Starting phenix.real_space_refine on Wed Mar 27 04:35:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d80_30611/03_2024/7d80_30611.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d80_30611/03_2024/7d80_30611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d80_30611/03_2024/7d80_30611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d80_30611/03_2024/7d80_30611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d80_30611/03_2024/7d80_30611.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d80_30611/03_2024/7d80_30611.pdb" } resolution = 4.1 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4758 5.49 5 S 161 5.16 5 C 76051 2.51 5 N 28031 2.21 5 O 41807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 3": "NH1" <-> "NH2" Residue "0 ARG 12": "NH1" <-> "NH2" Residue "0 ARG 14": "NH1" <-> "NH2" Residue "0 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 19": "NH1" <-> "NH2" Residue "0 ARG 21": "NH1" <-> "NH2" Residue "0 ARG 33": "NH1" <-> "NH2" Residue "0 ARG 41": "NH1" <-> "NH2" Residue "1 ARG 13": "NH1" <-> "NH2" Residue "1 ARG 30": "NH1" <-> "NH2" Residue "1 ARG 40": "NH1" <-> "NH2" Residue "1 ARG 42": "NH1" <-> "NH2" Residue "2 ARG 24": "NH1" <-> "NH2" Residue "3 GLU 21": "OE1" <-> "OE2" Residue "3 GLU 22": "OE1" <-> "OE2" Residue "3 GLU 95": "OE1" <-> "OE2" Residue "5 GLU 25": "OE1" <-> "OE2" Residue "5 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 101": "OE1" <-> "OE2" Residue "5 GLU 114": "OE1" <-> "OE2" Residue "5 GLU 116": "OE1" <-> "OE2" Residue "5 GLU 121": "OE1" <-> "OE2" Residue "5 GLU 124": "OE1" <-> "OE2" Residue "5 GLU 131": "OE1" <-> "OE2" Residue "5 GLU 153": "OE1" <-> "OE2" Residue "5 GLU 159": "OE1" <-> "OE2" Residue "5 GLU 175": "OE1" <-> "OE2" Residue "5 GLU 210": "OE1" <-> "OE2" Residue "5 GLU 251": "OE1" <-> "OE2" Residue "5 GLU 292": "OE1" <-> "OE2" Residue "5 GLU 326": "OE1" <-> "OE2" Residue "5 GLU 331": "OE1" <-> "OE2" Residue "5 GLU 338": "OE1" <-> "OE2" Residue "5 GLU 353": "OE1" <-> "OE2" Residue "5 GLU 364": "OE1" <-> "OE2" Residue "5 GLU 372": "OE1" <-> "OE2" Residue "5 GLU 393": "OE1" <-> "OE2" Residue "5 GLU 405": "OE1" <-> "OE2" Residue "5 GLU 409": "OE1" <-> "OE2" Residue "5 GLU 419": "OE1" <-> "OE2" Residue "5 GLU 421": "OE1" <-> "OE2" Residue "5 GLU 426": "OE1" <-> "OE2" Residue "6 ARG 10": "NH1" <-> "NH2" Residue "6 ARG 16": "NH1" <-> "NH2" Residue "6 ARG 52": "NH1" <-> "NH2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D GLU 161": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "G GLU 16": "OE1" <-> "OE2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "H GLU 40": "OE1" <-> "OE2" Residue "H GLU 74": "OE1" <-> "OE2" Residue "H GLU 129": "OE1" <-> "OE2" Residue "I GLU 124": "OE1" <-> "OE2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J ARG 124": "NH1" <-> "NH2" Residue "M GLU 25": "OE1" <-> "OE2" Residue "M ARG 56": "NH1" <-> "NH2" Residue "Q ARG 28": "NH1" <-> "NH2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q GLU 47": "OE1" <-> "OE2" Residue "W ARG 3": "NH1" <-> "NH2" Residue "W PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "b ARG 63": "NH1" <-> "NH2" Residue "b ARG 80": "NH1" <-> "NH2" Residue "b ARG 133": "NH1" <-> "NH2" Residue "b ARG 167": "NH1" <-> "NH2" Residue "b ARG 177": "NH1" <-> "NH2" Residue "b ARG 182": "NH1" <-> "NH2" Residue "b ARG 189": "NH1" <-> "NH2" Residue "b ARG 203": "NH1" <-> "NH2" Residue "b ARG 212": "NH1" <-> "NH2" Residue "c ARG 13": "NH1" <-> "NH2" Residue "c GLU 17": "OE1" <-> "OE2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 59": "NH1" <-> "NH2" Residue "c ARG 77": "NH1" <-> "NH2" Residue "c ARG 83": "NH1" <-> "NH2" Residue "c PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 168": "OE1" <-> "OE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c ARG 184": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 61": "NH1" <-> "NH2" Residue "d ARG 88": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ARG 162": "NH1" <-> "NH2" Residue "d ARG 170": "NH1" <-> "NH2" Residue "e ARG 71": "NH1" <-> "NH2" Residue "e ARG 80": "NH1" <-> "NH2" Residue "e ARG 92": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e ARG 110": "NH1" <-> "NH2" Residue "e ARG 112": "NH1" <-> "NH2" Residue "e ARG 115": "NH1" <-> "NH2" Residue "e ARG 133": "NH1" <-> "NH2" Residue "f ARG 3": "NH1" <-> "NH2" Residue "f ARG 153": "NH1" <-> "NH2" Residue "f ARG 163": "NH1" <-> "NH2" Residue "f ARG 170": "NH1" <-> "NH2" Residue "g ARG 27": "NH1" <-> "NH2" Residue "h GLU 130": "OE1" <-> "OE2" Residue "h GLU 141": "OE1" <-> "OE2" Residue "i GLU 9": "OE1" <-> "OE2" Residue "i ARG 13": "NH1" <-> "NH2" Residue "i ARG 37": "NH1" <-> "NH2" Residue "i ARG 96": "NH1" <-> "NH2" Residue "i ARG 120": "NH1" <-> "NH2" Residue "j GLU 45": "OE1" <-> "OE2" Residue "j GLU 121": "OE1" <-> "OE2" Residue "k ARG 21": "NH1" <-> "NH2" Residue "k ARG 33": "NH1" <-> "NH2" Residue "k ARG 41": "NH1" <-> "NH2" Residue "k ARG 47": "NH1" <-> "NH2" Residue "k ARG 60": "NH1" <-> "NH2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 115": "OE1" <-> "OE2" Residue "k ARG 126": "NH1" <-> "NH2" Residue "l ARG 10": "NH1" <-> "NH2" Residue "l ARG 18": "NH1" <-> "NH2" Residue "l ARG 40": "NH1" <-> "NH2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "l ARG 59": "NH1" <-> "NH2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "m ARG 8": "NH1" <-> "NH2" Residue "m ARG 12": "NH1" <-> "NH2" Residue "m ARG 17": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "m ARG 46": "NH1" <-> "NH2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "m ARG 64": "NH1" <-> "NH2" Residue "m ARG 69": "NH1" <-> "NH2" Residue "m ARG 71": "NH1" <-> "NH2" Residue "m PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 96": "NH1" <-> "NH2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "n ARG 10": "NH1" <-> "NH2" Residue "n ARG 16": "NH1" <-> "NH2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n ARG 81": "NH1" <-> "NH2" Residue "n ARG 94": "NH1" <-> "NH2" Residue "n ARG 102": "NH1" <-> "NH2" Residue "n ARG 111": "NH1" <-> "NH2" Residue "o GLU 11": "OE1" <-> "OE2" Residue "o ARG 21": "NH1" <-> "NH2" Residue "o ARG 39": "NH1" <-> "NH2" Residue "o ARG 62": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "o ARG 101": "NH1" <-> "NH2" Residue "o GLU 102": "OE1" <-> "OE2" Residue "o ARG 109": "NH1" <-> "NH2" Residue "p ARG 3": "NH1" <-> "NH2" Residue "p ARG 6": "NH1" <-> "NH2" Residue "p ARG 13": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "p ARG 48": "NH1" <-> "NH2" Residue "p ARG 70": "NH1" <-> "NH2" Residue "q ARG 21": "NH1" <-> "NH2" Residue "q ARG 68": "NH1" <-> "NH2" Residue "q GLU 70": "OE1" <-> "OE2" Residue "q ARG 78": "NH1" <-> "NH2" Residue "q ARG 79": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r ARG 88": "NH1" <-> "NH2" Residue "r ARG 95": "NH1" <-> "NH2" Residue "r ARG 110": "NH1" <-> "NH2" Residue "s ARG 6": "NH1" <-> "NH2" Residue "s ARG 7": "NH1" <-> "NH2" Residue "s GLU 37": "OE1" <-> "OE2" Residue "s ARG 82": "NH1" <-> "NH2" Residue "s ARG 86": "NH1" <-> "NH2" Residue "s ARG 94": "NH1" <-> "NH2" Residue "v ARG 3": "NH1" <-> "NH2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v ARG 18": "NH1" <-> "NH2" Residue "v ARG 37": "NH1" <-> "NH2" Residue "v ARG 50": "NH1" <-> "NH2" Residue "v ARG 57": "NH1" <-> "NH2" Residue "v ARG 74": "NH1" <-> "NH2" Residue "v GLU 76": "OE1" <-> "OE2" Residue "w GLU 17": "OE1" <-> "OE2" Residue "w ARG 29": "NH1" <-> "NH2" Residue "w ARG 47": "NH1" <-> "NH2" Residue "w ARG 52": "NH1" <-> "NH2" Residue "x ARG 11": "NH1" <-> "NH2" Residue "x ARG 30": "NH1" <-> "NH2" Residue "x ARG 45": "NH1" <-> "NH2" Residue "x GLU 58": "OE1" <-> "OE2" Residue "z PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 44": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150808 Number of models: 1 Model: "" Number of chains: 57 Chain: "0" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "1" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "2" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "3" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1346 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 160} Chain: "5" Number of atoms: 3386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3386 Classifications: {'peptide': 432} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 419} Chain: "6" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "A" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 283, 'rna2p_pyr': 152, 'rna3p_pur': 1391, 'rna3p_pyr': 1077} Link IDs: {'rna2p': 435, 'rna3p': 2467} Chain: "B" Number of atoms: 33015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33015 Classifications: {'RNA': 1539} Modifications used: {'rna2p_pur': 116, 'rna2p_pyr': 88, 'rna3p_pur': 758, 'rna3p_pyr': 577} Link IDs: {'rna2p': 204, 'rna3p': 1334} Chain: "C" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "D" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "F" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "G" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "H" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "I" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "J" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "K" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "L" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "M" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "N" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "O" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "P" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 710 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 87} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "R" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "S" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "U" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "V" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "W" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 764 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "X" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1392 Classifications: {'RNA': 65} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 26} Link IDs: {'rna2p': 7, 'rna3p': 57} Chain breaks: 6 Chain: "Z" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1406 Classifications: {'RNA': 66} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 30, 'rna3p_pyr': 27} Link IDs: {'rna2p': 9, 'rna3p': 56} Chain breaks: 7 Chain: "a" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "b" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "c" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "d" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "e" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "f" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "g" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 359 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "h" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "i" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "j" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "k" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "l" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "m" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "n" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "t" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "u" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 569 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "v" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "w" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "x" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "y" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1496 Classifications: {'RNA': 70} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 29, 'rna3p_pyr': 31} Link IDs: {'rna2p': 9, 'rna3p': 60} Chain breaks: 6 Chain: "z" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Time building chain proxies: 57.31, per 1000 atoms: 0.38 Number of scatterers: 150808 At special positions: 0 Unit cell: (331.2, 266.34, 224.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 161 16.00 P 4758 15.00 O 41807 8.00 N 28031 7.00 C 76051 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: 70.64 Conformation dependent library (CDL) restraints added in 6.9 seconds 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11434 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 81 sheets defined 27.2% alpha, 12.6% beta 738 base pairs and 1935 stacking pairs defined. Time for finding SS restraints: 46.87 Creating SS restraints... Processing helix chain '0' and resid 8 through 14 removed outlier: 3.716A pdb=" N ASN 0 13 " --> pdb=" O VAL 0 9 " (cutoff:3.500A) Processing helix chain '0' and resid 24 through 32 removed outlier: 4.284A pdb=" N ARG 0 28 " --> pdb=" O THR 0 24 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL 0 30 " --> pdb=" O ASN 0 26 " (cutoff:3.500A) Processing helix chain '1' and resid 7 through 11 removed outlier: 3.539A pdb=" N ALA 1 11 " --> pdb=" O ARG 1 8 " (cutoff:3.500A) Processing helix chain '1' and resid 32 through 36 removed outlier: 3.646A pdb=" N LYS 1 35 " --> pdb=" O ILE 1 32 " (cutoff:3.500A) Processing helix chain '1' and resid 37 through 43 removed outlier: 3.787A pdb=" N HIS 1 43 " --> pdb=" O LYS 1 39 " (cutoff:3.500A) Processing helix chain '1' and resid 54 through 62 removed outlier: 4.173A pdb=" N VAL 1 58 " --> pdb=" O ASP 1 54 " (cutoff:3.500A) Processing helix chain '3' and resid 10 through 14 removed outlier: 3.743A pdb=" N LEU 3 13 " --> pdb=" O ASP 3 10 " (cutoff:3.500A) Processing helix chain '3' and resid 26 through 32 removed outlier: 3.797A pdb=" N ILE 3 30 " --> pdb=" O GLU 3 26 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL 3 31 " --> pdb=" O ILE 3 27 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP 3 32 " --> pdb=" O GLN 3 28 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 26 through 32' Processing helix chain '3' and resid 35 through 40 Processing helix chain '3' and resid 49 through 52 removed outlier: 3.741A pdb=" N ASP 3 52 " --> pdb=" O THR 3 49 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 49 through 52' Processing helix chain '3' and resid 125 through 128 Processing helix chain '3' and resid 129 through 139 removed outlier: 3.889A pdb=" N ASP 3 135 " --> pdb=" O GLN 3 131 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N HIS 3 136 " --> pdb=" O HIS 3 132 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU 3 137 " --> pdb=" O GLU 3 133 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL 3 138 " --> pdb=" O MET 3 134 " (cutoff:3.500A) Processing helix chain '3' and resid 147 through 164 removed outlier: 3.807A pdb=" N GLN 3 152 " --> pdb=" O PRO 3 148 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL 3 158 " --> pdb=" O ILE 3 154 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU 3 159 " --> pdb=" O ARG 3 155 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU 3 161 " --> pdb=" O LYS 3 157 " (cutoff:3.500A) Processing helix chain '5' and resid 20 through 23 Processing helix chain '5' and resid 24 through 37 removed outlier: 3.778A pdb=" N GLU 5 31 " --> pdb=" O ALA 5 27 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL 5 33 " --> pdb=" O LYS 5 29 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN 5 34 " --> pdb=" O SER 5 30 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL 5 35 " --> pdb=" O GLU 5 31 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA 5 36 " --> pdb=" O LEU 5 32 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS 5 37 " --> pdb=" O VAL 5 33 " (cutoff:3.500A) Processing helix chain '5' and resid 50 through 59 removed outlier: 3.523A pdb=" N GLN 5 56 " --> pdb=" O ASN 5 52 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG 5 57 " --> pdb=" O ILE 5 53 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR 5 58 " --> pdb=" O VAL 5 54 " (cutoff:3.500A) Processing helix chain '5' and resid 66 through 80 removed outlier: 5.155A pdb=" N SER 5 72 " --> pdb=" O GLY 5 68 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE 5 75 " --> pdb=" O MET 5 71 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP 5 77 " --> pdb=" O ARG 5 73 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA 5 78 " --> pdb=" O ASN 5 74 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE 5 80 " --> pdb=" O ILE 5 76 " (cutoff:3.500A) Processing helix chain '5' and resid 133 through 141 removed outlier: 3.883A pdb=" N VAL 5 137 " --> pdb=" O THR 5 133 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP 5 138 " --> pdb=" O ASP 5 134 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLY 5 139 " --> pdb=" O ALA 5 135 " (cutoff:3.500A) Processing helix chain '5' and resid 249 through 253 Processing helix chain '5' and resid 262 through 265 Processing helix chain '5' and resid 266 through 271 removed outlier: 3.510A pdb=" N VAL 5 270 " --> pdb=" O LEU 5 266 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG 5 271 " --> pdb=" O ARG 5 267 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 266 through 271' Processing helix chain '5' and resid 280 through 285 Processing helix chain '5' and resid 287 through 292 removed outlier: 3.628A pdb=" N GLU 5 292 " --> pdb=" O SER 5 288 " (cutoff:3.500A) Processing helix chain '5' and resid 293 through 295 No H-bonds generated for 'chain '5' and resid 293 through 295' Processing helix chain '5' and resid 306 through 310 removed outlier: 3.698A pdb=" N GLU 5 310 " --> pdb=" O ILE 5 307 " (cutoff:3.500A) Processing helix chain '5' and resid 311 through 320 removed outlier: 4.340A pdb=" N GLN 5 320 " --> pdb=" O ARG 5 316 " (cutoff:3.500A) Processing helix chain '5' and resid 333 through 337 Processing helix chain '5' and resid 341 through 346 removed outlier: 3.539A pdb=" N VAL 5 346 " --> pdb=" O LYS 5 342 " (cutoff:3.500A) Processing helix chain '5' and resid 350 through 352 No H-bonds generated for 'chain '5' and resid 350 through 352' Processing helix chain '5' and resid 353 through 358 Processing helix chain '5' and resid 370 through 374 removed outlier: 4.042A pdb=" N GLU 5 373 " --> pdb=" O LEU 5 370 " (cutoff:3.500A) Processing helix chain '5' and resid 402 through 407 Processing helix chain '5' and resid 408 through 412 Processing helix chain '6' and resid 10 through 15 Processing helix chain '6' and resid 16 through 21 removed outlier: 4.353A pdb=" N HIS 6 19 " --> pdb=" O ARG 6 16 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP 6 20 " --> pdb=" O ARG 6 17 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA 6 21 " --> pdb=" O SER 6 18 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 16 through 21' Processing helix chain 'C' and resid 24 through 28 removed outlier: 3.698A pdb=" N LYS C 28 " --> pdb=" O PRO C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 63 removed outlier: 3.529A pdb=" N THR C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Proline residue: C 48 - end of helix removed outlier: 3.707A pdb=" N ASN C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLU C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 123 removed outlier: 3.757A pdb=" N VAL C 107 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLN C 109 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C 119 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 147 removed outlier: 3.880A pdb=" N SER C 147 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 154 removed outlier: 3.728A pdb=" N LYS C 152 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP C 153 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 178 removed outlier: 3.537A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 223 removed outlier: 3.603A pdb=" N THR C 211 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 212 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 219 " --> pdb=" O GLY C 215 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL C 221 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 11 removed outlier: 4.328A pdb=" N ARG D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 16 removed outlier: 3.648A pdb=" N LYS D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 45 removed outlier: 3.652A pdb=" N ASN D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 76 removed outlier: 3.792A pdb=" N ILE D 75 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.712A pdb=" N GLU D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 90 " --> pdb=" O LYS D 86 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL D 91 " --> pdb=" O LEU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 111 Processing helix chain 'D' and resid 112 through 125 removed outlier: 3.741A pdb=" N VAL D 116 " --> pdb=" O ASP D 112 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 135 through 140 removed outlier: 4.666A pdb=" N GLN D 139 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 135 through 140' Processing helix chain 'D' and resid 156 through 160 Processing helix chain 'E' and resid 7 through 11 Processing helix chain 'E' and resid 49 through 63 removed outlier: 3.759A pdb=" N VAL E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG E 63 " --> pdb=" O GLN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 80 Processing helix chain 'E' and resid 87 through 92 removed outlier: 4.330A pdb=" N LEU E 91 " --> pdb=" O GLY E 87 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 92' Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.572A pdb=" N GLY E 96 " --> pdb=" O LEU E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 96' Processing helix chain 'E' and resid 97 through 105 removed outlier: 3.536A pdb=" N VAL E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 119 removed outlier: 3.608A pdb=" N VAL E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 55 through 69 removed outlier: 3.636A pdb=" N GLN F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU F 65 " --> pdb=" O GLN F 61 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG F 69 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 117 removed outlier: 3.662A pdb=" N VAL F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 removed outlier: 3.687A pdb=" N VAL F 136 " --> pdb=" O PRO F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 149 through 156 removed outlier: 3.510A pdb=" N VAL F 153 " --> pdb=" O SER F 149 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS F 156 " --> pdb=" O MET F 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 15 Processing helix chain 'G' and resid 17 through 30 removed outlier: 3.613A pdb=" N ALA G 27 " --> pdb=" O GLU G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 81 removed outlier: 3.772A pdb=" N ILE G 71 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP G 72 " --> pdb=" O GLN G 68 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLU G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 31 removed outlier: 3.600A pdb=" N ASN H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 47 removed outlier: 3.543A pdb=" N ILE H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 63 removed outlier: 3.593A pdb=" N PHE H 62 " --> pdb=" O LEU H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 110 removed outlier: 3.856A pdb=" N ASN H 97 " --> pdb=" O PRO H 93 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA H 98 " --> pdb=" O VAL H 94 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL H 105 " --> pdb=" O MET H 101 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU H 106 " --> pdb=" O ARG H 102 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 122 removed outlier: 3.504A pdb=" N ARG H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 135 through 147 removed outlier: 3.837A pdb=" N HIS H 142 " --> pdb=" O ARG H 138 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA H 147 " --> pdb=" O ARG H 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 19 removed outlier: 3.570A pdb=" N LEU I 11 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG I 13 " --> pdb=" O ASP I 9 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY I 17 " --> pdb=" O ARG I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 44 removed outlier: 4.957A pdb=" N VAL I 39 " --> pdb=" O ALA I 35 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU I 43 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 92 removed outlier: 3.629A pdb=" N GLU I 91 " --> pdb=" O ARG I 88 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU I 92 " --> pdb=" O LYS I 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 88 through 92' Processing helix chain 'I' and resid 94 through 99 removed outlier: 4.008A pdb=" N ALA I 97 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 117 removed outlier: 3.948A pdb=" N ARG I 117 " --> pdb=" O ASP I 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 113 through 117' Processing helix chain 'J' and resid 35 through 39 removed outlier: 4.369A pdb=" N PHE J 39 " --> pdb=" O LEU J 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 35 through 39' Processing helix chain 'J' and resid 72 through 87 removed outlier: 3.680A pdb=" N ALA J 78 " --> pdb=" O GLY J 74 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE J 83 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR J 84 " --> pdb=" O ARG J 80 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG J 85 " --> pdb=" O HIS J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 95 removed outlier: 3.541A pdb=" N ARG J 95 " --> pdb=" O ASP J 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 33 removed outlier: 3.519A pdb=" N ASP K 19 " --> pdb=" O HIS K 15 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLN K 20 " --> pdb=" O ARG K 16 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA K 21 " --> pdb=" O LEU K 17 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR K 28 " --> pdb=" O GLU K 24 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR K 32 " --> pdb=" O THR K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 85 removed outlier: 3.589A pdb=" N VAL K 84 " --> pdb=" O THR K 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 58 removed outlier: 3.791A pdb=" N LYS L 57 " --> pdb=" O GLY L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 72 removed outlier: 3.666A pdb=" N ALA L 63 " --> pdb=" O THR L 59 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN L 64 " --> pdb=" O PRO L 60 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU L 68 " --> pdb=" O GLN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 102 removed outlier: 3.607A pdb=" N ALA L 99 " --> pdb=" O SER L 95 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU L 100 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN L 101 " --> pdb=" O ILE L 97 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA L 102 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 10 removed outlier: 3.829A pdb=" N ARG M 9 " --> pdb=" O ASN M 5 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS M 10 " --> pdb=" O GLN M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 118 removed outlier: 3.824A pdb=" N TYR M 117 " --> pdb=" O ALA M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 37 removed outlier: 3.674A pdb=" N ALA N 37 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 53 Processing helix chain 'N' and resid 58 through 62 removed outlier: 3.540A pdb=" N LYS N 62 " --> pdb=" O GLU N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 83 removed outlier: 4.399A pdb=" N ARG N 79 " --> pdb=" O MET N 75 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 90 removed outlier: 4.215A pdb=" N ARG N 90 " --> pdb=" O TYR N 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 9 Processing helix chain 'O' and resid 9 through 20 removed outlier: 3.973A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA O 15 " --> pdb=" O VAL O 11 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU O 16 " --> pdb=" O LYS O 12 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP O 18 " --> pdb=" O VAL O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 29 Processing helix chain 'O' and resid 42 through 47 removed outlier: 3.927A pdb=" N LEU O 46 " --> pdb=" O TRP O 42 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS O 47 " --> pdb=" O ASN O 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 42 through 47' Processing helix chain 'O' and resid 82 through 90 removed outlier: 3.979A pdb=" N GLU O 86 " --> pdb=" O ILE O 82 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA O 87 " --> pdb=" O LYS O 83 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG O 90 " --> pdb=" O GLU O 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 16 removed outlier: 3.963A pdb=" N ALA P 9 " --> pdb=" O THR P 5 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LYS P 10 " --> pdb=" O GLU P 6 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE P 11 " --> pdb=" O ALA P 7 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL P 12 " --> pdb=" O THR P 8 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER P 13 " --> pdb=" O ALA P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 45 removed outlier: 3.967A pdb=" N ALA P 30 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR P 33 " --> pdb=" O VAL P 29 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY P 41 " --> pdb=" O ASN P 37 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N HIS P 42 " --> pdb=" O HIS P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 72 removed outlier: 5.090A pdb=" N GLY P 55 " --> pdb=" O HIS P 51 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU P 56 " --> pdb=" O SER P 52 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG P 63 " --> pdb=" O MET P 59 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU P 67 " --> pdb=" O ARG P 63 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 80 removed outlier: 3.571A pdb=" N TYR P 78 " --> pdb=" O ASP P 74 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR P 79 " --> pdb=" O VAL P 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 61 removed outlier: 3.847A pdb=" N TRP Q 60 " --> pdb=" O ARG Q 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 73 Processing helix chain 'S' and resid 28 through 33 removed outlier: 3.735A pdb=" N ILE S 33 " --> pdb=" O LYS S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 63 removed outlier: 3.783A pdb=" N GLN S 54 " --> pdb=" O LYS S 50 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU S 55 " --> pdb=" O TYR S 51 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA S 56 " --> pdb=" O GLN S 52 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG S 57 " --> pdb=" O ARG S 53 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA S 62 " --> pdb=" O ALA S 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 20 removed outlier: 3.734A pdb=" N LYS T 18 " --> pdb=" O HIS T 14 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU T 20 " --> pdb=" O LEU T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 41 through 45 removed outlier: 3.787A pdb=" N MET T 44 " --> pdb=" O PHE T 41 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE T 45 " --> pdb=" O PRO T 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 41 through 45' Processing helix chain 'T' and resid 70 through 75 removed outlier: 3.586A pdb=" N GLU T 73 " --> pdb=" O LYS T 70 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE T 74 " --> pdb=" O LEU T 71 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA T 75 " --> pdb=" O GLY T 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 70 through 75' Processing helix chain 'U' and resid 5 through 7 No H-bonds generated for 'chain 'U' and resid 5 through 7' Processing helix chain 'U' and resid 8 through 42 removed outlier: 3.701A pdb=" N SER U 14 " --> pdb=" O ARG U 10 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU U 15 " --> pdb=" O ALA U 11 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG U 29 " --> pdb=" O ARG U 25 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE U 31 " --> pdb=" O MET U 27 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL U 35 " --> pdb=" O PHE U 31 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA U 38 " --> pdb=" O LYS U 34 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA U 41 " --> pdb=" O ALA U 37 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY U 42 " --> pdb=" O ALA U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 59 Proline residue: U 56 - end of helix Processing helix chain 'U' and resid 60 through 64 Processing helix chain 'U' and resid 69 through 84 removed outlier: 3.762A pdb=" N GLN U 82 " --> pdb=" O ASN U 78 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN U 84 " --> pdb=" O THR U 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 23 removed outlier: 3.611A pdb=" N ARG V 21 " --> pdb=" O ARG V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 27 through 32 Processing helix chain 'V' and resid 43 through 51 removed outlier: 3.601A pdb=" N ARG V 47 " --> pdb=" O THR V 43 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA V 48 " --> pdb=" O GLU V 44 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LYS V 49 " --> pdb=" O ARG V 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 23 Processing helix chain 'W' and resid 43 through 51 removed outlier: 3.705A pdb=" N GLN W 48 " --> pdb=" O LYS W 44 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS W 49 " --> pdb=" O ALA W 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 135 No H-bonds generated for 'chain 'b' and resid 133 through 135' Processing helix chain 'b' and resid 199 through 203 removed outlier: 3.538A pdb=" N ARG b 203 " --> pdb=" O HIS b 200 " (cutoff:3.500A) Processing helix chain 'b' and resid 209 through 214 removed outlier: 3.518A pdb=" N ARG b 214 " --> pdb=" O ALA b 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 72 removed outlier: 4.042A pdb=" N HIS c 67 " --> pdb=" O PRO c 63 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS c 70 " --> pdb=" O GLY c 66 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA c 71 " --> pdb=" O HIS c 67 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 102 removed outlier: 3.545A pdb=" N LEU c 100 " --> pdb=" O SER c 97 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA c 102 " --> pdb=" O GLU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 181 through 184 removed outlier: 3.626A pdb=" N ARG c 184 " --> pdb=" O ASP c 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 181 through 184' Processing helix chain 'd' and resid 24 through 37 removed outlier: 3.573A pdb=" N HIS d 29 " --> pdb=" O GLU d 25 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN d 30 " --> pdb=" O ALA d 26 " (cutoff:3.500A) Processing helix chain 'd' and resid 99 through 104 Processing helix chain 'd' and resid 130 through 141 removed outlier: 3.733A pdb=" N LEU d 134 " --> pdb=" O LYS d 130 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET d 141 " --> pdb=" O LYS d 137 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 160 removed outlier: 3.531A pdb=" N ALA d 160 " --> pdb=" O ASN d 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 178 through 183 removed outlier: 3.807A pdb=" N PHE d 183 " --> pdb=" O SER d 179 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 198 removed outlier: 3.510A pdb=" N LYS d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 9 Processing helix chain 'e' and resid 11 through 19 removed outlier: 3.590A pdb=" N LYS e 15 " --> pdb=" O GLU e 11 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET e 17 " --> pdb=" O VAL e 13 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR e 18 " --> pdb=" O LYS e 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 24 through 28 removed outlier: 3.562A pdb=" N VAL e 28 " --> pdb=" O VAL e 25 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 56 removed outlier: 3.732A pdb=" N ASP e 51 " --> pdb=" O LYS e 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA e 54 " --> pdb=" O LEU e 50 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP e 56 " --> pdb=" O ASN e 52 " (cutoff:3.500A) Processing helix chain 'e' and resid 94 through 101 Processing helix chain 'e' and resid 106 through 111 Processing helix chain 'e' and resid 163 through 171 Processing helix chain 'f' and resid 3 through 7 removed outlier: 3.697A pdb=" N ALA f 7 " --> pdb=" O ARG f 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 3 through 7' Processing helix chain 'f' and resid 60 through 79 removed outlier: 3.851A pdb=" N THR f 67 " --> pdb=" O ALA f 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA f 68 " --> pdb=" O GLN f 64 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG f 69 " --> pdb=" O ALA f 65 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE f 77 " --> pdb=" O ASN f 73 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY f 78 " --> pdb=" O SER f 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 139 through 149 removed outlier: 3.653A pdb=" N ARG f 149 " --> pdb=" O ALA f 145 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 28 removed outlier: 3.679A pdb=" N ASN g 28 " --> pdb=" O GLY g 24 " (cutoff:3.500A) Processing helix chain 'g' and resid 30 through 34 Processing helix chain 'h' and resid 34 through 39 removed outlier: 3.840A pdb=" N GLU h 37 " --> pdb=" O ASN h 34 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE h 38 " --> pdb=" O ILE h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 75 through 80 removed outlier: 3.659A pdb=" N LEU h 79 " --> pdb=" O PRO h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 102 through 107 removed outlier: 4.260A pdb=" N LEU h 106 " --> pdb=" O SER h 102 " (cutoff:3.500A) Processing helix chain 'i' and resid 25 through 36 removed outlier: 4.828A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG i 34 " --> pdb=" O THR i 30 " (cutoff:3.500A) Processing helix chain 'i' and resid 89 through 96 Processing helix chain 'i' and resid 97 through 99 No H-bonds generated for 'chain 'i' and resid 97 through 99' Processing helix chain 'i' and resid 100 through 107 removed outlier: 4.055A pdb=" N LYS i 106 " --> pdb=" O GLU i 102 " (cutoff:3.500A) Processing helix chain 'i' and resid 132 through 136 Processing helix chain 'j' and resid 104 through 108 removed outlier: 3.739A pdb=" N ARG j 108 " --> pdb=" O ARG j 105 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 118 removed outlier: 3.596A pdb=" N ILE j 116 " --> pdb=" O PHE j 112 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU j 118 " --> pdb=" O LYS j 114 " (cutoff:3.500A) Processing helix chain 'k' and resid 132 through 138 removed outlier: 3.641A pdb=" N ALA k 138 " --> pdb=" O ALA k 134 " (cutoff:3.500A) Processing helix chain 'l' and resid 43 through 48 removed outlier: 3.884A pdb=" N GLU l 47 " --> pdb=" O ALA l 43 " (cutoff:3.500A) Processing helix chain 'l' and resid 50 through 55 Processing helix chain 'l' and resid 109 through 121 removed outlier: 3.535A pdb=" N PHE l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LYS l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) Processing helix chain 'l' and resid 122 through 124 No H-bonds generated for 'chain 'l' and resid 122 through 124' Processing helix chain 'm' and resid 20 through 25 Processing helix chain 'm' and resid 27 through 32 Processing helix chain 'm' and resid 38 through 42 Processing helix chain 'm' and resid 43 through 46 Processing helix chain 'm' and resid 47 through 52 Processing helix chain 'm' and resid 53 through 56 removed outlier: 3.982A pdb=" N LYS m 56 " --> pdb=" O THR m 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 53 through 56' Processing helix chain 'm' and resid 64 through 69 removed outlier: 3.517A pdb=" N ALA m 68 " --> pdb=" O ARG m 64 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG m 69 " --> pdb=" O LEU m 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 64 through 69' Processing helix chain 'm' and resid 72 through 79 Processing helix chain 'm' and resid 82 through 87 removed outlier: 3.841A pdb=" N PHE m 87 " --> pdb=" O LEU m 83 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 17 removed outlier: 5.516A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG n 15 " --> pdb=" O ALA n 11 " (cutoff:3.500A) Processing helix chain 'n' and resid 17 through 22 removed outlier: 3.797A pdb=" N LEU n 21 " --> pdb=" O LYS n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 60 removed outlier: 3.938A pdb=" N GLU n 60 " --> pdb=" O LYS n 56 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 83 removed outlier: 3.741A pdb=" N VAL n 74 " --> pdb=" O ALA n 70 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS n 76 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU n 80 " --> pdb=" O LYS n 76 " (cutoff:3.500A) Processing helix chain 'n' and resid 84 through 86 No H-bonds generated for 'chain 'n' and resid 84 through 86' Processing helix chain 'n' and resid 101 through 111 removed outlier: 3.638A pdb=" N ALA n 105 " --> pdb=" O GLY n 101 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA n 110 " --> pdb=" O LEU n 106 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 9 Processing helix chain 'o' and resid 10 through 13 Processing helix chain 'o' and resid 53 through 57 removed outlier: 3.796A pdb=" N HIS o 56 " --> pdb=" O ARG o 53 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER o 57 " --> pdb=" O GLY o 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 53 through 57' Processing helix chain 'o' and resid 104 through 108 Processing helix chain 'p' and resid 6 through 19 removed outlier: 3.505A pdb=" N ARG p 11 " --> pdb=" O GLY p 7 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA p 12 " --> pdb=" O VAL p 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS p 14 " --> pdb=" O ALA p 10 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS p 16 " --> pdb=" O ALA p 12 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE p 17 " --> pdb=" O ARG p 13 " (cutoff:3.500A) Processing helix chain 'p' and resid 25 through 29 removed outlier: 4.131A pdb=" N SER p 29 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 48 through 57 removed outlier: 4.831A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 72 removed outlier: 4.646A pdb=" N ALA p 63 " --> pdb=" O GLN p 59 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG p 64 " --> pdb=" O LEU p 60 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA p 67 " --> pdb=" O ALA p 63 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG p 70 " --> pdb=" O ASN p 66 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASN p 72 " --> pdb=" O ALA p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 79 through 86 Processing helix chain 'p' and resid 93 through 102 removed outlier: 3.567A pdb=" N ALA p 99 " --> pdb=" O LEU p 95 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL p 100 " --> pdb=" O ALA p 96 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE p 101 " --> pdb=" O ASP p 97 " (cutoff:3.500A) Processing helix chain 'p' and resid 102 through 114 removed outlier: 3.563A pdb=" N PHE p 106 " --> pdb=" O ASP p 102 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR p 107 " --> pdb=" O LYS p 103 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU p 111 " --> pdb=" O THR p 107 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS p 112 " --> pdb=" O ALA p 108 " (cutoff:3.500A) Processing helix chain 'r' and resid 42 through 56 removed outlier: 3.868A pdb=" N LEU r 46 " --> pdb=" O LYS r 42 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LYS r 48 " --> pdb=" O ALA r 44 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU r 51 " --> pdb=" O VAL r 47 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA r 56 " --> pdb=" O GLU r 52 " (cutoff:3.500A) Processing helix chain 't' and resid 12 through 21 removed outlier: 4.219A pdb=" N ALA t 16 " --> pdb=" O GLN t 12 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG t 18 " --> pdb=" O LYS t 14 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG t 19 " --> pdb=" O GLY t 15 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU t 20 " --> pdb=" O ALA t 16 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 51 removed outlier: 3.706A pdb=" N ASN t 49 " --> pdb=" O ASP t 45 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 58 removed outlier: 3.798A pdb=" N TYR t 57 " --> pdb=" O ALA t 54 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER t 58 " --> pdb=" O GLU t 55 " (cutoff:3.500A) Processing helix chain 'v' and resid 54 through 63 removed outlier: 4.725A pdb=" N ASP v 60 " --> pdb=" O MET v 56 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS v 61 " --> pdb=" O ARG v 57 " (cutoff:3.500A) Processing helix chain 'v' and resid 63 through 68 Processing helix chain 'w' and resid 4 through 8 Processing helix chain 'w' and resid 13 through 22 removed outlier: 3.508A pdb=" N LEU w 22 " --> pdb=" O LEU w 18 " (cutoff:3.500A) Processing helix chain 'w' and resid 26 through 34 removed outlier: 3.621A pdb=" N MET w 30 " --> pdb=" O PHE w 26 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA w 32 " --> pdb=" O LEU w 28 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER w 34 " --> pdb=" O MET w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 39 through 42 removed outlier: 3.735A pdb=" N LEU w 42 " --> pdb=" O GLN w 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 39 through 42' Processing helix chain 'w' and resid 43 through 48 Processing helix chain 'w' and resid 50 through 61 removed outlier: 3.691A pdb=" N GLU w 59 " --> pdb=" O THR w 55 " (cutoff:3.500A) Processing helix chain 'x' and resid 17 through 22 Processing helix chain 'x' and resid 23 through 28 Processing helix chain 'x' and resid 43 through 51 Processing sheet with id=AA1, first strand: chain '1' and resid 15 through 16 removed outlier: 3.515A pdb=" N LYS 1 15 " --> pdb=" O LYS 1 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 14 through 17 Processing sheet with id=AA3, first strand: chain '3' and resid 45 through 47 removed outlier: 3.778A pdb=" N LEU 3 46 " --> pdb=" O VAL 3 59 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL 3 59 " --> pdb=" O LEU 3 46 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE 3 60 " --> pdb=" O LEU 3 70 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU 3 70 " --> pdb=" O ILE 3 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain '3' and resid 73 through 83 removed outlier: 6.757A pdb=" N ARG 3 109 " --> pdb=" O PRO 3 75 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LEU 3 77 " --> pdb=" O LYS 3 107 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LYS 3 107 " --> pdb=" O LEU 3 77 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU 3 79 " --> pdb=" O LYS 3 105 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS 3 105 " --> pdb=" O GLU 3 79 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER 3 81 " --> pdb=" O ALA 3 103 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ALA 3 103 " --> pdb=" O SER 3 81 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE 3 108 " --> pdb=" O LEU 3 120 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU 3 120 " --> pdb=" O ILE 3 108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 86 through 88 Processing sheet with id=AA6, first strand: chain '5' and resid 5 through 6 Processing sheet with id=AA7, first strand: chain '5' and resid 93 through 97 removed outlier: 3.625A pdb=" N VAL 5 93 " --> pdb=" O SER 5 106 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N THR 5 104 " --> pdb=" O GLY 5 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '5' and resid 124 through 125 Processing sheet with id=AA9, first strand: chain '5' and resid 187 through 188 removed outlier: 7.246A pdb=" N ASP 5 167 " --> pdb=" O LEU 5 237 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU 5 237 " --> pdb=" O ASP 5 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '6' and resid 28 through 30 Processing sheet with id=AB2, first strand: chain '6' and resid 48 through 49 removed outlier: 3.812A pdb=" N ARG 6 52 " --> pdb=" O TYR 6 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 69 through 70 removed outlier: 6.622A pdb=" N PHE C 69 " --> pdb=" O VAL C 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 161 through 163 removed outlier: 6.521A pdb=" N LEU C 161 " --> pdb=" O PHE C 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 52 through 56 removed outlier: 6.550A pdb=" N HIS D 69 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE D 55 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR D 67 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE D 68 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 168 through 169 Processing sheet with id=AB7, first strand: chain 'F' and resid 14 through 15 Processing sheet with id=AB8, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AB9, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AC1, first strand: chain 'G' and resid 43 through 44 removed outlier: 4.439A pdb=" N GLY G 43 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL G 60 " --> pdb=" O PHE G 8 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL G 7 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER G 87 " --> pdb=" O VAL G 7 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 73 through 76 Processing sheet with id=AC3, first strand: chain 'I' and resid 24 through 28 removed outlier: 3.637A pdb=" N GLU I 58 " --> pdb=" O GLU I 52 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 75 through 77 Processing sheet with id=AC5, first strand: chain 'I' and resid 75 through 77 removed outlier: 7.034A pdb=" N VAL I 103 " --> pdb=" O ILE I 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 6 through 8 removed outlier: 3.516A pdb=" N PHE J 20 " --> pdb=" O TYR J 64 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 29 through 30 Processing sheet with id=AC8, first strand: chain 'K' and resid 45 through 46 removed outlier: 3.788A pdb=" N ARG K 45 " --> pdb=" O THR K 69 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 49 through 52 Processing sheet with id=AD1, first strand: chain 'L' and resid 43 through 46 removed outlier: 6.505A pdb=" N LEU L 82 " --> pdb=" O ILE L 107 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASN L 109 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 31 through 32 Processing sheet with id=AD3, first strand: chain 'M' and resid 52 through 56 Processing sheet with id=AD4, first strand: chain 'Q' and resid 50 through 52 removed outlier: 5.943A pdb=" N ARG Q 35 " --> pdb=" O VAL Q 21 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL Q 21 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY Q 37 " --> pdb=" O VAL Q 19 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG Q 5 " --> pdb=" O VAL Q 20 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL Q 2 " --> pdb=" O THR Q 66 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 11 through 12 removed outlier: 3.795A pdb=" N ARG R 11 " --> pdb=" O ALA R 24 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 28 through 30 Processing sheet with id=AD7, first strand: chain 'R' and resid 58 through 63 removed outlier: 7.089A pdb=" N VAL R 58 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL R 78 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU R 60 " --> pdb=" O VAL R 76 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'T' and resid 47 through 52 removed outlier: 3.690A pdb=" N LEU T 47 " --> pdb=" O VAL T 62 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'W' and resid 29 through 30 removed outlier: 3.848A pdb=" N VAL W 57 " --> pdb=" O THR W 86 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'W' and resid 33 through 34 removed outlier: 3.961A pdb=" N LYS W 81 " --> pdb=" O VAL W 34 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 67 through 70 removed outlier: 3.706A pdb=" N ARG W 73 " --> pdb=" O HIS W 70 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'b' and resid 3 through 5 Processing sheet with id=AE4, first strand: chain 'b' and resid 34 through 35 Processing sheet with id=AE5, first strand: chain 'b' and resid 101 through 105 removed outlier: 6.972A pdb=" N ILE b 91 " --> pdb=" O LEU b 81 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU b 81 " --> pdb=" O ILE b 91 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU b 93 " --> pdb=" O GLU b 79 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'b' and resid 129 through 131 removed outlier: 3.702A pdb=" N VAL b 165 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N THR b 173 " --> pdb=" O VAL b 165 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N MET b 181 " --> pdb=" O VAL b 268 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 169 through 171 removed outlier: 3.563A pdb=" N VAL c 170 " --> pdb=" O GLY c 111 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS c 204 " --> pdb=" O ASP c 108 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LYS c 8 " --> pdb=" O GLU c 28 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU c 28 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY c 10 " --> pdb=" O VAL c 26 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL c 189 " --> pdb=" O THR c 25 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU c 188 " --> pdb=" O VAL c 178 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'c' and resid 80 through 83 removed outlier: 3.611A pdb=" N ARG c 33 " --> pdb=" O THR c 51 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'd' and resid 2 through 4 Processing sheet with id=AF1, first strand: chain 'd' and resid 168 through 171 removed outlier: 3.597A pdb=" N ASP d 168 " --> pdb=" O VAL d 146 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'e' and resid 66 through 67 removed outlier: 3.588A pdb=" N CYS e 87 " --> pdb=" O MET e 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'e' and resid 66 through 67 removed outlier: 3.588A pdb=" N CYS e 87 " --> pdb=" O MET e 38 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR e 35 " --> pdb=" O THR e 155 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR e 155 " --> pdb=" O THR e 35 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL e 132 " --> pdb=" O LEU e 152 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'f' and resid 16 through 20 removed outlier: 4.057A pdb=" N VAL f 23 " --> pdb=" O ASN f 20 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG f 35 " --> pdb=" O ILE f 24 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'f' and resid 41 through 44 removed outlier: 3.544A pdb=" N LYS f 44 " --> pdb=" O THR f 51 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR f 51 " --> pdb=" O LYS f 44 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'f' and resid 130 through 135 Processing sheet with id=AF7, first strand: chain 'f' and resid 95 through 99 removed outlier: 3.651A pdb=" N ALA f 97 " --> pdb=" O ASN f 104 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL f 102 " --> pdb=" O LYS f 99 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 4 through 5 Processing sheet with id=AF9, first strand: chain 'i' and resid 53 through 55 removed outlier: 6.676A pdb=" N TRP i 15 " --> pdb=" O GLN i 138 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'i' and resid 73 through 77 Processing sheet with id=AG2, first strand: chain 'j' and resid 7 through 8 removed outlier: 6.355A pdb=" N GLU j 45 " --> pdb=" O ARG j 17 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL j 19 " --> pdb=" O ILE j 43 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE j 43 " --> pdb=" O VAL j 19 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS j 21 " --> pdb=" O ILE j 41 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE j 41 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS j 23 " --> pdb=" O ILE j 39 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE j 39 " --> pdb=" O LYS j 23 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'j' and resid 62 through 64 removed outlier: 6.357A pdb=" N ALA j 83 " --> pdb=" O VAL j 63 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'j' and resid 69 through 70 removed outlier: 3.711A pdb=" N VAL j 69 " --> pdb=" O ILE j 77 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL j 76 " --> pdb=" O VAL o 73 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ARG o 62 " --> pdb=" O VAL o 47 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL o 47 " --> pdb=" O ARG o 62 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N ILE o 64 " --> pdb=" O GLY o 45 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N GLY o 45 " --> pdb=" O ILE o 64 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'k' and resid 74 through 76 removed outlier: 6.964A pdb=" N ALA k 75 " --> pdb=" O LYS k 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'k' and resid 89 through 90 Processing sheet with id=AG7, first strand: chain 'l' and resid 62 through 65 removed outlier: 6.409A pdb=" N VAL l 101 " --> pdb=" O ALA l 35 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA l 35 " --> pdb=" O VAL l 101 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU l 33 " --> pdb=" O TYR l 103 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE l 31 " --> pdb=" O MET l 105 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL l 131 " --> pdb=" O GLY l 32 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'l' and resid 40 through 42 removed outlier: 3.956A pdb=" N ASN l 88 " --> pdb=" O GLU l 75 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE l 73 " --> pdb=" O GLU l 90 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TRP l 92 " --> pdb=" O LYS l 71 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS l 71 " --> pdb=" O TRP l 92 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'm' and resid 33 through 37 Processing sheet with id=AH1, first strand: chain 'n' and resid 47 through 52 removed outlier: 6.938A pdb=" N VAL n 39 " --> pdb=" O LEU n 48 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ALA n 50 " --> pdb=" O ALA n 37 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA n 37 " --> pdb=" O ALA n 50 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU n 26 " --> pdb=" O ASP n 93 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'q' and resid 13 through 14 removed outlier: 6.400A pdb=" N VAL q 4 " --> pdb=" O LEU q 39 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'q' and resid 19 through 22 removed outlier: 6.687A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'q' and resid 68 through 75 removed outlier: 5.414A pdb=" N GLN q 91 " --> pdb=" O GLY q 69 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS q 71 " --> pdb=" O HIS q 89 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N HIS q 89 " --> pdb=" O LYS q 71 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS q 73 " --> pdb=" O GLN q 87 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN q 87 " --> pdb=" O LYS q 73 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'r' and resid 3 through 10 removed outlier: 5.600A pdb=" N ILE r 4 " --> pdb=" O VAL r 107 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL r 107 " --> pdb=" O ILE r 4 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS r 6 " --> pdb=" O VAL r 105 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL r 105 " --> pdb=" O LYS r 6 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ARG r 8 " --> pdb=" O ILE r 103 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE r 103 " --> pdb=" O ARG r 8 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE r 75 " --> pdb=" O THR r 104 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS r 73 " --> pdb=" O VAL r 106 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER r 108 " --> pdb=" O VAL r 71 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL r 71 " --> pdb=" O SER r 108 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'r' and resid 82 through 83 Processing sheet with id=AH7, first strand: chain 'r' and resid 86 through 87 Processing sheet with id=AH8, first strand: chain 's' and resid 65 through 66 removed outlier: 7.046A pdb=" N LYS s 33 " --> pdb=" O VAL s 28 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL s 28 " --> pdb=" O LYS s 33 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ILE s 35 " --> pdb=" O LYS s 26 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL s 11 " --> pdb=" O GLY s 23 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N GLU s 10 " --> pdb=" O PHE s 73 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE s 72 " --> pdb=" O ASP s 81 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 's' and resid 41 through 45 Processing sheet with id=AI1, first strand: chain 's' and resid 83 through 84 Processing sheet with id=AI2, first strand: chain 't' and resid 3 through 8 removed outlier: 7.273A pdb=" N ASN t 5 " --> pdb=" O ASP t 43 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ASP t 43 " --> pdb=" O ASN t 5 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU t 41 " --> pdb=" O GLU t 7 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLN t 87 " --> pdb=" O LYS t 25 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE t 89 " --> pdb=" O PRO t 27 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS t 88 " --> pdb=" O GLN t 78 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP t 76 " --> pdb=" O ASP t 90 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL t 92 " --> pdb=" O ALA t 74 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ALA t 74 " --> pdb=" O VAL t 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE t 70 " --> pdb=" O ILE t 63 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE t 4 " --> pdb=" O VAL t 64 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'u' and resid 22 through 23 removed outlier: 3.591A pdb=" N VAL u 38 " --> pdb=" O LEU u 59 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'u' and resid 30 through 31 removed outlier: 3.864A pdb=" N GLY u 65 " --> pdb=" O VAL u 31 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG u 77 " --> pdb=" O LYS u 72 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'v' and resid 14 through 18 removed outlier: 3.951A pdb=" N THR v 25 " --> pdb=" O ASN v 17 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'v' and resid 38 through 39 Processing sheet with id=AI7, first strand: chain 'x' and resid 35 through 38 Processing sheet with id=AI8, first strand: chain 'z' and resid 7 through 8 removed outlier: 3.650A pdb=" N GLU z 7 " --> pdb=" O LYS z 25 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'z' and resid 20 through 21 1031 hydrogen bonds defined for protein. 2730 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1705 hydrogen bonds 2614 hydrogen bond angles 0 basepair planarities 738 basepair parallelities 1935 stacking parallelities Total time for adding SS restraints: 185.91 Time building geometry restraints manager: 76.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 14729 1.30 - 1.43: 71989 1.43 - 1.56: 67186 1.56 - 1.69: 9495 1.69 - 1.82: 292 Bond restraints: 163691 Sorted by residual: bond pdb=" O3' U B 701 " pdb=" P A B 702 " ideal model delta sigma weight residual 1.607 1.548 0.059 1.50e-02 4.44e+03 1.54e+01 bond pdb=" C5 A A 783 " pdb=" C6 A A 783 " ideal model delta sigma weight residual 1.406 1.339 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C5 A A 761 " pdb=" C6 A A 761 " ideal model delta sigma weight residual 1.406 1.345 0.061 2.00e-02 2.50e+03 9.18e+00 bond pdb=" C5 A Z 76 " pdb=" C6 A Z 76 " ideal model delta sigma weight residual 1.406 1.351 0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" C5 G A 467 " pdb=" C6 G A 467 " ideal model delta sigma weight residual 1.419 1.364 0.055 2.00e-02 2.50e+03 7.46e+00 ... (remaining 163686 not shown) Histogram of bond angle deviations from ideal: 96.90 - 105.29: 23850 105.29 - 113.69: 104630 113.69 - 122.08: 79918 122.08 - 130.48: 34259 130.48 - 138.87: 1873 Bond angle restraints: 244530 Sorted by residual: angle pdb=" C LEU S 67 " pdb=" N LEU S 68 " pdb=" CA LEU S 68 " ideal model delta sigma weight residual 122.31 138.87 -16.56 2.34e+00 1.83e-01 5.01e+01 angle pdb=" N ILE h 109 " pdb=" CA ILE h 109 " pdb=" C ILE h 109 " ideal model delta sigma weight residual 111.91 105.78 6.13 8.90e-01 1.26e+00 4.75e+01 angle pdb=" N ILE 1 32 " pdb=" CA ILE 1 32 " pdb=" C ILE 1 32 " ideal model delta sigma weight residual 109.34 122.49 -13.15 2.08e+00 2.31e-01 4.00e+01 angle pdb=" C ASN F 77 " pdb=" N ASN F 78 " pdb=" CA ASN F 78 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C4' A B 702 " pdb=" C3' A B 702 " pdb=" O3' A B 702 " ideal model delta sigma weight residual 113.00 121.33 -8.33 1.50e+00 4.44e-01 3.08e+01 ... (remaining 244525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 92103 35.93 - 71.86: 11344 71.86 - 107.79: 1397 107.79 - 143.72: 13 143.72 - 179.66: 24 Dihedral angle restraints: 104881 sinusoidal: 87161 harmonic: 17720 Sorted by residual: dihedral pdb=" CA THR c 151 " pdb=" C THR c 151 " pdb=" N PRO c 152 " pdb=" CA PRO c 152 " ideal model delta harmonic sigma weight residual -180.00 -107.67 -72.33 0 5.00e+00 4.00e-02 2.09e+02 dihedral pdb=" CA THR R 70 " pdb=" C THR R 70 " pdb=" N LYS R 71 " pdb=" CA LYS R 71 " ideal model delta harmonic sigma weight residual -180.00 -108.96 -71.04 0 5.00e+00 4.00e-02 2.02e+02 dihedral pdb=" CA ASP f 47 " pdb=" C ASP f 47 " pdb=" N ASN f 48 " pdb=" CA ASN f 48 " ideal model delta harmonic sigma weight residual -180.00 -120.22 -59.78 0 5.00e+00 4.00e-02 1.43e+02 ... (remaining 104878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 27980 0.084 - 0.167: 2979 0.167 - 0.251: 227 0.251 - 0.335: 29 0.335 - 0.418: 8 Chirality restraints: 31223 Sorted by residual: chirality pdb=" CB ILE I 75 " pdb=" CA ILE I 75 " pdb=" CG1 ILE I 75 " pdb=" CG2 ILE I 75 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C3' A A 244 " pdb=" C4' A A 244 " pdb=" O3' A A 244 " pdb=" C2' A A 244 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" CB VAL c 142 " pdb=" CA VAL c 142 " pdb=" CG1 VAL c 142 " pdb=" CG2 VAL c 142 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.37e+00 ... (remaining 31220 not shown) Planarity restraints: 13326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR c 151 " 0.086 5.00e-02 4.00e+02 1.28e-01 2.61e+01 pdb=" N PRO c 152 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO c 152 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO c 152 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR b 246 " -0.062 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO b 247 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO b 247 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO b 247 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY i 112 " 0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO i 113 " -0.155 5.00e-02 4.00e+02 pdb=" CA PRO i 113 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO i 113 " 0.049 5.00e-02 4.00e+02 ... (remaining 13323 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 17 2.23 - 2.90: 57450 2.90 - 3.56: 237390 3.56 - 4.23: 432121 4.23 - 4.90: 606132 Nonbonded interactions: 1333110 Sorted by model distance: nonbonded pdb=" O2' U A2506 " pdb=" O4' C A2507 " model vdw 1.560 2.440 nonbonded pdb=" OP1 G A2508 " pdb=" O5' A Z 76 " model vdw 1.820 3.040 nonbonded pdb=" N6 A A2572 " pdb=" OE1 GLN c 150 " model vdw 1.929 2.520 nonbonded pdb=" N2 G A1358 " pdb=" OP2 U A1372 " model vdw 2.015 2.520 nonbonded pdb=" O2' G A2576 " pdb=" OP2 C A2579 " model vdw 2.051 2.440 ... (remaining 1333105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.150 Extract box with map and model: 12.850 Check model and map are aligned: 1.620 Set scattering table: 1.060 Process input model: 463.450 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.420 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 487.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 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 : 0.011 0.101 163691 Z= 0.670 Angle : 1.035 16.563 244530 Z= 0.512 Chirality : 0.053 0.418 31223 Planarity : 0.007 0.128 13326 Dihedral : 23.705 179.655 93447 Min Nonbonded Distance : 1.560 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.74 % Favored : 86.92 % Rotamer: Outliers : 0.88 % Allowed : 11.20 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.45 % 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: -5.50 (0.08), residues: 6114 helix: -4.80 (0.05), residues: 1561 sheet: -3.34 (0.14), residues: 913 loop : -3.31 (0.08), residues: 3640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP b 213 HIS 0.015 0.002 HIS u 46 PHE 0.031 0.003 PHE c 118 TYR 0.026 0.003 TYR b 171 ARG 0.015 0.001 ARG q 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1186 time to evaluate : 5.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 395 MET cc_start: -0.2070 (ptt) cc_final: -0.2304 (ptt) REVERT: 5 398 MET cc_start: 0.2269 (mtp) cc_final: 0.0539 (mmt) REVERT: 5 399 ARG cc_start: 0.4950 (ptt180) cc_final: 0.3466 (mtt180) REVERT: H 31 MET cc_start: 0.6014 (ptm) cc_final: 0.5364 (ttt) REVERT: H 101 MET cc_start: 0.5413 (mtm) cc_final: 0.4983 (mtm) REVERT: L 100 LEU cc_start: 0.8045 (mt) cc_final: 0.7752 (mt) REVERT: N 74 SER cc_start: 0.7563 (p) cc_final: 0.7142 (p) REVERT: O 96 LEU cc_start: 0.7234 (tp) cc_final: 0.7003 (tp) REVERT: W 79 ASP cc_start: 0.7310 (p0) cc_final: 0.6792 (p0) REVERT: h 40 LYS cc_start: 0.7199 (ptmm) cc_final: 0.6932 (ptmm) REVERT: h 117 MET cc_start: 0.1133 (tpt) cc_final: -0.0366 (tpt) REVERT: j 73 ASP cc_start: 0.6633 (p0) cc_final: 0.6320 (p0) REVERT: j 93 GLN cc_start: 0.5849 (mm110) cc_final: 0.5222 (mm-40) REVERT: u 56 ASP cc_start: 0.5599 (p0) cc_final: 0.5358 (p0) REVERT: u 71 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.6960 (p) outliers start: 45 outliers final: 17 residues processed: 1225 average time/residue: 1.5025 time to fit residues: 3136.1592 Evaluate side-chains 712 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 694 time to evaluate : 6.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 905 optimal weight: 6.9990 chunk 812 optimal weight: 20.0000 chunk 450 optimal weight: 40.0000 chunk 277 optimal weight: 5.9990 chunk 548 optimal weight: 20.0000 chunk 434 optimal weight: 30.0000 chunk 840 optimal weight: 7.9990 chunk 325 optimal weight: 5.9990 chunk 510 optimal weight: 20.0000 chunk 625 optimal weight: 30.0000 chunk 973 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 6 GLN 0 16 HIS ** 3 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 298 ASN 5 328 GLN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN D 123 GLN ** E 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 GLN ** G 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN J 126 GLN M 77 HIS M 96 HIS ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 63 GLN Q 79 ASN ** R 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 HIS U 3 ASN ** U 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN W 91 GLN b 117 GLN ** b 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 32 ASN c 49 GLN c 148 GLN d 9 GLN ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 GLN e 63 GLN f 116 GLN f 143 GLN ** g 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 31 GLN i 47 HIS j 88 ASN ** j 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN k 54 GLN ** l 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 38 GLN o 56 HIS p 37 GLN p 44 GLN p 71 GLN p 72 ASN r 7 HIS r 102 HIS s 69 ASN s 74 ASN t 49 ASN ** v 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 23 ASN ** v 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 45 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 163691 Z= 0.256 Angle : 0.690 14.728 244530 Z= 0.347 Chirality : 0.037 0.308 31223 Planarity : 0.006 0.205 13326 Dihedral : 24.120 179.787 81155 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.37 % Favored : 90.37 % Rotamer: Outliers : 0.14 % Allowed : 5.75 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.30 % 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: -4.60 (0.09), residues: 6114 helix: -3.63 (0.09), residues: 1612 sheet: -2.84 (0.14), residues: 967 loop : -2.90 (0.09), residues: 3535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP b 213 HIS 0.010 0.001 HIS b 230 PHE 0.027 0.002 PHE b 30 TYR 0.023 0.002 TYR b 96 ARG 0.047 0.001 ARG L 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 909 time to evaluate : 6.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 26 ASN cc_start: 0.7900 (m-40) cc_final: 0.7362 (m-40) REVERT: 5 274 MET cc_start: -0.3460 (mpp) cc_final: -0.4577 (ptt) REVERT: 5 395 MET cc_start: -0.1878 (ptt) cc_final: -0.2159 (ptt) REVERT: 5 399 ARG cc_start: 0.4868 (ptt180) cc_final: 0.3306 (mtt180) REVERT: D 142 MET cc_start: 0.7077 (mmt) cc_final: 0.6793 (mmt) REVERT: F 71 MET cc_start: 0.6105 (mmm) cc_final: 0.5362 (mmm) REVERT: G 90 MET cc_start: 0.6179 (mmt) cc_final: 0.5956 (mmm) REVERT: H 31 MET cc_start: 0.6155 (ptm) cc_final: 0.5485 (ttp) REVERT: H 72 THR cc_start: 0.7905 (m) cc_final: 0.7348 (t) REVERT: W 37 ASP cc_start: 0.6942 (p0) cc_final: 0.6639 (p0) REVERT: W 79 ASP cc_start: 0.7056 (p0) cc_final: 0.6839 (p0) REVERT: e 18 THR cc_start: 0.8200 (p) cc_final: 0.7613 (p) REVERT: h 117 MET cc_start: -0.0075 (tpt) cc_final: -0.1149 (tpt) REVERT: l 9 PHE cc_start: 0.7718 (m-10) cc_final: 0.7193 (m-80) REVERT: l 41 LEU cc_start: 0.7409 (mm) cc_final: 0.6916 (mm) REVERT: p 17 ILE cc_start: 0.6842 (tt) cc_final: 0.6557 (tt) REVERT: r 38 TYR cc_start: 0.7382 (m-10) cc_final: 0.7133 (m-10) outliers start: 7 outliers final: 0 residues processed: 916 average time/residue: 1.4192 time to fit residues: 2229.3046 Evaluate side-chains 633 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 633 time to evaluate : 6.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 541 optimal weight: 0.5980 chunk 302 optimal weight: 20.0000 chunk 810 optimal weight: 6.9990 chunk 662 optimal weight: 0.9990 chunk 268 optimal weight: 40.0000 chunk 975 optimal weight: 6.9990 chunk 1053 optimal weight: 1.9990 chunk 868 optimal weight: 8.9990 chunk 967 optimal weight: 20.0000 chunk 332 optimal weight: 20.0000 chunk 782 optimal weight: 0.1980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 35 GLN 3 96 GLN ** 3 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 ASN F 73 ASN ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN ** K 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 HIS ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 9 HIS Q 63 GLN R 9 GLN ** R 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 9 ASN W 70 HIS b 226 ASN ** b 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 97 ASN d 115 GLN g 18 GLN ** l 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 88 ASN ** n 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 77 HIS ** s 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 ASN s 74 ASN ** v 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 25 GLN w 36 GLN ** w 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 34 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 163691 Z= 0.146 Angle : 0.551 13.530 244530 Z= 0.285 Chirality : 0.032 0.273 31223 Planarity : 0.005 0.160 13326 Dihedral : 23.919 179.142 81155 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.22 % Favored : 90.56 % Rotamer: Outliers : 0.04 % Allowed : 5.36 % Favored : 94.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.22 % 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: -4.03 (0.09), residues: 6114 helix: -2.96 (0.10), residues: 1627 sheet: -2.42 (0.15), residues: 891 loop : -2.68 (0.09), residues: 3596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP W 80 HIS 0.008 0.001 HIS G 11 PHE 0.036 0.001 PHE H 26 TYR 0.027 0.002 TYR V 38 ARG 0.021 0.001 ARG r 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 904 time to evaluate : 6.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 96 GLN cc_start: 0.7588 (mm110) cc_final: 0.6823 (mm110) REVERT: 5 395 MET cc_start: -0.2132 (ptt) cc_final: -0.2424 (ptt) REVERT: 5 399 ARG cc_start: 0.4845 (ptt180) cc_final: 0.3299 (mtt180) REVERT: 6 12 LYS cc_start: 0.6721 (mmpt) cc_final: 0.6412 (mmmt) REVERT: I 83 LEU cc_start: 0.7584 (tp) cc_final: 0.6715 (tt) REVERT: U 27 MET cc_start: 0.7710 (ppp) cc_final: 0.7479 (ppp) REVERT: V 5 LYS cc_start: 0.5968 (mmtt) cc_final: 0.5562 (mmtt) REVERT: b 114 ASP cc_start: 0.6038 (m-30) cc_final: 0.5420 (m-30) REVERT: b 181 MET cc_start: 0.5953 (mmp) cc_final: 0.5557 (mmm) REVERT: c 2 ILE cc_start: 0.7640 (mp) cc_final: 0.7363 (mp) REVERT: h 117 MET cc_start: 0.0223 (tpt) cc_final: -0.0654 (tpt) REVERT: i 67 ASN cc_start: 0.5959 (t0) cc_final: 0.5715 (t0) REVERT: i 81 ILE cc_start: 0.7922 (tp) cc_final: 0.7249 (tp) REVERT: l 41 LEU cc_start: 0.7419 (mm) cc_final: 0.6922 (mm) REVERT: m 20 MET cc_start: 0.5252 (tpt) cc_final: 0.5019 (tpp) REVERT: n 89 ASP cc_start: 0.6867 (m-30) cc_final: 0.6646 (m-30) REVERT: o 13 MET cc_start: 0.7446 (mmp) cc_final: 0.6969 (mmm) REVERT: q 77 PHE cc_start: 0.7850 (t80) cc_final: 0.7647 (t80) REVERT: r 11 ARG cc_start: 0.7931 (tpt170) cc_final: 0.7617 (tpt170) REVERT: v 11 ARG cc_start: 0.6243 (tpt170) cc_final: 0.5994 (mmt180) outliers start: 2 outliers final: 1 residues processed: 906 average time/residue: 1.3935 time to fit residues: 2151.9875 Evaluate side-chains 641 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 640 time to evaluate : 6.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 963 optimal weight: 5.9990 chunk 733 optimal weight: 7.9990 chunk 506 optimal weight: 40.0000 chunk 107 optimal weight: 20.0000 chunk 465 optimal weight: 50.0000 chunk 654 optimal weight: 0.0770 chunk 978 optimal weight: 20.0000 chunk 1036 optimal weight: 30.0000 chunk 511 optimal weight: 50.0000 chunk 927 optimal weight: 20.0000 chunk 279 optimal weight: 20.0000 overall best weight: 10.8150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN F 70 ASN ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 HIS K 58 ASN L 64 GLN ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 28 GLN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 HIS R 9 GLN ** R 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 HIS W 48 GLN ** b 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 GLN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 2 GLN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 38 GLN p 37 GLN p 52 GLN ** s 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 74 ASN u 46 HIS ** v 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 163691 Z= 0.327 Angle : 0.669 11.093 244530 Z= 0.342 Chirality : 0.036 0.326 31223 Planarity : 0.006 0.099 13326 Dihedral : 24.189 179.802 81155 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 27.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.19 % Favored : 89.63 % Rotamer: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.22 % 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: -3.56 (0.10), residues: 6114 helix: -2.24 (0.11), residues: 1606 sheet: -2.44 (0.15), residues: 1007 loop : -2.44 (0.10), residues: 3501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP b 213 HIS 0.015 0.002 HIS b 230 PHE 0.030 0.002 PHE i 89 TYR 0.030 0.002 TYR 6 48 ARG 0.012 0.001 ARG r 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 795 time to evaluate : 6.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 143 MET cc_start: 0.6689 (tpt) cc_final: 0.3805 (tpt) REVERT: 5 1 MET cc_start: 0.1328 (ttm) cc_final: 0.0618 (tpt) REVERT: 5 312 ASP cc_start: 0.4517 (p0) cc_final: 0.4207 (p0) REVERT: 5 399 ARG cc_start: 0.5039 (ptt180) cc_final: 0.3403 (mtt180) REVERT: 5 428 MET cc_start: 0.5551 (mmp) cc_final: 0.5314 (mmm) REVERT: 6 12 LYS cc_start: 0.7293 (mmpt) cc_final: 0.6417 (mmmt) REVERT: D 142 MET cc_start: 0.7202 (mmt) cc_final: 0.6855 (mmt) REVERT: G 1 MET cc_start: 0.6395 (ppp) cc_final: 0.5799 (ppp) REVERT: H 31 MET cc_start: 0.7273 (ttp) cc_final: 0.5954 (tpp) REVERT: H 101 MET cc_start: 0.5392 (ttt) cc_final: 0.4798 (ttt) REVERT: L 53 ARG cc_start: 0.6504 (tpp-160) cc_final: 0.5918 (tpm170) REVERT: L 125 LYS cc_start: 0.5090 (ptpt) cc_final: 0.3599 (pttt) REVERT: U 28 MET cc_start: 0.6886 (mmp) cc_final: 0.6627 (mmm) REVERT: V 5 LYS cc_start: 0.5788 (mmtt) cc_final: 0.5394 (mmtt) REVERT: W 37 ASP cc_start: 0.7592 (p0) cc_final: 0.7169 (p0) REVERT: W 79 ASP cc_start: 0.7085 (p0) cc_final: 0.6871 (p0) REVERT: c 18 ASP cc_start: 0.7915 (p0) cc_final: 0.7500 (p0) REVERT: h 117 MET cc_start: 0.1259 (tpt) cc_final: 0.0579 (tpt) REVERT: i 81 ILE cc_start: 0.7959 (tp) cc_final: 0.7160 (tp) REVERT: l 41 LEU cc_start: 0.7413 (mm) cc_final: 0.7066 (mm) REVERT: n 89 ASP cc_start: 0.7217 (m-30) cc_final: 0.6799 (m-30) REVERT: o 13 MET cc_start: 0.8062 (mmp) cc_final: 0.7807 (mmp) REVERT: r 38 TYR cc_start: 0.7933 (m-10) cc_final: 0.7520 (m-10) REVERT: x 47 MET cc_start: 0.7793 (mmm) cc_final: 0.7592 (mmt) outliers start: 2 outliers final: 0 residues processed: 796 average time/residue: 1.3818 time to fit residues: 1881.1723 Evaluate side-chains 579 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 579 time to evaluate : 6.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 862 optimal weight: 0.6980 chunk 588 optimal weight: 50.0000 chunk 15 optimal weight: 0.5980 chunk 771 optimal weight: 30.0000 chunk 427 optimal weight: 40.0000 chunk 884 optimal weight: 50.0000 chunk 716 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 529 optimal weight: 7.9990 chunk 930 optimal weight: 30.0000 chunk 261 optimal weight: 20.0000 overall best weight: 9.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 151 GLN ** 5 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 429 ASN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN J 126 GLN M 72 HIS ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 ASN S 54 GLN ** U 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 HIS ** b 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 163 GLN b 200 HIS ** b 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 260 ASN ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 GLN ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 80 HIS j 89 ASN ** j 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 38 GLN p 52 GLN q 82 HIS ** s 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 74 ASN ** t 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 19 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 163691 Z= 0.271 Angle : 0.599 12.045 244530 Z= 0.308 Chirality : 0.034 0.279 31223 Planarity : 0.005 0.105 13326 Dihedral : 24.307 179.940 81155 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 24.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.85 % Favored : 89.99 % Rotamer: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.24 % 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: -3.33 (0.10), residues: 6114 helix: -1.91 (0.12), residues: 1654 sheet: -2.39 (0.15), residues: 989 loop : -2.33 (0.10), residues: 3471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.002 TRP H 103 HIS 0.009 0.001 HIS b 230 PHE 0.028 0.002 PHE D 37 TYR 0.045 0.002 TYR U 36 ARG 0.014 0.001 ARG i 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 779 time to evaluate : 5.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 MET cc_start: 0.6866 (mmm) cc_final: 0.6621 (tpp) REVERT: 3 74 ASN cc_start: 0.7870 (m-40) cc_final: 0.7480 (m-40) REVERT: 3 143 MET cc_start: 0.6942 (tpt) cc_final: 0.5900 (tpt) REVERT: 5 1 MET cc_start: 0.2336 (ttm) cc_final: 0.1361 (tpt) REVERT: 5 274 MET cc_start: -0.3690 (mpp) cc_final: -0.5086 (ptt) REVERT: 5 399 ARG cc_start: 0.4903 (ptt180) cc_final: 0.3317 (mtt180) REVERT: C 9 MET cc_start: 0.7230 (ppp) cc_final: 0.6544 (ppp) REVERT: D 142 MET cc_start: 0.7315 (mmt) cc_final: 0.7045 (mmt) REVERT: F 36 LEU cc_start: 0.8481 (tp) cc_final: 0.8239 (tp) REVERT: G 1 MET cc_start: 0.7006 (ppp) cc_final: 0.6725 (ppp) REVERT: H 31 MET cc_start: 0.7609 (ttp) cc_final: 0.5781 (tpp) REVERT: H 72 THR cc_start: 0.7961 (m) cc_final: 0.7724 (t) REVERT: L 53 ARG cc_start: 0.6058 (tpp-160) cc_final: 0.5033 (tpt170) REVERT: L 125 LYS cc_start: 0.4213 (ptpt) cc_final: 0.2769 (pttt) REVERT: R 25 ILE cc_start: 0.8103 (mm) cc_final: 0.7872 (mm) REVERT: V 5 LYS cc_start: 0.5987 (mmtt) cc_final: 0.5500 (mmtt) REVERT: W 1 MET cc_start: 0.5522 (mpp) cc_final: 0.5010 (mpp) REVERT: W 37 ASP cc_start: 0.7757 (p0) cc_final: 0.7345 (p0) REVERT: b 153 GLN cc_start: 0.6881 (mp10) cc_final: 0.6167 (mp10) REVERT: c 2 ILE cc_start: 0.8041 (mp) cc_final: 0.7669 (mp) REVERT: c 18 ASP cc_start: 0.7496 (p0) cc_final: 0.7156 (p0) REVERT: h 117 MET cc_start: 0.1691 (tpt) cc_final: 0.0715 (tpt) REVERT: i 81 ILE cc_start: 0.7917 (tp) cc_final: 0.7095 (tp) REVERT: l 41 LEU cc_start: 0.7267 (mm) cc_final: 0.6812 (mm) REVERT: q 77 PHE cc_start: 0.8094 (t80) cc_final: 0.7864 (t80) REVERT: s 89 ASP cc_start: 0.8079 (p0) cc_final: 0.7863 (p0) outliers start: 2 outliers final: 1 residues processed: 780 average time/residue: 1.3458 time to fit residues: 1808.8986 Evaluate side-chains 573 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 572 time to evaluate : 6.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 348 optimal weight: 20.0000 chunk 933 optimal weight: 5.9990 chunk 204 optimal weight: 20.0000 chunk 608 optimal weight: 50.0000 chunk 255 optimal weight: 20.0000 chunk 1037 optimal weight: 4.9990 chunk 861 optimal weight: 6.9990 chunk 480 optimal weight: 50.0000 chunk 86 optimal weight: 20.0000 chunk 343 optimal weight: 20.0000 chunk 544 optimal weight: 9.9990 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 151 GLN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 GLN ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 HIS ** b 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 260 ASN ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 GLN ** i 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 86 GLN j 89 ASN ** j 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 38 GLN p 52 GLN ** s 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 74 ASN ** t 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 163691 Z= 0.281 Angle : 0.613 12.493 244530 Z= 0.312 Chirality : 0.034 0.315 31223 Planarity : 0.005 0.091 13326 Dihedral : 24.335 179.637 81155 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 28.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.35 % Favored : 89.45 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.18 % 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: -3.13 (0.10), residues: 6114 helix: -1.62 (0.12), residues: 1654 sheet: -2.45 (0.14), residues: 1047 loop : -2.20 (0.10), residues: 3413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 213 HIS 0.012 0.002 HIS t 44 PHE 0.031 0.002 PHE L 52 TYR 0.026 0.002 TYR S 32 ARG 0.025 0.001 ARG N 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 742 time to evaluate : 6.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 MET cc_start: 0.7177 (mmm) cc_final: 0.6852 (mmm) REVERT: 0 26 ASN cc_start: 0.8139 (m110) cc_final: 0.7667 (m110) REVERT: 3 74 ASN cc_start: 0.7945 (m-40) cc_final: 0.7580 (m-40) REVERT: 5 1 MET cc_start: 0.2001 (ttm) cc_final: 0.1310 (tpt) REVERT: 5 274 MET cc_start: -0.3345 (mpp) cc_final: -0.5323 (ptp) REVERT: 5 399 ARG cc_start: 0.4992 (ptt180) cc_final: 0.3351 (mtt180) REVERT: C 9 MET cc_start: 0.6958 (ppp) cc_final: 0.6475 (ppp) REVERT: D 142 MET cc_start: 0.7346 (mmt) cc_final: 0.7076 (mmt) REVERT: H 31 MET cc_start: 0.7660 (ttp) cc_final: 0.5869 (tpp) REVERT: L 53 ARG cc_start: 0.5447 (tpp-160) cc_final: 0.4577 (tpt170) REVERT: L 125 LYS cc_start: 0.4577 (ptpt) cc_final: 0.3286 (pttt) REVERT: M 18 LYS cc_start: 0.8243 (tmmt) cc_final: 0.7899 (tttt) REVERT: R 25 ILE cc_start: 0.8216 (mm) cc_final: 0.7991 (mm) REVERT: V 5 LYS cc_start: 0.6156 (mmtt) cc_final: 0.5900 (mmtp) REVERT: W 1 MET cc_start: 0.5508 (mpp) cc_final: 0.4820 (mpp) REVERT: W 37 ASP cc_start: 0.7664 (p0) cc_final: 0.7207 (p0) REVERT: b 153 GLN cc_start: 0.6833 (mp10) cc_final: 0.6070 (mp10) REVERT: b 181 MET cc_start: 0.5904 (mmp) cc_final: 0.5433 (mmm) REVERT: c 18 ASP cc_start: 0.7828 (p0) cc_final: 0.7490 (p0) REVERT: e 17 MET cc_start: 0.7441 (tmm) cc_final: 0.6689 (tmm) REVERT: h 117 MET cc_start: 0.1779 (tpt) cc_final: 0.0548 (tpt) REVERT: i 81 ILE cc_start: 0.8265 (tp) cc_final: 0.7448 (tp) REVERT: l 41 LEU cc_start: 0.7572 (mm) cc_final: 0.7126 (mm) REVERT: m 14 SER cc_start: 0.7529 (p) cc_final: 0.7142 (p) REVERT: o 13 MET cc_start: 0.7809 (mmp) cc_final: 0.7587 (mmp) outliers start: 0 outliers final: 0 residues processed: 742 average time/residue: 1.3432 time to fit residues: 1713.0607 Evaluate side-chains 549 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 549 time to evaluate : 6.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 999 optimal weight: 4.9990 chunk 116 optimal weight: 20.0000 chunk 590 optimal weight: 50.0000 chunk 757 optimal weight: 50.0000 chunk 586 optimal weight: 8.9990 chunk 873 optimal weight: 6.9990 chunk 579 optimal weight: 1.9990 chunk 1033 optimal weight: 8.9990 chunk 646 optimal weight: 1.9990 chunk 629 optimal weight: 6.9990 chunk 477 optimal weight: 40.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN ** 3 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 54 HIS ** 3 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 ASN M 72 HIS ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 56 GLN ** U 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 260 ASN ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 2 GLN j 93 GLN n 38 GLN p 52 GLN s 69 ASN s 74 ASN t 24 ASN ** v 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 163691 Z= 0.165 Angle : 0.531 12.116 244530 Z= 0.273 Chirality : 0.031 0.229 31223 Planarity : 0.005 0.118 13326 Dihedral : 24.232 179.818 81155 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.39 % Favored : 90.45 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.10), residues: 6114 helix: -1.35 (0.13), residues: 1656 sheet: -2.29 (0.15), residues: 1009 loop : -2.08 (0.10), residues: 3449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP b 213 HIS 0.013 0.001 HIS b 230 PHE 0.023 0.001 PHE D 37 TYR 0.022 0.001 TYR U 36 ARG 0.011 0.000 ARG L 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 743 time to evaluate : 6.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 MET cc_start: 0.7223 (mmm) cc_final: 0.6961 (tpp) REVERT: 3 74 ASN cc_start: 0.7854 (m-40) cc_final: 0.7516 (m-40) REVERT: 3 96 GLN cc_start: 0.8507 (mm110) cc_final: 0.7306 (mm-40) REVERT: 5 1 MET cc_start: 0.2121 (ttm) cc_final: 0.1382 (tpt) REVERT: 5 274 MET cc_start: -0.3360 (mpp) cc_final: -0.5309 (ptp) REVERT: 5 399 ARG cc_start: 0.4948 (ptt180) cc_final: 0.3319 (mtt180) REVERT: C 9 MET cc_start: 0.6721 (ppp) cc_final: 0.6368 (ppp) REVERT: D 142 MET cc_start: 0.7133 (mmt) cc_final: 0.6853 (mmt) REVERT: G 1 MET cc_start: 0.6911 (ppp) cc_final: 0.6657 (ppp) REVERT: H 31 MET cc_start: 0.7697 (ttp) cc_final: 0.5951 (tpp) REVERT: L 125 LYS cc_start: 0.4328 (ptpt) cc_final: 0.2990 (pttt) REVERT: M 18 LYS cc_start: 0.8310 (tmmt) cc_final: 0.7950 (tttt) REVERT: V 5 LYS cc_start: 0.6509 (mmtt) cc_final: 0.6119 (mmtt) REVERT: W 1 MET cc_start: 0.5322 (mpp) cc_final: 0.4869 (mpp) REVERT: W 37 ASP cc_start: 0.7570 (p0) cc_final: 0.7121 (p0) REVERT: b 181 MET cc_start: 0.5992 (mmp) cc_final: 0.5452 (mmm) REVERT: e 17 MET cc_start: 0.7192 (tmm) cc_final: 0.6457 (tmm) REVERT: g 18 GLN cc_start: 0.7765 (mm110) cc_final: 0.7450 (mm110) REVERT: h 117 MET cc_start: 0.1609 (tpt) cc_final: 0.0171 (tpt) REVERT: i 81 ILE cc_start: 0.8030 (tp) cc_final: 0.7127 (tp) REVERT: l 41 LEU cc_start: 0.7627 (mm) cc_final: 0.7227 (mm) outliers start: 0 outliers final: 0 residues processed: 743 average time/residue: 1.3505 time to fit residues: 1729.8984 Evaluate side-chains 563 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 563 time to evaluate : 6.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 639 optimal weight: 6.9990 chunk 412 optimal weight: 40.0000 chunk 617 optimal weight: 10.0000 chunk 311 optimal weight: 30.0000 chunk 203 optimal weight: 20.0000 chunk 200 optimal weight: 20.0000 chunk 656 optimal weight: 9.9990 chunk 703 optimal weight: 6.9990 chunk 510 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 812 optimal weight: 0.3980 overall best weight: 6.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 26 ASN ** 3 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 GLN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 ASN ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 ASN ** U 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 260 ASN ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 2 GLN i 86 GLN j 89 ASN n 38 GLN ** o 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 52 GLN s 74 ASN ** v 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 163691 Z= 0.210 Angle : 0.549 12.045 244530 Z= 0.282 Chirality : 0.032 0.232 31223 Planarity : 0.005 0.166 13326 Dihedral : 24.197 179.762 81155 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 24.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.99 % Favored : 89.86 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.10), residues: 6114 helix: -1.25 (0.13), residues: 1643 sheet: -2.22 (0.15), residues: 1011 loop : -2.03 (0.10), residues: 3460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP b 213 HIS 0.010 0.001 HIS b 230 PHE 0.030 0.001 PHE L 52 TYR 0.012 0.001 TYR b 96 ARG 0.012 0.001 ARG L 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 718 time to evaluate : 6.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 MET cc_start: 0.7270 (mmm) cc_final: 0.6953 (tpp) REVERT: 3 74 ASN cc_start: 0.7886 (m-40) cc_final: 0.7571 (m-40) REVERT: 5 1 MET cc_start: 0.2332 (ttm) cc_final: 0.1529 (tpt) REVERT: 5 274 MET cc_start: -0.3225 (mpp) cc_final: -0.5195 (ptp) REVERT: 5 399 ARG cc_start: 0.4995 (ptt180) cc_final: 0.3281 (mtt180) REVERT: C 9 MET cc_start: 0.6789 (ppp) cc_final: 0.6438 (ppp) REVERT: D 142 MET cc_start: 0.7194 (mmt) cc_final: 0.6924 (mmt) REVERT: F 71 MET cc_start: 0.3736 (mmp) cc_final: 0.3087 (mmp) REVERT: H 31 MET cc_start: 0.7767 (ttp) cc_final: 0.6036 (tpp) REVERT: L 53 ARG cc_start: 0.4957 (tpm170) cc_final: 0.3746 (tpm170) REVERT: L 125 LYS cc_start: 0.4148 (ptpt) cc_final: 0.2803 (pttt) REVERT: R 17 MET cc_start: 0.2392 (tpt) cc_final: 0.1923 (tpt) REVERT: V 5 LYS cc_start: 0.6440 (mmtt) cc_final: 0.5977 (mmtp) REVERT: W 1 MET cc_start: 0.5079 (mpp) cc_final: 0.4481 (mpp) REVERT: W 37 ASP cc_start: 0.7650 (p0) cc_final: 0.7298 (p0) REVERT: b 181 MET cc_start: 0.5987 (mmp) cc_final: 0.5537 (mmm) REVERT: e 17 MET cc_start: 0.7323 (tmm) cc_final: 0.6605 (tmm) REVERT: g 18 GLN cc_start: 0.7856 (mm110) cc_final: 0.7537 (mm110) REVERT: h 117 MET cc_start: 0.1544 (tpt) cc_final: -0.0063 (tpt) REVERT: i 81 ILE cc_start: 0.7968 (tp) cc_final: 0.6985 (tp) REVERT: l 41 LEU cc_start: 0.7594 (mm) cc_final: 0.7176 (mm) REVERT: m 24 MET cc_start: 0.6427 (mmt) cc_final: 0.5958 (mmp) outliers start: 0 outliers final: 0 residues processed: 718 average time/residue: 1.4432 time to fit residues: 1803.5780 Evaluate side-chains 540 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 540 time to evaluate : 6.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 939 optimal weight: 0.0970 chunk 989 optimal weight: 10.0000 chunk 903 optimal weight: 4.9990 chunk 962 optimal weight: 30.0000 chunk 579 optimal weight: 20.0000 chunk 419 optimal weight: 50.0000 chunk 756 optimal weight: 60.0000 chunk 295 optimal weight: 40.0000 chunk 870 optimal weight: 30.0000 chunk 910 optimal weight: 8.9990 chunk 959 optimal weight: 20.0000 overall best weight: 8.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 26 ASN ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 HIS F 70 ASN ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 ASN ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 260 ASN ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 2 GLN n 38 GLN p 52 GLN q 12 HIS s 74 ASN ** v 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 45 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.5728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 163691 Z= 0.251 Angle : 0.579 12.406 244530 Z= 0.297 Chirality : 0.033 0.589 31223 Planarity : 0.005 0.145 13326 Dihedral : 24.262 179.491 81155 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 27.85 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.32 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.10), residues: 6114 helix: -1.30 (0.12), residues: 1668 sheet: -2.22 (0.15), residues: 984 loop : -2.01 (0.10), residues: 3462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP e 97 HIS 0.010 0.001 HIS b 230 PHE 0.027 0.002 PHE E 107 TYR 0.022 0.002 TYR i 75 ARG 0.013 0.001 ARG F 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 694 time to evaluate : 6.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 MET cc_start: 0.7319 (mmm) cc_final: 0.6987 (tpp) REVERT: 3 74 ASN cc_start: 0.7924 (m-40) cc_final: 0.7594 (m-40) REVERT: 5 1 MET cc_start: 0.2699 (ttm) cc_final: 0.1837 (tpt) REVERT: 5 274 MET cc_start: -0.3083 (mpp) cc_final: -0.5138 (ptp) REVERT: 5 399 ARG cc_start: 0.4993 (ptt180) cc_final: 0.3245 (mtt180) REVERT: C 9 MET cc_start: 0.6967 (ppp) cc_final: 0.6647 (ppp) REVERT: D 142 MET cc_start: 0.7175 (mmt) cc_final: 0.6936 (mmt) REVERT: H 31 MET cc_start: 0.7875 (ttp) cc_final: 0.6101 (tpp) REVERT: L 13 ARG cc_start: 0.7178 (ttp80) cc_final: 0.6356 (ttp80) REVERT: L 53 ARG cc_start: 0.4348 (tpm170) cc_final: 0.2470 (tpt170) REVERT: L 125 LYS cc_start: 0.3869 (ptpt) cc_final: 0.2571 (pttt) REVERT: N 64 VAL cc_start: 0.3903 (t) cc_final: 0.3678 (t) REVERT: R 17 MET cc_start: 0.2298 (tpt) cc_final: 0.1928 (tpt) REVERT: V 5 LYS cc_start: 0.6474 (mmtt) cc_final: 0.6111 (mmtt) REVERT: W 1 MET cc_start: 0.5519 (mpp) cc_final: 0.5096 (mpp) REVERT: b 60 GLN cc_start: 0.7458 (mp10) cc_final: 0.6915 (mp10) REVERT: b 153 GLN cc_start: 0.6607 (mp10) cc_final: 0.6223 (mp10) REVERT: b 181 MET cc_start: 0.6045 (mmp) cc_final: 0.5610 (mmm) REVERT: e 17 MET cc_start: 0.7536 (tmm) cc_final: 0.6846 (tmm) REVERT: f 114 ASP cc_start: 0.6971 (t0) cc_final: 0.6699 (t0) REVERT: h 117 MET cc_start: 0.1752 (tpt) cc_final: 0.0325 (tpt) REVERT: i 81 ILE cc_start: 0.7934 (tp) cc_final: 0.7066 (tp) REVERT: l 41 LEU cc_start: 0.7594 (mm) cc_final: 0.7120 (mm) REVERT: t 3 THR cc_start: 0.7856 (t) cc_final: 0.7625 (p) REVERT: x 57 VAL cc_start: 0.8660 (t) cc_final: 0.8197 (p) REVERT: z 8 LYS cc_start: 0.6189 (ptpt) cc_final: 0.5656 (pttt) outliers start: 0 outliers final: 0 residues processed: 694 average time/residue: 1.3570 time to fit residues: 1630.3616 Evaluate side-chains 541 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 541 time to evaluate : 6.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 632 optimal weight: 10.0000 chunk 1018 optimal weight: 9.9990 chunk 621 optimal weight: 20.0000 chunk 483 optimal weight: 40.0000 chunk 707 optimal weight: 8.9990 chunk 1067 optimal weight: 40.0000 chunk 982 optimal weight: 5.9990 chunk 850 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 656 optimal weight: 9.9990 chunk 521 optimal weight: 8.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 ASN ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 260 ASN ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 2 GLN ** g 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 107 ASN n 38 GLN o 77 HIS p 52 GLN s 74 ASN ** v 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.5947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 163691 Z= 0.250 Angle : 0.581 12.971 244530 Z= 0.297 Chirality : 0.033 0.232 31223 Planarity : 0.005 0.083 13326 Dihedral : 24.301 179.568 81155 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 28.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.35 % Favored : 89.48 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.10), residues: 6114 helix: -1.32 (0.12), residues: 1684 sheet: -2.24 (0.15), residues: 979 loop : -1.93 (0.10), residues: 3451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP b 213 HIS 0.008 0.001 HIS b 230 PHE 0.024 0.002 PHE L 52 TYR 0.016 0.002 TYR l 103 ARG 0.010 0.001 ARG L 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12228 Ramachandran restraints generated. 6114 Oldfield, 0 Emsley, 6114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 6.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 MET cc_start: 0.7302 (mmm) cc_final: 0.7053 (tpp) REVERT: 3 74 ASN cc_start: 0.7955 (m-40) cc_final: 0.7602 (m-40) REVERT: 5 1 MET cc_start: 0.2960 (ttm) cc_final: 0.2028 (tpt) REVERT: 5 274 MET cc_start: -0.3058 (mpp) cc_final: -0.5150 (ptp) REVERT: 5 399 ARG cc_start: 0.4912 (ptt180) cc_final: 0.3098 (mtt180) REVERT: C 9 MET cc_start: 0.7213 (ppp) cc_final: 0.6810 (ppp) REVERT: D 142 MET cc_start: 0.7191 (mmt) cc_final: 0.6944 (mmt) REVERT: G 74 LEU cc_start: 0.8730 (tp) cc_final: 0.8523 (tp) REVERT: H 31 MET cc_start: 0.7671 (ttp) cc_final: 0.6027 (tpp) REVERT: L 53 ARG cc_start: 0.4718 (tpm170) cc_final: 0.3118 (tpt170) REVERT: L 125 LYS cc_start: 0.3601 (ptpt) cc_final: 0.2264 (pttt) REVERT: R 17 MET cc_start: 0.2417 (tpt) cc_final: 0.2083 (tpt) REVERT: V 5 LYS cc_start: 0.6464 (mmtt) cc_final: 0.6118 (mmtt) REVERT: W 1 MET cc_start: 0.5422 (mpp) cc_final: 0.4984 (mpp) REVERT: b 60 GLN cc_start: 0.7360 (mp10) cc_final: 0.6876 (mp10) REVERT: b 153 GLN cc_start: 0.6510 (mp10) cc_final: 0.6129 (mp10) REVERT: b 181 MET cc_start: 0.6068 (mmp) cc_final: 0.5600 (mmm) REVERT: e 17 MET cc_start: 0.7602 (tmm) cc_final: 0.6913 (tmm) REVERT: g 18 GLN cc_start: 0.7943 (mm110) cc_final: 0.7642 (mm110) REVERT: h 117 MET cc_start: 0.1374 (tpt) cc_final: 0.0106 (tpt) REVERT: i 81 ILE cc_start: 0.7980 (tp) cc_final: 0.7102 (tp) REVERT: l 41 LEU cc_start: 0.7582 (mm) cc_final: 0.7131 (mm) REVERT: m 24 MET cc_start: 0.6135 (mmp) cc_final: 0.5693 (mmp) REVERT: t 3 THR cc_start: 0.8009 (t) cc_final: 0.7736 (p) REVERT: x 57 VAL cc_start: 0.8631 (t) cc_final: 0.8204 (p) REVERT: z 8 LYS cc_start: 0.6368 (ptpt) cc_final: 0.5612 (pttt) outliers start: 0 outliers final: 0 residues processed: 687 average time/residue: 1.3250 time to fit residues: 1585.0154 Evaluate side-chains 533 residues out of total 5098 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 533 time to evaluate : 6.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 675 optimal weight: 10.0000 chunk 905 optimal weight: 1.9990 chunk 260 optimal weight: 20.0000 chunk 784 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 236 optimal weight: 20.0000 chunk 851 optimal weight: 30.0000 chunk 356 optimal weight: 20.0000 chunk 874 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 overall best weight: 12.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 2 GLN i 76 HIS ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 38 GLN ** o 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 52 GLN s 74 ASN ** w 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.036336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.021890 restraints weight = 2034506.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.021995 restraints weight = 1077990.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 77)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.021255 restraints weight = 767417.288| |-----------------------------------------------------------------------------| r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 163691 Z= 0.340 Angle : 0.671 15.129 244530 Z= 0.341 Chirality : 0.036 0.238 31223 Planarity : 0.006 0.099 13326 Dihedral : 24.480 179.539 81155 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 36.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.65 % Favored : 88.16 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.10), residues: 6114 helix: -1.50 (0.12), residues: 1677 sheet: -2.34 (0.15), residues: 972 loop : -1.99 (0.10), residues: 3465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP b 213 HIS 0.010 0.002 HIS b 230 PHE 0.019 0.002 PHE F 33 TYR 0.026 0.002 TYR p 45 ARG 0.015 0.001 ARG F 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30135.29 seconds wall clock time: 535 minutes 54.12 seconds (32154.12 seconds total)