CYS cc_start: 0.8101 (p) cc_final: 0.7414 (p) REVERT: s 46 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: s 52 GLN cc_start: 0.7426 (mt0) cc_final: 0.7224 (mt0) REVERT: u 1 MET cc_start: 0.7605 (ptp) cc_final: 0.7395 (ptp) REVERT: u 73 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9044 (mm) REVERT: v 78 GLU cc_start: 0.7533 (tp30) cc_final: 0.7295 (tp30) REVERT: v 96 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: w 71 LYS cc_start: 0.9069 (mtpt) cc_final: 0.8687 (mtmt) REVERT: x 66 MET cc_start: 0.7394 (ptp) cc_final: 0.6923 (pmm) REVERT: x 80 TYR cc_start: 0.4109 (OUTLIER) cc_final: 0.1902 (t80) REVERT: y 25 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7985 (ttp-110) REVERT: z 9 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7226 (ttp-110) REVERT: z 14 TRP cc_start: 0.9111 (t60) cc_final: 0.8782 (t60) REVERT: z 21 TYR cc_start: 0.7547 (m-80) cc_final: 0.7229 (m-80) REVERT: z 22 ARG cc_start: 0.8071 (ttt-90) cc_final: 0.7203 (ttt-90) REVERT: Z 1 MET cc_start: 0.5404 (tmm) cc_final: 0.4789 (tmm) REVERT: Z 5 LYS cc_start: 0.7947 (tttt) cc_final: 0.7606 (tttm) REVERT: Z 33 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8084 (mt0) REVERT: Z 38 GLU cc_start: 0.7679 (mp0) cc_final: 0.7371 (mp0) REVERT: Z 43 ILE cc_start: 0.9322 (mm) cc_final: 0.9011 (mm) REVERT: b 37 LYS cc_start: 0.8883 (pttp) cc_final: 0.8567 (mmpt) REVERT: b 39 MET cc_start: 0.7423 (mmm) cc_final: 0.6866 (mtm) REVERT: b 52 TYR cc_start: 0.6835 (t80) cc_final: 0.6627 (t80) REVERT: c 37 ARG cc_start: 0.7136 (mmt180) cc_final: 0.6888 (mmt180) REVERT: c 51 GLU cc_start: 0.7995 (pm20) cc_final: 0.6987 (pm20) REVERT: e 29 LYS cc_start: 0.7196 (tttt) cc_final: 0.6789 (tmtt) REVERT: A 47 LEU cc_start: 0.4548 (OUTLIER) cc_final: 0.4311 (mt) REVERT: A 79 LYS cc_start: 0.3094 (mttt) cc_final: 0.1656 (mptt) REVERT: B 7 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8312 (mmtt) REVERT: B 97 TYR cc_start: 0.8856 (m-10) cc_final: 0.8480 (m-10) REVERT: B 112 GLN cc_start: 0.6952 (mp10) cc_final: 0.6359 (mp10) REVERT: B 171 ASP cc_start: 0.8169 (t0) cc_final: 0.7776 (t0) REVERT: B 237 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7416 (pp20) REVERT: C 152 LYS cc_start: 0.9026 (mtpp) cc_final: 0.8750 (ttpp) REVERT: D 7 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.5126 (t80) REVERT: D 161 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7085 (tm-30) REVERT: D 205 ARG cc_start: 0.8276 (tmt170) cc_final: 0.7720 (ttt180) REVERT: E 71 THR cc_start: 0.7701 (p) cc_final: 0.7367 (p) REVERT: E 74 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6900 (mttt) REVERT: E 80 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6561 (m-80) REVERT: E 164 GLU cc_start: 0.7700 (mm-30) cc_final: 0.6722 (pt0) REVERT: F 121 ILE cc_start: 0.8782 (mp) cc_final: 0.8549 (mt) REVERT: F 139 GLN cc_start: 0.8087 (tp40) cc_final: 0.7713 (tp40) REVERT: G 23 PRO cc_start: 0.9196 (Cg_exo) cc_final: 0.8846 (Cg_endo) REVERT: G 33 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.7504 (mtt-85) REVERT: J 17 ASP cc_start: 0.8167 (t70) cc_final: 0.7938 (t0) REVERT: K 12 ASP cc_start: 0.8569 (p0) cc_final: 0.8366 (p0) REVERT: K 13 ASN cc_start: 0.6436 (p0) cc_final: 0.6211 (p0) REVERT: L 7 ARG cc_start: 0.7584 (mmp-170) cc_final: 0.7011 (mmp-170) REVERT: L 102 ARG cc_start: 0.8748 (mtp-110) cc_final: 0.8373 (mtp-110) REVERT: L 112 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8512 (tp) REVERT: M 32 TYR cc_start: 0.7745 (m-80) cc_final: 0.7488 (m-80) REVERT: N 4 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6809 (tm) REVERT: N 43 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8034 (mm-30) REVERT: N 107 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8286 (p0) REVERT: O 84 GLN cc_start: 0.7672 (tp40) cc_final: 0.6675 (tm-30) REVERT: O 93 LYS cc_start: 0.8554 (tptp) cc_final: 0.7708 (tppp) REVERT: O 94 TYR cc_start: 0.8485 (t80) cc_final: 0.7796 (t80) REVERT: P 29 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.6294 (mmp-170) REVERT: P 32 TYR cc_start: 0.5742 (OUTLIER) cc_final: 0.4334 (p90) REVERT: P 85 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.6797 (tppt) REVERT: Q 17 ILE cc_start: 0.9560 (mm) cc_final: 0.9335 (mt) REVERT: Q 71 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8174 (mm-40) REVERT: R 74 LYS cc_start: 0.8370 (pttm) cc_final: 0.8164 (pttm) REVERT: R 76 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7925 (ptmm) REVERT: R 81 TYR cc_start: 0.6753 (OUTLIER) cc_final: 0.5269 (t80) REVERT: T 29 TRP cc_start: 0.8362 (m100) cc_final: 0.7779 (m100) REVERT: U 35 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6948 (t80) REVERT: U 38 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.6650 (mm) REVERT: U 46 LYS cc_start: 0.7582 (mttt) cc_final: 0.6572 (ttmt) REVERT: V 56 VAL cc_start: 0.9281 (t) cc_final: 0.8949 (p) REVERT: V 87 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7276 (p0) REVERT: 5 108 ASN cc_start: 0.7659 (p0) cc_final: 0.7161 (p0) REVERT: 5 130 ARG cc_start: 0.7506 (mtm180) cc_final: 0.7161 (mtm-85) outliers start: 396 outliers final: 306 residues processed: 1669 average time/residue: 1.3626 time to fit residues: 3904.6784 Evaluate side-chains 1764 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 1425 time to evaluate : 6.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 81 VAL Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain g residue 113 HIS Chi-restraints excluded: chain g residue 162 ILE Chi-restraints excluded: chain g residue 165 VAL Chi-restraints excluded: chain g residue 185 ILE Chi-restraints excluded: chain g residue 187 LEU Chi-restraints excluded: chain g residue 193 ASP Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 222 ILE Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 62 ASP Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 89 GLU Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain h residue 192 THR Chi-restraints excluded: chain i residue 4 TYR Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain i residue 137 SER Chi-restraints excluded: chain i residue 158 ILE Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 36 ASP Chi-restraints excluded: chain j residue 67 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 115 VAL Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain j residue 120 THR Chi-restraints excluded: chain j residue 139 LEU Chi-restraints excluded: chain j residue 147 ASP Chi-restraints excluded: chain k residue 15 ASP Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain k residue 98 LEU Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 16 LEU Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 84 ASN Chi-restraints excluded: chain l residue 86 GLN Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 141 VAL Chi-restraints excluded: chain l residue 151 TYR Chi-restraints excluded: chain m residue 19 VAL Chi-restraints excluded: chain m residue 35 ILE Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 100 ILE Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 120 THR Chi-restraints excluded: chain m residue 123 GLU Chi-restraints excluded: chain n residue 4 TYR Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain n residue 103 THR Chi-restraints excluded: chain o residue 23 ILE Chi-restraints excluded: chain o residue 24 VAL Chi-restraints excluded: chain o residue 47 PHE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 GLN Chi-restraints excluded: chain p residue 25 TYR Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 75 TYR Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 87 THR Chi-restraints excluded: chain p residue 114 VAL Chi-restraints excluded: chain q residue 7 ILE Chi-restraints excluded: chain q residue 22 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 93 LEU Chi-restraints excluded: chain q residue 122 THR Chi-restraints excluded: chain r residue 12 ASN Chi-restraints excluded: chain r residue 17 VAL Chi-restraints excluded: chain r residue 32 GLU Chi-restraints excluded: chain r residue 70 LEU Chi-restraints excluded: chain r residue 86 CYS Chi-restraints excluded: chain r residue 91 ARG Chi-restraints excluded: chain r residue 103 THR Chi-restraints excluded: chain s residue 36 PHE Chi-restraints excluded: chain s residue 37 PHE Chi-restraints excluded: chain s residue 46 GLU Chi-restraints excluded: chain s residue 60 SER Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 29 ASP Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 45 THR Chi-restraints excluded: chain u residue 68 ASP Chi-restraints excluded: chain u residue 69 THR Chi-restraints excluded: chain u residue 73 LEU Chi-restraints excluded: chain u residue 74 LEU Chi-restraints excluded: chain v residue 5 VAL Chi-restraints excluded: chain v residue 35 VAL Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 46 ASP Chi-restraints excluded: chain v residue 57 VAL Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 90 ILE Chi-restraints excluded: chain v residue 94 ASN Chi-restraints excluded: chain v residue 96 GLU Chi-restraints excluded: chain w residue 36 ASN Chi-restraints excluded: chain w residue 39 VAL Chi-restraints excluded: chain w residue 59 SER Chi-restraints excluded: chain w residue 83 GLU Chi-restraints excluded: chain x residue 41 VAL Chi-restraints excluded: chain x residue 67 VAL Chi-restraints excluded: chain x residue 80 TYR Chi-restraints excluded: chain y residue 25 ARG Chi-restraints excluded: chain y residue 26 ASN Chi-restraints excluded: chain y residue 31 SER Chi-restraints excluded: chain y residue 36 LEU Chi-restraints excluded: chain y residue 73 HIS Chi-restraints excluded: chain y residue 86 ARG Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 18 ILE Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 82 LEU Chi-restraints excluded: chain Y residue 35 LEU Chi-restraints excluded: chain Y residue 47 ASN Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 42 PHE Chi-restraints excluded: chain b residue 13 LYS Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 15 THR Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 148 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain J residue 131 GLN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 112 GLU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 7 ILE Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 29 ARG Chi-restraints excluded: chain P residue 32 TYR Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 85 LYS Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 60 GLU Chi-restraints excluded: chain R residue 81 TYR Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 26 TYR Chi-restraints excluded: chain T residue 30 VAL Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain V residue 23 LYS Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 54 HIS Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain 5 residue 8 ARG Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 5 residue 40 ASP Chi-restraints excluded: chain 5 residue 53 LEU Chi-restraints excluded: chain 5 residue 72 ASP Chi-restraints excluded: chain 5 residue 81 LEU Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 133 LYS 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: 8.9990 chunk 624 optimal weight: 2.9990 chunk 314 optimal weight: 7.9990 chunk 205 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 664 optimal weight: 5.9990 chunk 711 optimal weight: 6.9990 chunk 516 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 821 optimal weight: 0.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 38 GLN ** j 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 124 GLN ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 37 ASN u 76 GLN w 63 GLN y 18 GLN 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** ** B 87 ASN ** 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 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 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** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN T 41 ASN T 55 ASN T 58 HIS ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 ASN ** 5 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.576 167513 Z= 0.277 Angle : 0.858 103.270 250789 Z= 0.396 Chirality : 0.038 0.346 31882 Planarity : 0.006 0.202 13445 Dihedral : 26.050 179.902 85259 Min Nonbonded Distance : 1.036 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.52 % Allowed : 15.28 % Favored : 84.20 % Rotamer: Outliers : 7.18 % Allowed : 29.11 % Favored : 63.71 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 2.11 % 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: -3.41 (0.10), residues: 5779 helix: -0.90 (0.12), residues: 1655 sheet: -2.46 (0.16), residues: 921 loop : -3.06 (0.10), residues: 3203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP m 138 HIS 0.023 0.001 HIS L 128 PHE 0.035 0.002 PHE g 57 TYR 0.022 0.002 TYR v 95 ARG 0.016 0.001 ARG Z 55 *********************** 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 1808 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 1464 time to evaluate : 6.530 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: g 28 PHE cc_start: 0.8692 (t80) cc_final: 0.8317 (t80) REVERT: g 49 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7433 (mm-30) REVERT: g 76 GLN cc_start: 0.7114 (mp10) cc_final: 0.6521 (mt0) REVERT: g 113 HIS cc_start: 0.8522 (OUTLIER) cc_final: 0.7407 (m-70) REVERT: g 169 LYS cc_start: 0.7855 (tppt) cc_final: 0.7465 (mmtm) REVERT: h 5 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8196 (pt) REVERT: h 17 ASP cc_start: 0.7668 (p0) cc_final: 0.7451 (p0) REVERT: h 54 ARG cc_start: 0.7566 (ptp90) cc_final: 0.7171 (ptp90) REVERT: h 123 GLN cc_start: 0.8545 (mm110) cc_final: 0.8151 (mp10) REVERT: h 136 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7654 (tp40) REVERT: i 5 ILE cc_start: 0.5505 (OUTLIER) cc_final: 0.5249 (tp) REVERT: i 42 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8222 (tm-30) REVERT: i 76 ARG cc_start: 0.8620 (ttt-90) cc_final: 0.8348 (ttt90) REVERT: i 77 ASN cc_start: 0.8294 (m-40) cc_final: 0.7841 (m-40) REVERT: i 101 LEU cc_start: 0.8787 (tp) cc_final: 0.8473 (tp) REVERT: i 134 ASP cc_start: 0.7579 (p0) cc_final: 0.7339 (p0) REVERT: j 118 ILE cc_start: 0.9042 (tp) cc_final: 0.8652 (tp) REVERT: j 127 ASN cc_start: 0.8593 (t0) cc_final: 0.8302 (t0) REVERT: k 33 TYR cc_start: 0.8353 (m-80) cc_final: 0.8106 (m-10) REVERT: k 59 TYR cc_start: 0.7033 (t80) cc_final: 0.6733 (t80) REVERT: k 69 GLU cc_start: 0.7133 (pp20) cc_final: 0.6285 (pp20) REVERT: k 86 ARG cc_start: 0.6742 (mtt90) cc_final: 0.6332 (mtt90) REVERT: l 12 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7772 (mm) REVERT: l 144 MET cc_start: 0.7964 (tpp) cc_final: 0.7461 (tpp) REVERT: m 18 ARG cc_start: 0.8370 (mmp-170) cc_final: 0.8132 (mmp-170) REVERT: m 48 TYR cc_start: 0.8697 (p90) cc_final: 0.7573 (p90) REVERT: m 98 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8092 (mttt) REVERT: m 123 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: n 4 TYR cc_start: 0.6963 (OUTLIER) cc_final: 0.5731 (m-80) REVERT: n 42 ARG cc_start: 0.7445 (ttp-170) cc_final: 0.6623 (tmm160) REVERT: n 49 PRO cc_start: 0.9049 (Cg_exo) cc_final: 0.8805 (Cg_endo) REVERT: n 121 ARG cc_start: 0.7582 (tpt-90) cc_final: 0.7344 (tpt90) REVERT: o 29 ARG cc_start: 0.6031 (mtp-110) cc_final: 0.5309 (mtt-85) REVERT: o 84 GLN cc_start: 0.6409 (OUTLIER) cc_final: 0.5217 (mp10) REVERT: p 20 TYR cc_start: 0.8266 (m-80) cc_final: 0.8010 (m-80) REVERT: p 25 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.6996 (m-80) REVERT: p 75 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7426 (m-10) REVERT: p 116 HIS cc_start: 0.7791 (m170) cc_final: 0.7126 (m-70) REVERT: r 82 MET cc_start: 0.4835 (ttt) cc_final: 0.4416 (ttt) REVERT: s 4 LYS cc_start: 0.8806 (tppt) cc_final: 0.8278 (tptp) REVERT: s 36 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7691 (t80) REVERT: s 37 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8368 (m-80) REVERT: s 40 CYS cc_start: 0.7999 (p) cc_final: 0.7264 (p) REVERT: s 46 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: s 52 GLN cc_start: 0.7519 (mt0) cc_final: 0.7306 (mt0) REVERT: t 37 ASN cc_start: 0.8189 (m-40) cc_final: 0.7227 (t0) REVERT: t 62 GLN cc_start: 0.8738 (tp-100) cc_final: 0.8297 (mm-40) REVERT: u 17 TYR cc_start: 0.8916 (m-80) cc_final: 0.8687 (m-80) REVERT: u 73 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8956 (mm) REVERT: v 93 GLN cc_start: 0.7574 (mm-40) cc_final: 0.6847 (mm-40) REVERT: v 96 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: w 71 LYS cc_start: 0.9090 (mtpt) cc_final: 0.8710 (mtmt) REVERT: x 65 ASN cc_start: 0.8220 (p0) cc_final: 0.7901 (m-40) REVERT: x 66 MET cc_start: 0.7332 (ptp) cc_final: 0.6869 (pmm) REVERT: x 71 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8766 (mm) REVERT: x 80 TYR cc_start: 0.3916 (OUTLIER) cc_final: 0.1781 (t80) REVERT: y 18 GLN cc_start: 0.8658 (mt0) cc_final: 0.8454 (mt0) REVERT: z 3 LYS cc_start: 0.8351 (mtmt) cc_final: 0.8089 (mtmm) REVERT: z 14 TRP cc_start: 0.9055 (t60) cc_final: 0.8757 (t60) REVERT: z 22 ARG cc_start: 0.8255 (ttt-90) cc_final: 0.7425 (ttt-90) REVERT: X 57 GLU cc_start: 0.8266 (tp30) cc_final: 0.7984 (tp30) REVERT: Y 26 ARG cc_start: 0.8149 (tmm160) cc_final: 0.7587 (tmm160) REVERT: Z 1 MET cc_start: 0.5058 (tmm) cc_final: 0.4502 (tmm) REVERT: Z 33 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7946 (mt0) REVERT: Z 43 ILE cc_start: 0.9307 (mm) cc_final: 0.8999 (mm) REVERT: b 37 LYS cc_start: 0.8895 (pttp) cc_final: 0.8552 (mmtm) REVERT: b 39 MET cc_start: 0.7315 (mmm) cc_final: 0.6812 (mtm) REVERT: c 37 ARG cc_start: 0.7089 (mmt180) cc_final: 0.6799 (mmt180) REVERT: c 51 GLU cc_start: 0.7917 (pm20) cc_final: 0.6851 (pm20) REVERT: e 29 LYS cc_start: 0.6448 (tttt) cc_final: 0.6078 (tmmt) REVERT: A 47 LEU cc_start: 0.4658 (OUTLIER) cc_final: 0.4299 (mt) REVERT: A 79 LYS cc_start: 0.2859 (mttt) cc_final: 0.1489 (mptt) REVERT: A 85 GLU cc_start: 0.3839 (tt0) cc_final: 0.3563 (tt0) REVERT: B 7 LYS cc_start: 0.8600 (mmtt) cc_final: 0.8296 (mmtt) REVERT: B 97 TYR cc_start: 0.8673 (m-80) cc_final: 0.8209 (m-10) REVERT: B 112 GLN cc_start: 0.7050 (mp10) cc_final: 0.6524 (mp10) REVERT: B 171 ASP cc_start: 0.8103 (t0) cc_final: 0.7790 (t0) REVERT: B 237 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7138 (pp20) REVERT: C 152 LYS cc_start: 0.8810 (mtpp) cc_final: 0.8330 (tttt) REVERT: C 168 MET cc_start: 0.7332 (mmt) cc_final: 0.6829 (mmt) REVERT: D 7 TYR cc_start: 0.6393 (OUTLIER) cc_final: 0.4884 (t80) REVERT: D 161 GLU cc_start: 0.7602 (tm-30) cc_final: 0.6913 (tm-30) REVERT: D 162 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7938 (mt) REVERT: D 181 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8214 (mt) REVERT: D 205 ARG cc_start: 0.8275 (tmt170) cc_final: 0.7686 (ttt180) REVERT: E 71 THR cc_start: 0.7589 (p) cc_final: 0.7247 (p) REVERT: E 80 PHE cc_start: 0.7268 (OUTLIER) cc_final: 0.6499 (m-80) REVERT: F 86 GLU cc_start: 0.7485 (mm-30) cc_final: 0.6592 (pm20) REVERT: F 121 ILE cc_start: 0.8740 (mp) cc_final: 0.8520 (mt) REVERT: F 139 GLN cc_start: 0.7954 (tp40) cc_final: 0.7560 (tp40) REVERT: G 22 LYS cc_start: 0.8192 (ttmt) cc_final: 0.7803 (ttpt) REVERT: G 23 PRO cc_start: 0.9259 (Cg_exo) cc_final: 0.9042 (Cg_endo) REVERT: J 17 ASP cc_start: 0.8085 (t70) cc_final: 0.7824 (t0) REVERT: J 89 LYS cc_start: 0.8784 (ttmm) cc_final: 0.8505 (ttmm) REVERT: K 13 ASN cc_start: 0.6864 (p0) cc_final: 0.6394 (p0) REVERT: K 70 LYS cc_start: 0.8188 (tttm) cc_final: 0.7933 (ttpp) REVERT: L 7 ARG cc_start: 0.7567 (mmp-170) cc_final: 0.6953 (mmp-170) REVERT: L 102 ARG cc_start: 0.8760 (mtp-110) cc_final: 0.8394 (mtp-110) REVERT: N 43 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7964 (mm-30) REVERT: O 17 ARG cc_start: 0.5725 (mpp-170) cc_final: 0.4444 (mpt180) REVERT: O 84 GLN cc_start: 0.7596 (tp40) cc_final: 0.6648 (tm-30) REVERT: O 93 LYS cc_start: 0.8532 (tptp) cc_final: 0.7656 (tppp) REVERT: O 94 TYR cc_start: 0.8421 (t80) cc_final: 0.7607 (t80) REVERT: P 85 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.6638 (tppt) REVERT: Q 17 ILE cc_start: 0.9459 (mm) cc_final: 0.9207 (mt) REVERT: R 23 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7428 (mt-10) REVERT: R 74 LYS cc_start: 0.8214 (pttm) cc_final: 0.7998 (pttm) REVERT: R 76 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7817 (ptmm) REVERT: R 81 TYR cc_start: 0.6339 (OUTLIER) cc_final: 0.4851 (t80) REVERT: T 29 TRP cc_start: 0.8303 (m100) cc_final: 0.7744 (m100) REVERT: U 35 TYR cc_start: 0.6984 (OUTLIER) cc_final: 0.6722 (t80) REVERT: U 38 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.6567 (mm) REVERT: U 46 LYS cc_start: 0.7567 (mttt) cc_final: 0.6624 (ttmt) REVERT: V 56 VAL cc_start: 0.9229 (t) cc_final: 0.8894 (p) REVERT: V 77 ASP cc_start: 0.6788 (t0) cc_final: 0.6340 (p0) REVERT: V 87 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7192 (p0) REVERT: 5 47 ARG cc_start: 0.6666 (tpp-160) cc_final: 0.5779 (tmm-80) REVERT: 5 108 ASN cc_start: 0.7550 (p0) cc_final: 0.6974 (p0) REVERT: 5 130 ARG cc_start: 0.7531 (mtm180) cc_final: 0.7176 (mtm-85) outliers start: 344 outliers final: 280 residues processed: 1653 average time/residue: 1.4977 time to fit residues: 4277.7685 Evaluate side-chains 1724 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 1416 time to evaluate : 6.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 15 VAL Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain g residue 113 HIS Chi-restraints excluded: chain g residue 165 VAL Chi-restraints excluded: chain g residue 185 ILE Chi-restraints excluded: chain g residue 187 LEU Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain i residue 4 TYR Chi-restraints excluded: chain i residue 5 ILE Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain i residue 137 SER Chi-restraints excluded: chain i residue 158 ILE Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 36 ASP Chi-restraints excluded: chain j residue 67 VAL Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 115 VAL Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain j residue 120 THR Chi-restraints excluded: chain j residue 147 ASP Chi-restraints excluded: chain k residue 15 ASP Chi-restraints excluded: chain k residue 19 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 98 LEU Chi-restraints excluded: chain l residue 12 LEU Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 84 ASN Chi-restraints excluded: chain l residue 118 VAL Chi-restraints excluded: chain l residue 141 VAL Chi-restraints excluded: chain l residue 151 TYR Chi-restraints excluded: chain m residue 19 VAL Chi-restraints excluded: chain m residue 35 ILE Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 100 ILE Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 120 THR Chi-restraints excluded: chain m residue 123 GLU Chi-restraints excluded: chain n residue 4 TYR Chi-restraints excluded: chain n residue 16 ARG Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain n residue 103 THR Chi-restraints excluded: chain o residue 14 LYS Chi-restraints excluded: chain o residue 23 ILE Chi-restraints excluded: chain o residue 24 VAL Chi-restraints excluded: chain o residue 47 PHE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 GLN Chi-restraints excluded: chain p residue 25 TYR Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 75 TYR Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 87 THR Chi-restraints excluded: chain p residue 114 VAL Chi-restraints excluded: chain q residue 7 ILE Chi-restraints excluded: chain q residue 22 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 37 CYS Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 93 LEU Chi-restraints excluded: chain q residue 122 THR Chi-restraints excluded: chain r residue 12 ASN Chi-restraints excluded: chain r residue 17 VAL Chi-restraints excluded: chain r residue 32 GLU Chi-restraints excluded: chain r residue 86 CYS Chi-restraints excluded: chain r residue 103 THR Chi-restraints excluded: chain s residue 16 PHE Chi-restraints excluded: chain s residue 36 PHE Chi-restraints excluded: chain s residue 37 PHE Chi-restraints excluded: chain s residue 46 GLU Chi-restraints excluded: chain s residue 60 SER Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 45 THR Chi-restraints excluded: chain u residue 68 ASP Chi-restraints excluded: chain u residue 69 THR Chi-restraints excluded: chain u residue 73 LEU Chi-restraints excluded: chain v residue 5 VAL Chi-restraints excluded: chain v residue 35 VAL Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 46 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 90 ILE Chi-restraints excluded: chain v residue 96 GLU Chi-restraints excluded: chain w residue 36 ASN Chi-restraints excluded: chain w residue 39 VAL Chi-restraints excluded: chain x residue 31 ILE Chi-restraints excluded: chain x residue 41 VAL Chi-restraints excluded: chain x residue 71 LEU Chi-restraints excluded: chain x residue 80 TYR Chi-restraints excluded: chain y residue 26 ASN Chi-restraints excluded: chain y residue 31 SER Chi-restraints excluded: chain y residue 36 LEU Chi-restraints excluded: chain y residue 85 MET Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain y residue 104 LEU Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 18 ILE Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 37 ILE Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 47 ASN Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 42 PHE Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain b residue 13 LYS Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 62 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 112 GLU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 32 TYR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 43 GLN Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 85 LYS Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 60 GLU Chi-restraints excluded: chain R residue 81 TYR Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 26 TYR Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain U residue 35 TYR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain V residue 23 LYS Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 54 HIS Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain 5 residue 8 ARG Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 5 residue 40 ASP Chi-restraints excluded: chain 5 residue 72 ASP Chi-restraints excluded: chain 5 residue 81 LEU Chi-restraints excluded: chain 5 residue 117 LEU Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 133 LYS Chi-restraints excluded: chain 5 residue 137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 950 optimal weight: 2.9990 chunk 1000 optimal weight: 9.9990 chunk 913 optimal weight: 7.9990 chunk 973 optimal weight: 0.9980 chunk 586 optimal weight: 10.0000 chunk 424 optimal weight: 5.9990 chunk 764 optimal weight: 1.9990 chunk 298 optimal weight: 0.9980 chunk 879 optimal weight: 5.9990 chunk 920 optimal weight: 2.9990 chunk 970 optimal weight: 10.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 38 GLN ** j 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 117 ASN v 94 ASN w 63 GLN y 42 GLN ** X 19 GLN ** 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 180 ASN ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN L 70 GLN O 16 ASN ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS T 41 ASN ** T 87 GLN ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.573 167513 Z= 0.266 Angle : 0.834 103.300 250789 Z= 0.382 Chirality : 0.036 0.339 31882 Planarity : 0.006 0.204 13445 Dihedral : 25.942 179.053 85257 Min Nonbonded Distance : 1.061 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.50 % Allowed : 15.75 % Favored : 83.75 % Rotamer: Outliers : 6.47 % Allowed : 30.30 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.49 % 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: -3.25 (0.11), residues: 5779 helix: -0.77 (0.13), residues: 1648 sheet: -2.33 (0.17), residues: 901 loop : -2.98 (0.10), residues: 3230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP m 138 HIS 0.019 0.001 HIS L 128 PHE 0.041 0.002 PHE i 93 TYR 0.019 0.002 TYR p 59 ARG 0.009 0.001 ARG Z 55 *********************** 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 1772 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1462 time to evaluate : 6.530 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: g 28 PHE cc_start: 0.8674 (t80) cc_final: 0.8282 (t80) REVERT: g 49 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7298 (mm-30) REVERT: g 113 HIS cc_start: 0.8494 (OUTLIER) cc_final: 0.7382 (m-70) REVERT: g 169 LYS cc_start: 0.8024 (tppt) cc_final: 0.7488 (mmtm) REVERT: h 5 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8080 (pt) REVERT: h 17 ASP cc_start: 0.7669 (p0) cc_final: 0.7390 (p0) REVERT: h 54 ARG cc_start: 0.7559 (ptp90) cc_final: 0.7163 (ptp90) REVERT: h 123 GLN cc_start: 0.8576 (mm110) cc_final: 0.8173 (mp10) REVERT: h 125 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7284 (mt-10) REVERT: h 136 GLN cc_start: 0.7760 (tm-30) cc_final: 0.6923 (tp-100) REVERT: i 42 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8341 (tm-30) REVERT: i 76 ARG cc_start: 0.8567 (ttt-90) cc_final: 0.8303 (ttt90) REVERT: i 101 LEU cc_start: 0.8691 (tp) cc_final: 0.8371 (tp) REVERT: i 138 TYR cc_start: 0.9009 (t80) cc_final: 0.8543 (t80) REVERT: j 118 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8702 (tp) REVERT: j 127 ASN cc_start: 0.8773 (t0) cc_final: 0.8379 (t0) REVERT: k 1 MET cc_start: 0.6658 (tpp) cc_final: 0.6334 (tpp) REVERT: k 33 TYR cc_start: 0.8382 (m-80) cc_final: 0.8103 (m-10) REVERT: k 59 TYR cc_start: 0.6969 (t80) cc_final: 0.6677 (t80) REVERT: k 69 GLU cc_start: 0.7096 (pp20) cc_final: 0.6231 (pp20) REVERT: k 86 ARG cc_start: 0.6609 (mtt90) cc_final: 0.6199 (mtt90) REVERT: l 144 MET cc_start: 0.8012 (tpp) cc_final: 0.7526 (tpp) REVERT: m 48 TYR cc_start: 0.8665 (p90) cc_final: 0.7727 (p90) REVERT: m 78 GLN cc_start: 0.7202 (mt0) cc_final: 0.6707 (mt0) REVERT: m 123 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: n 4 TYR cc_start: 0.6949 (OUTLIER) cc_final: 0.5740 (m-80) REVERT: n 38 GLN cc_start: 0.8078 (tt0) cc_final: 0.7736 (tp40) REVERT: n 42 ARG cc_start: 0.7401 (ttp-170) cc_final: 0.6559 (tmm160) REVERT: n 121 ARG cc_start: 0.7532 (tpt-90) cc_final: 0.7327 (tpt90) REVERT: o 29 ARG cc_start: 0.5880 (mtp-110) cc_final: 0.5258 (mtt-85) REVERT: o 84 GLN cc_start: 0.6343 (OUTLIER) cc_final: 0.5152 (mp10) REVERT: p 20 TYR cc_start: 0.8241 (m-80) cc_final: 0.7970 (m-80) REVERT: p 25 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.6983 (m-80) REVERT: p 75 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7249 (m-10) REVERT: p 116 HIS cc_start: 0.7774 (m170) cc_final: 0.7339 (m-70) REVERT: s 4 LYS cc_start: 0.8852 (tppt) cc_final: 0.8283 (tptp) REVERT: s 35 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7895 (tpp80) REVERT: s 36 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7706 (t80) REVERT: s 37 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8392 (m-80) REVERT: s 40 CYS cc_start: 0.7932 (p) cc_final: 0.7236 (p) REVERT: t 37 ASN cc_start: 0.8315 (m-40) cc_final: 0.7396 (t0) REVERT: u 17 TYR cc_start: 0.8878 (m-80) cc_final: 0.8629 (m-80) REVERT: u 73 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8919 (mm) REVERT: v 93 GLN cc_start: 0.7570 (mm-40) cc_final: 0.7292 (mm-40) REVERT: w 23 LYS cc_start: 0.6952 (tttp) cc_final: 0.6504 (tttt) REVERT: w 61 LYS cc_start: 0.8686 (tttp) cc_final: 0.8471 (ttmt) REVERT: w 71 LYS cc_start: 0.9103 (mtpt) cc_final: 0.8784 (mtmt) REVERT: x 66 MET cc_start: 0.7295 (ptp) cc_final: 0.6902 (pmm) REVERT: x 71 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8678 (mm) REVERT: x 80 TYR cc_start: 0.3879 (OUTLIER) cc_final: 0.1924 (t80) REVERT: z 14 TRP cc_start: 0.9075 (t60) cc_final: 0.8789 (t60) REVERT: z 22 ARG cc_start: 0.8233 (ttt-90) cc_final: 0.7408 (ttt-90) REVERT: W 60 PHE cc_start: 0.8952 (p90) cc_final: 0.8596 (p90) REVERT: X 57 GLU cc_start: 0.8325 (tp30) cc_final: 0.7986 (tp30) REVERT: Y 26 ARG cc_start: 0.8177 (tmm160) cc_final: 0.7681 (tmm160) REVERT: Y 33 MET cc_start: 0.6607 (mmm) cc_final: 0.6285 (mtt) REVERT: Y 34 GLU cc_start: 0.6198 (pm20) cc_final: 0.5506 (pm20) REVERT: Z 1 MET cc_start: 0.5027 (tmm) cc_final: 0.4340 (tmm) REVERT: Z 33 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: Z 43 ILE cc_start: 0.9344 (mm) cc_final: 0.9076 (mm) REVERT: b 37 LYS cc_start: 0.8865 (pttp) cc_final: 0.8452 (mmtm) REVERT: b 39 MET cc_start: 0.7164 (mmm) cc_final: 0.6899 (mtm) REVERT: c 36 LEU cc_start: 0.7292 (pt) cc_final: 0.6480 (mt) REVERT: c 51 GLU cc_start: 0.7879 (pm20) cc_final: 0.6842 (pm20) REVERT: e 29 LYS cc_start: 0.6283 (tttt) cc_final: 0.5924 (tmmt) REVERT: e 43 GLN cc_start: 0.7435 (mt0) cc_final: 0.7233 (mt0) REVERT: A 24 GLU cc_start: 0.6180 (mt-10) cc_final: 0.5945 (mt-10) REVERT: A 47 LEU cc_start: 0.4684 (OUTLIER) cc_final: 0.4330 (mt) REVERT: A 79 LYS cc_start: 0.3029 (mttt) cc_final: 0.1580 (mptt) REVERT: A 85 GLU cc_start: 0.3787 (tt0) cc_final: 0.3496 (tt0) REVERT: B 7 LYS cc_start: 0.8587 (mmtt) cc_final: 0.8286 (mmtt) REVERT: B 112 GLN cc_start: 0.7043 (mp10) cc_final: 0.6525 (mp10) REVERT: B 171 ASP cc_start: 0.8101 (t0) cc_final: 0.7833 (t0) REVERT: B 237 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7272 (pp20) REVERT: C 152 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8476 (tttp) REVERT: C 168 MET cc_start: 0.7272 (mmt) cc_final: 0.6873 (mmt) REVERT: C 181 LEU cc_start: 0.9253 (mt) cc_final: 0.9001 (mt) REVERT: D 7 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.4892 (t80) REVERT: D 161 GLU cc_start: 0.7580 (tm-30) cc_final: 0.6908 (tm-30) REVERT: D 162 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7822 (mt) REVERT: D 205 ARG cc_start: 0.8265 (tmt170) cc_final: 0.7761 (ttt180) REVERT: E 29 TRP cc_start: 0.8247 (m100) cc_final: 0.7813 (m100) REVERT: E 71 THR cc_start: 0.7267 (p) cc_final: 0.6935 (p) REVERT: E 80 PHE cc_start: 0.7137 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: F 121 ILE cc_start: 0.8711 (mp) cc_final: 0.8490 (mt) REVERT: F 139 GLN cc_start: 0.7891 (tp40) cc_final: 0.7532 (tp40) REVERT: G 22 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7830 (ttpt) REVERT: J 17 ASP cc_start: 0.7970 (t70) cc_final: 0.7717 (t0) REVERT: J 33 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8994 (mp) REVERT: J 89 LYS cc_start: 0.8816 (ttmm) cc_final: 0.8595 (ttmm) REVERT: K 13 ASN cc_start: 0.6796 (p0) cc_final: 0.6381 (p0) REVERT: K 38 VAL cc_start: 0.9272 (t) cc_final: 0.9001 (p) REVERT: K 70 LYS cc_start: 0.8149 (tttm) cc_final: 0.7901 (ttpp) REVERT: L 7 ARG cc_start: 0.7536 (mmp-170) cc_final: 0.6964 (mmp-170) REVERT: L 102 ARG cc_start: 0.8835 (mtp-110) cc_final: 0.8418 (mtp-110) REVERT: N 43 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7916 (mm-30) REVERT: O 17 ARG cc_start: 0.6103 (mpp-170) cc_final: 0.4871 (mpt180) REVERT: O 67 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7764 (mtm-85) REVERT: O 84 GLN cc_start: 0.7607 (tp40) cc_final: 0.6782 (tm-30) REVERT: O 93 LYS cc_start: 0.8561 (tptp) cc_final: 0.7629 (tppp) REVERT: O 94 TYR cc_start: 0.8386 (t80) cc_final: 0.7598 (t80) REVERT: P 1 MET cc_start: 0.5132 (ptt) cc_final: 0.4901 (ptm) REVERT: Q 17 ILE cc_start: 0.9397 (mm) cc_final: 0.9177 (mt) REVERT: Q 34 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8620 (mmmt) REVERT: R 23 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7493 (mt-10) REVERT: R 76 LYS cc_start: 0.8195 (ttpt) cc_final: 0.7804 (ptmm) REVERT: R 81 TYR cc_start: 0.6120 (OUTLIER) cc_final: 0.4782 (t80) REVERT: T 29 TRP cc_start: 0.8330 (m100) cc_final: 0.7782 (m100) REVERT: U 38 ILE cc_start: 0.7205 (OUTLIER) cc_final: 0.6363 (mm) REVERT: U 46 LYS cc_start: 0.7512 (mttt) cc_final: 0.6525 (ttmt) REVERT: V 56 VAL cc_start: 0.9190 (t) cc_final: 0.8853 (p) REVERT: V 77 ASP cc_start: 0.6752 (t0) cc_final: 0.6258 (p0) REVERT: V 87 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7124 (p0) REVERT: 5 18 GLU cc_start: 0.6708 (pm20) cc_final: 0.6387 (pm20) REVERT: 5 47 ARG cc_start: 0.6676 (tpp-160) cc_final: 0.5690 (tmm-80) REVERT: 5 108 ASN cc_start: 0.7266 (p0) cc_final: 0.6758 (p0) REVERT: 5 130 ARG cc_start: 0.7469 (mtm180) cc_final: 0.7077 (mtm-85) REVERT: f 18 ARG cc_start: 0.8342 (tmm-80) cc_final: 0.7922 (ttp80) REVERT: f 36 GLN cc_start: 0.8372 (tt0) cc_final: 0.8112 (tt0) outliers start: 310 outliers final: 254 residues processed: 1623 average time/residue: 1.3977 time to fit residues: 3872.6693 Evaluate side-chains 1689 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1412 time to evaluate : 8.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain g residue 113 HIS Chi-restraints excluded: chain g residue 165 VAL Chi-restraints excluded: chain g residue 185 ILE Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain i residue 4 TYR Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain i residue 71 SER Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain i residue 127 THR Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain i residue 137 SER Chi-restraints excluded: chain i residue 158 ILE Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 36 ASP Chi-restraints excluded: chain j residue 67 VAL Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 115 VAL Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain j residue 118 ILE Chi-restraints excluded: chain j residue 120 THR Chi-restraints excluded: chain j residue 147 ASP Chi-restraints excluded: chain k residue 15 ASP Chi-restraints excluded: chain k residue 19 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 98 LEU Chi-restraints excluded: chain l residue 16 LEU Chi-restraints excluded: chain l residue 17 VAL Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 84 ASN Chi-restraints excluded: chain l residue 141 VAL Chi-restraints excluded: chain l residue 151 TYR Chi-restraints excluded: chain m residue 35 ILE Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 100 ILE Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 120 THR Chi-restraints excluded: chain m residue 123 GLU Chi-restraints excluded: chain n residue 4 TYR Chi-restraints excluded: chain n residue 16 ARG Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain o residue 23 ILE Chi-restraints excluded: chain o residue 24 VAL Chi-restraints excluded: chain o residue 47 PHE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 71 LEU Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 GLN Chi-restraints excluded: chain p residue 25 TYR Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 75 TYR Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 87 THR Chi-restraints excluded: chain p residue 114 VAL Chi-restraints excluded: chain p residue 117 ASN Chi-restraints excluded: chain q residue 22 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 37 CYS Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 93 LEU Chi-restraints excluded: chain q residue 122 THR Chi-restraints excluded: chain r residue 12 ASN Chi-restraints excluded: chain r residue 86 CYS Chi-restraints excluded: chain r residue 103 THR Chi-restraints excluded: chain s residue 16 PHE Chi-restraints excluded: chain s residue 36 PHE Chi-restraints excluded: chain s residue 37 PHE Chi-restraints excluded: chain s residue 46 GLU Chi-restraints excluded: chain s residue 60 SER Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 68 ASP Chi-restraints excluded: chain u residue 69 THR Chi-restraints excluded: chain u residue 73 LEU Chi-restraints excluded: chain v residue 5 VAL Chi-restraints excluded: chain v residue 35 VAL Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 46 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 90 ILE Chi-restraints excluded: chain w residue 36 ASN Chi-restraints excluded: chain w residue 39 VAL Chi-restraints excluded: chain w residue 59 SER Chi-restraints excluded: chain x residue 31 ILE Chi-restraints excluded: chain x residue 41 VAL Chi-restraints excluded: chain x residue 71 LEU Chi-restraints excluded: chain x residue 80 TYR Chi-restraints excluded: chain y residue 10 LEU Chi-restraints excluded: chain y residue 26 ASN Chi-restraints excluded: chain y residue 31 SER Chi-restraints excluded: chain y residue 36 LEU Chi-restraints excluded: chain y residue 85 MET Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain Y residue 47 ASN Chi-restraints excluded: chain Z residue 33 GLN Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 42 PHE Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain b residue 13 LYS Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 GLU Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 47 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 134 ARG Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 91 GLN Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 32 TYR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 80 ILE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 60 GLU Chi-restraints excluded: chain R residue 81 TYR Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 26 TYR Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain V residue 23 LYS Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 87 ASP Chi-restraints excluded: chain 5 residue 8 ARG Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 5 residue 40 ASP Chi-restraints excluded: chain 5 residue 72 ASP Chi-restraints excluded: chain 5 residue 81 LEU Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 133 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 639 optimal weight: 6.9990 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: 0.8980 chunk 859 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 664 optimal weight: 7.9990 chunk 527 optimal weight: 6.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- 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 77 ASN ** i 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 82 HIS ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 77 ASN u 76 GLN ** w 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 46 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN D 40 GLN D 182 ASN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 16 ASN ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 ASN T 55 ASN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 82 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.573 167513 Z= 0.537 Angle : 1.033 103.387 250789 Z= 0.482 Chirality : 0.046 0.424 31882 Planarity : 0.008 0.201 13445 Dihedral : 26.139 179.780 85257 Min Nonbonded Distance : 0.974 Molprobity Statistics. All-atom Clashscore : 25.89 Ramachandran Plot: Outliers : 0.62 % Allowed : 17.70 % Favored : 81.68 % Rotamer: Outliers : 6.83 % Allowed : 29.90 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % 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: -3.63 (0.10), residues: 5779 helix: -1.19 (0.12), residues: 1657 sheet: -2.50 (0.16), residues: 907 loop : -3.17 (0.10), residues: 3215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP m 138 HIS 0.019 0.002 HIS p 116 PHE 0.039 0.003 PHE i 93 TYR 0.032 0.003 TYR x 80 ARG 0.011 0.001 ARG Z 55 ********************** 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 1760 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 1433 time to evaluate : 6.476 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: g 28 PHE cc_start: 0.8781 (t80) cc_final: 0.8425 (t80) REVERT: g 49 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7468 (mm-30) REVERT: g 113 HIS cc_start: 0.8518 (OUTLIER) cc_final: 0.8004 (m-70) REVERT: g 169 LYS cc_start: 0.7747 (tppt) cc_final: 0.7395 (mmtm) REVERT: g 187 LEU cc_start: 0.7684 (tt) cc_final: 0.7374 (mt) REVERT: h 5 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8453 (pt) REVERT: h 54 ARG cc_start: 0.7505 (ptp90) cc_final: 0.6954 (ptp90) REVERT: h 123 GLN cc_start: 0.8527 (mm110) cc_final: 0.8027 (mp10) REVERT: h 136 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7574 (tp-100) REVERT: h 142 MET cc_start: 0.7317 (mmp) cc_final: 0.7102 (mmp) REVERT: i 42 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8241 (tm-30) REVERT: i 77 ASN cc_start: 0.8345 (m110) cc_final: 0.8088 (m-40) REVERT: i 101 LEU cc_start: 0.8952 (tp) cc_final: 0.8589 (tp) REVERT: i 103 ASN cc_start: 0.8907 (t0) cc_final: 0.8616 (t0) REVERT: i 138 TYR cc_start: 0.9084 (t80) cc_final: 0.8559 (t80) REVERT: j 118 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8771 (tp) REVERT: j 127 ASN cc_start: 0.8895 (t0) cc_final: 0.8665 (t0) REVERT: k 33 TYR cc_start: 0.8436 (m-80) cc_final: 0.8138 (m-10) REVERT: k 54 LYS cc_start: 0.7826 (mtmm) cc_final: 0.7616 (mtpt) REVERT: l 126 ASP cc_start: 0.7255 (m-30) cc_final: 0.7035 (m-30) REVERT: m 123 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: n 4 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.5852 (m-80) REVERT: n 34 ASN cc_start: 0.7336 (m-40) cc_final: 0.7077 (m-40) REVERT: n 38 GLN cc_start: 0.8073 (tt0) cc_final: 0.7752 (tp40) REVERT: o 84 GLN cc_start: 0.6451 (OUTLIER) cc_final: 0.5605 (mp10) REVERT: p 25 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7054 (m-80) REVERT: p 75 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7661 (m-10) REVERT: p 116 HIS cc_start: 0.7595 (m170) cc_final: 0.7256 (m-70) REVERT: r 58 GLU cc_start: 0.7745 (pp20) cc_final: 0.7205 (pp20) REVERT: r 82 MET cc_start: 0.5749 (ttt) cc_final: 0.5515 (ttt) REVERT: r 94 ARG cc_start: 0.6510 (ttm-80) cc_final: 0.6236 (ttm110) REVERT: s 4 LYS cc_start: 0.8931 (tppt) cc_final: 0.8343 (tptp) REVERT: s 36 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7990 (t80) REVERT: s 37 PHE cc_start: 0.8830 (OUTLIER) cc_final: 0.8465 (m-80) REVERT: s 46 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: t 37 ASN cc_start: 0.8407 (m-40) cc_final: 0.7460 (t0) REVERT: u 12 LYS cc_start: 0.9048 (mtmt) cc_final: 0.8738 (mttt) REVERT: u 73 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9009 (mm) REVERT: w 23 LYS cc_start: 0.6931 (tttp) cc_final: 0.6516 (tttt) REVERT: w 61 LYS cc_start: 0.8692 (tttp) cc_final: 0.8459 (ttmt) REVERT: w 71 LYS cc_start: 0.9086 (mtpt) cc_final: 0.8677 (mtmt) REVERT: x 66 MET cc_start: 0.7416 (ptp) cc_final: 0.6933 (pmm) REVERT: x 71 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8835 (mm) REVERT: x 80 TYR cc_start: 0.4412 (OUTLIER) cc_final: 0.2146 (t80) REVERT: y 25 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8010 (ttp-110) REVERT: y 42 GLN cc_start: 0.7748 (tp40) cc_final: 0.7487 (tp40) REVERT: z 14 TRP cc_start: 0.9055 (t60) cc_final: 0.8756 (t60) REVERT: z 21 TYR cc_start: 0.7497 (m-80) cc_final: 0.7254 (m-80) REVERT: z 22 ARG cc_start: 0.8073 (ttt-90) cc_final: 0.7110 (ttt-90) REVERT: Y 26 ARG cc_start: 0.8201 (tmm160) cc_final: 0.7792 (tmm160) REVERT: Y 33 MET cc_start: 0.7264 (mmm) cc_final: 0.6619 (mtt) REVERT: Z 1 MET cc_start: 0.4663 (tmm) cc_final: 0.4317 (tmm) REVERT: Z 43 ILE cc_start: 0.9305 (mm) cc_final: 0.9007 (mm) REVERT: b 37 LYS cc_start: 0.8854 (pttp) cc_final: 0.8555 (mmpt) REVERT: b 39 MET cc_start: 0.7488 (mmm) cc_final: 0.7007 (mtm) REVERT: c 37 ARG cc_start: 0.7147 (mmt180) cc_final: 0.6893 (mmt180) REVERT: c 51 GLU cc_start: 0.7850 (pm20) cc_final: 0.6845 (pm20) REVERT: e 26 LYS cc_start: 0.8576 (mmmt) cc_final: 0.7852 (mtmt) REVERT: e 29 LYS cc_start: 0.7138 (tttt) cc_final: 0.6805 (tmtt) REVERT: A 47 LEU cc_start: 0.4541 (OUTLIER) cc_final: 0.4324 (mt) REVERT: A 79 LYS cc_start: 0.2541 (mttt) cc_final: 0.1577 (mptt) REVERT: B 7 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8317 (mmtt) REVERT: B 97 TYR cc_start: 0.8843 (m-80) cc_final: 0.8556 (m-10) REVERT: B 112 GLN cc_start: 0.7039 (mp10) cc_final: 0.6509 (mp10) REVERT: B 171 ASP cc_start: 0.8158 (t0) cc_final: 0.7786 (t0) REVERT: B 237 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7518 (pp20) REVERT: C 103 ASP cc_start: 0.7630 (m-30) cc_final: 0.6809 (m-30) REVERT: C 168 MET cc_start: 0.7410 (mmt) cc_final: 0.6642 (mmp) REVERT: D 7 TYR cc_start: 0.6674 (OUTLIER) cc_final: 0.5136 (t80) REVERT: D 161 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7050 (tm-30) REVERT: D 205 ARG cc_start: 0.8340 (tmt170) cc_final: 0.7834 (ttt180) REVERT: E 71 THR cc_start: 0.7694 (p) cc_final: 0.7352 (p) REVERT: E 80 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.6565 (m-80) REVERT: F 86 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6514 (pm20) REVERT: F 121 ILE cc_start: 0.8848 (mp) cc_final: 0.8600 (mt) REVERT: F 139 GLN cc_start: 0.7955 (tp40) cc_final: 0.7585 (tp40) REVERT: F 140 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7864 (mtpt) REVERT: G 22 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7986 (ttpt) REVERT: G 35 LEU cc_start: 0.8065 (mt) cc_final: 0.7792 (mp) REVERT: J 17 ASP cc_start: 0.8078 (t70) cc_final: 0.7862 (t0) REVERT: K 9 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6768 (tp30) REVERT: K 13 ASN cc_start: 0.6877 (p0) cc_final: 0.6517 (p0) REVERT: L 7 ARG cc_start: 0.7602 (mmp-170) cc_final: 0.7002 (mmp-170) REVERT: L 102 ARG cc_start: 0.8763 (mtp-110) cc_final: 0.8387 (mtp-110) REVERT: M 83 MET cc_start: 0.5683 (OUTLIER) cc_final: 0.5328 (mpp) REVERT: N 4 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6791 (tm) REVERT: N 18 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8609 (tt) REVERT: O 84 GLN cc_start: 0.7632 (tp40) cc_final: 0.6791 (tm-30) REVERT: O 93 LYS cc_start: 0.8491 (tptp) cc_final: 0.7620 (tppp) REVERT: O 94 TYR cc_start: 0.8496 (t80) cc_final: 0.7860 (t80) REVERT: P 29 ARG cc_start: 0.6634 (OUTLIER) cc_final: 0.5968 (mmp80) REVERT: P 32 TYR cc_start: 0.5967 (OUTLIER) cc_final: 0.4448 (p90) REVERT: P 85 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7011 (tppt) REVERT: Q 17 ILE cc_start: 0.9573 (mm) cc_final: 0.9357 (mt) REVERT: Q 38 THR cc_start: 0.8865 (m) cc_final: 0.8413 (m) REVERT: R 76 LYS cc_start: 0.8321 (ttpt) cc_final: 0.7902 (ptmm) REVERT: R 81 TYR cc_start: 0.6742 (OUTLIER) cc_final: 0.5159 (t80) REVERT: T 29 TRP cc_start: 0.8375 (m100) cc_final: 0.7643 (m100) REVERT: T 54 VAL cc_start: 0.8833 (t) cc_final: 0.8567 (p) REVERT: U 38 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.6766 (mm) REVERT: U 46 LYS cc_start: 0.7670 (mttt) cc_final: 0.6610 (ttmt) REVERT: V 56 VAL cc_start: 0.9328 (t) cc_final: 0.8963 (p) REVERT: V 77 ASP cc_start: 0.6849 (t0) cc_final: 0.6222 (p0) REVERT: 5 108 ASN cc_start: 0.7830 (p0) cc_final: 0.7138 (p0) REVERT: 5 109 GLU cc_start: 0.6557 (pm20) cc_final: 0.6202 (pm20) REVERT: 5 130 ARG cc_start: 0.7522 (mtm180) cc_final: 0.7145 (mtm-85) outliers start: 327 outliers final: 270 residues processed: 1618 average time/residue: 1.3866 time to fit residues: 3846.4938 Evaluate side-chains 1711 residues out of total 4902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1413 time to evaluate : 6.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 103 THR Chi-restraints excluded: chain g residue 113 HIS Chi-restraints excluded: chain g residue 140 HIS Chi-restraints excluded: chain g residue 165 VAL Chi-restraints excluded: chain g residue 185 ILE Chi-restraints excluded: chain g residue 215 LEU Chi-restraints excluded: chain g residue 230 VAL Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 62 ASP Chi-restraints excluded: chain h residue 64 VAL Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain i residue 4 TYR Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain i residue 71 SER Chi-restraints excluded: chain i residue 88 VAL Chi-restraints excluded: chain i residue 131 ARG Chi-restraints excluded: chain i residue 137 SER Chi-restraints excluded: chain i residue 158 ILE Chi-restraints excluded: chain i residue 193 ASP Chi-restraints excluded: chain j residue 32 VAL Chi-restraints excluded: chain j residue 36 ASP Chi-restraints excluded: chain j residue 67 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 98 THR Chi-restraints excluded: chain j residue 115 VAL Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain j residue 118 ILE Chi-restraints excluded: chain j residue 120 THR Chi-restraints excluded: chain j residue 147 ASP Chi-restraints excluded: chain k residue 15 ASP Chi-restraints excluded: chain k residue 19 LEU Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain k residue 83 ASP Chi-restraints excluded: chain k residue 98 LEU Chi-restraints excluded: chain l residue 16 LEU Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 84 ASN Chi-restraints excluded: chain l residue 141 VAL Chi-restraints excluded: chain l residue 151 TYR Chi-restraints excluded: chain m residue 35 ILE Chi-restraints excluded: chain m residue 87 SER Chi-restraints excluded: chain m residue 93 VAL Chi-restraints excluded: chain m residue 97 VAL Chi-restraints excluded: chain m residue 100 ILE Chi-restraints excluded: chain m residue 113 SER Chi-restraints excluded: chain m residue 114 THR Chi-restraints excluded: chain m residue 120 THR Chi-restraints excluded: chain m residue 123 GLU Chi-restraints excluded: chain n residue 4 TYR Chi-restraints excluded: chain n residue 16 ARG Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain n residue 103 THR Chi-restraints excluded: chain o residue 23 ILE Chi-restraints excluded: chain o residue 24 VAL Chi-restraints excluded: chain o residue 47 PHE Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain o residue 84 GLN Chi-restraints excluded: chain o residue 96 ILE Chi-restraints excluded: chain p residue 25 TYR Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 33 THR Chi-restraints excluded: chain p residue 75 TYR Chi-restraints excluded: chain p residue 84 VAL Chi-restraints excluded: chain p residue 87 THR Chi-restraints excluded: chain p residue 114 VAL Chi-restraints excluded: chain q residue 7 ILE Chi-restraints excluded: chain q residue 22 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 52 LEU Chi-restraints excluded: chain q residue 93 LEU Chi-restraints excluded: chain q residue 122 THR Chi-restraints excluded: chain r residue 12 ASN Chi-restraints excluded: chain r residue 17 VAL Chi-restraints excluded: chain r residue 32 GLU Chi-restraints excluded: chain r residue 70 LEU Chi-restraints excluded: chain r residue 86 CYS Chi-restraints excluded: chain r residue 103 THR Chi-restraints excluded: chain s residue 36 PHE Chi-restraints excluded: chain s residue 37 PHE Chi-restraints excluded: chain s residue 46 GLU Chi-restraints excluded: chain s residue 60 SER Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 44 THR Chi-restraints excluded: chain u residue 45 THR Chi-restraints excluded: chain u residue 68 ASP Chi-restraints excluded: chain u residue 69 THR Chi-restraints excluded: chain u residue 73 LEU Chi-restraints excluded: chain v residue 5 VAL Chi-restraints excluded: chain v residue 35 VAL Chi-restraints excluded: chain v residue 36 ILE Chi-restraints excluded: chain v residue 46 ASP Chi-restraints excluded: chain v residue 60 ILE Chi-restraints excluded: chain v residue 90 ILE Chi-restraints excluded: chain w residue 39 VAL Chi-restraints excluded: chain w residue 59 SER Chi-restraints excluded: chain x residue 41 VAL Chi-restraints excluded: chain x residue 71 LEU Chi-restraints excluded: chain x residue 80 TYR Chi-restraints excluded: chain y residue 25 ARG Chi-restraints excluded: chain y residue 26 ASN Chi-restraints excluded: chain y residue 31 SER Chi-restraints excluded: chain y residue 36 LEU Chi-restraints excluded: chain y residue 85 MET Chi-restraints excluded: chain y residue 91 LEU Chi-restraints excluded: chain z residue 17 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain X residue 13 ILE Chi-restraints excluded: chain X residue 18 ILE Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 46 LEU Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain X residue 94 LEU Chi-restraints excluded: chain Y residue 47 ASN Chi-restraints excluded: chain Y residue 51 ARG Chi-restraints excluded: chain a residue 24 THR Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 42 PHE Chi-restraints excluded: chain a residue 59 PHE Chi-restraints excluded: chain b residue 13 LYS Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 57 VAL Chi-restraints excluded: chain c residue 14 THR Chi-restraints excluded: chain c residue 30 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 237 GLU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 35 GLN Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 70 VAL Chi-restraints excluded: chain E residue 80 PHE Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 99 MET Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 132 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 80 SER Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 4 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 38 HIS Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 50 ASP Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 60 ILE Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 9 GLU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 GLU Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain M residue 13 GLN Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 29 PHE Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 89 ASN Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 109 VAL Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 59 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 29 ARG Chi-restraints excluded: chain P residue 32 TYR Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain P residue 44 ASP Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 85 LYS Chi-restraints excluded: chain P residue 107 ASP Chi-restraints excluded: chain Q residue 18 LEU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 37 VAL Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 60 GLU Chi-restraints excluded: chain R residue 81 TYR Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 103 ILE Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain T residue 12 VAL Chi-restraints excluded: chain T residue 26 TYR Chi-restraints excluded: chain T residue 56 THR Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain V residue 23 LYS Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 69 THR Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain 5 residue 8 ARG Chi-restraints excluded: chain 5 residue 39 VAL Chi-restraints excluded: chain 5 residue 40 ASP Chi-restraints excluded: chain 5 residue 72 ASP Chi-restraints excluded: chain 5 residue 81 LEU Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 119 LEU Chi-restraints excluded: chain 5 residue 133 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1084 random chunks: chunk 683 optimal weight: 2.9990 chunk 916 optimal weight: 0.0670 chunk 263 optimal weight: 0.5980 chunk 792 optimal weight: 0.3980 chunk 126 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 861 optimal weight: 0.9990 chunk 360 optimal weight: 0.7980 chunk 884 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 158 optimal weight: 3.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- 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 181 ASN ** i 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 124 GLN ** o 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 76 GLN w 63 GLN y 18 GLN X 19 GLN ** c 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** 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 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN L 70 GLN M 12 GLN ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 72 HIS T 41 ASN T 55 ASN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.131334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110896 restraints weight = 344764.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112208 restraints weight = 179937.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113032 restraints weight = 118051.111| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.576 167513 Z= 0.225 Angle : 0.830 103.235 250789 Z= 0.378 Chirality : 0.036 0.383 31882 Planarity : 0.006 0.204 13445 Dihedral : 25.899 179.362 85257 Min Nonbonded Distance : 1.077 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.90 % Favored : 85.65 % Rotamer: Outliers : 4.99 % Allowed : 31.80 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.47 % 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: -3.24 (0.11), residues: 5779 helix: -0.76 (0.13), residues: 1630 sheet: -2.33 (0.17), residues: 921 loop : -2.95 (0.10), residues: 3228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP l 103 HIS 0.016 0.002 HIS L 128 PHE 0.035 0.002 PHE i 93 TYR 0.024 0.002 TYR V 9 ARG 0.017 0.001 ARG Q 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51215.47 seconds wall clock time: 890 minutes 19.82 seconds (53419.82 seconds total)