Starting phenix.real_space_refine on Tue Mar 26 22:58:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5b_12734/03_2024/7o5b_12734_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5b_12734/03_2024/7o5b_12734.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5b_12734/03_2024/7o5b_12734_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5b_12734/03_2024/7o5b_12734_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5b_12734/03_2024/7o5b_12734_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5b_12734/03_2024/7o5b_12734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5b_12734/03_2024/7o5b_12734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5b_12734/03_2024/7o5b_12734_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o5b_12734/03_2024/7o5b_12734_updated.pdb" } resolution = 3.33 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= 0.025 sd= 0.127 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 4883 5.49 5 S 140 5.16 5 C 75216 2.51 5 N 27958 2.21 5 O 42225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "q GLU 91": "OE1" <-> "OE2" Residue "Z GLU 30": "OE1" <-> "OE2" Residue "Z GLU 115": "OE1" <-> "OE2" Residue "Z ASP 123": "OD1" <-> "OD2" Residue "Z GLU 236": "OE1" <-> "OE2" Residue "a GLU 47": "OE1" <-> "OE2" Residue "b TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 11": "OE1" <-> "OE2" Residue "c PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 94": "OE1" <-> "OE2" Residue "c TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 98": "OD1" <-> "OD2" Residue "c PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 163": "OD1" <-> "OD2" Residue "c PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 85": "OE1" <-> "OE2" Residue "e GLU 32": "OE1" <-> "OE2" Residue "e GLU 61": "OE1" <-> "OE2" Residue "e GLU 92": "OE1" <-> "OE2" Residue "e TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 142": "OE1" <-> "OE2" Residue "f GLU 56": "OE1" <-> "OE2" Residue "f TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 73": "OE1" <-> "OE2" Residue "i TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 26": "OE1" <-> "OE2" Residue "j GLU 80": "OE1" <-> "OE2" Residue "j GLU 111": "OE1" <-> "OE2" Residue "k ASP 23": "OD1" <-> "OD2" Residue "k GLU 34": "OE1" <-> "OE2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k ASP 55": "OD1" <-> "OD2" Residue "k PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 110": "OD1" <-> "OD2" Residue "l TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 16": "OE1" <-> "OE2" Residue "o GLU 28": "OE1" <-> "OE2" Residue "r PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 3": "OD1" <-> "OD2" Residue "s GLU 15": "OE1" <-> "OE2" Residue "s GLU 38": "OE1" <-> "OE2" Residue "s ASP 41": "OD1" <-> "OD2" Residue "s GLU 44": "OE1" <-> "OE2" Residue "s PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 72": "OD1" <-> "OD2" Residue "t GLU 77": "OE1" <-> "OE2" Residue "u TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 78": "OE1" <-> "OE2" Residue "w GLU 24": "OE1" <-> "OE2" Residue "w PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 5": "OE1" <-> "OE2" Residue "x ASP 39": "OD1" <-> "OD2" Residue "x GLU 58": "OE1" <-> "OE2" Residue "0 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 54": "OD1" <-> "OD2" Residue "6 PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 91": "OD1" <-> "OD2" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E GLU 151": "OE1" <-> "OE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "G GLU 94": "OE1" <-> "OE2" Residue "H GLU 23": "OE1" <-> "OE2" Residue "H TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 91": "OD1" <-> "OD2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "L PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "N PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 34": "OD1" <-> "OD2" Residue "O GLU 41": "OE1" <-> "OE2" Residue "P TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 68": "OD1" <-> "OD2" Residue "Q GLU 51": "OE1" <-> "OE2" Residue "Q PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 73": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150422 Number of models: 1 Model: "" Number of chains: 57 Chain: "U" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 13, 'rna3p': 63} Chain: "V" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 177 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 6} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "W" Number of atoms: 5685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 5685 Classifications: {'RNA': 266} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 136, 'rna3p_pyr': 115} Link IDs: {'rna2p': 15, 'rna3p': 250} Chain: "g" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 1911 Classifications: {'peptide': 403} Incomplete info: {'backbone_only': 90, 'truncation_to_alanine': 252} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 388} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1239 Unresolved non-hydrogen angles: 1613 Unresolved non-hydrogen dihedrals: 922 Unresolved non-hydrogen chiralities: 208 Planarities with less than four sites: {'GLN:plan1': 23, 'HIS:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 12, 'ASP:plan': 24, 'PHE:plan': 10, 'GLU:plan': 33, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 546 Chain: "h" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 189 Classifications: {'peptide': 43} Incomplete info: {'backbone_only': 1, 'n_c_alpha_c_only': 17, 'truncation_to_alanine': 19} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 39} Chain breaks: 1 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 78 Chain: "p" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "q" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 981 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 10, 'TRANS': 122} Chain: "X" Number of atoms: 61997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2887, 61997 Inner-chain residues flagged as termini: ['pdbres=" G X 328 "', 'pdbres=" G X1220 "'] Classifications: {'RNA': 2887} Modifications used: {'5*END': 3, 'rna2p_pur': 296, 'rna2p_pyr': 160, 'rna3p_pur': 1381, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 456, 'rna3p': 2430} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2392 Classifications: {'RNA': 112} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 6, 'rna3p_pur': 50, 'rna3p_pyr': 46} Link IDs: {'rna2p': 16, 'rna3p': 95} Chain: "Z" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "a" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1569 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "b" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "c" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1386 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "d" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "e" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1123 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "f" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "i" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1081 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "j" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1076 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "k" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "l" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "m" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 944 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "n" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "o" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "r" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "s" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 725 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "t" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 762 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "u" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 630 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "w" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "x" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "0" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "1" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "2" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "4" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 499 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "A" Number of atoms: 32891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1533, 32891 Classifications: {'RNA': 1533} Modifications used: {'rna2p_pur': 124, 'rna2p_pyr': 89, 'rna3p_pur': 746, 'rna3p_pyr': 574} Link IDs: {'rna2p': 212, 'rna3p': 1320} Chain: "B" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1757 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "C" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 3, 'TRANS': 202} Chain: "D" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1568 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "E" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1218 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "F" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 755 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1181 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "H" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1036 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "I" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 966 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "J" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 761 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "K" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 838 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "L" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1052 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "M" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 868 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "N" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 497 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "O" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 710 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "P" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "Q" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 691 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "R" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "S" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "T" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 637 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain: "g" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'G4P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 55.17, per 1000 atoms: 0.37 Number of scatterers: 150422 At special positions: 0 Unit cell: (272.163, 329.349, 242.511, 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 140 16.00 P 4883 15.00 O 42225 8.00 N 27958 7.00 C 75216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 27 " - pdb=" SG CYS N 43 " distance=2.05 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: 60.05 Conformation dependent library (CDL) restraints added in 7.8 seconds 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10788 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 183 helices and 72 sheets defined 39.2% alpha, 17.3% beta 1560 base pairs and 2414 stacking pairs defined. Time for finding SS restraints: 73.61 Creating SS restraints... Processing helix chain 'g' and resid 2 through 16 removed outlier: 4.182A pdb=" N GLN g 10 " --> pdb=" O ASP g 6 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR g 11 " --> pdb=" O ARG g 7 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS g 14 " --> pdb=" O GLN g 10 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE g 15 " --> pdb=" O THR g 11 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 41 Processing helix chain 'g' and resid 43 through 63 removed outlier: 3.690A pdb=" N GLY g 60 " --> pdb=" O GLU g 56 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP g 62 " --> pdb=" O ALA g 58 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL g 63 " --> pdb=" O VAL g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 86 removed outlier: 3.587A pdb=" N GLY g 86 " --> pdb=" O THR g 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 112 through 126 Processing helix chain 'g' and resid 142 through 155 Processing helix chain 'g' and resid 166 through 182 Processing helix chain 'g' and resid 197 through 212 removed outlier: 3.781A pdb=" N GLU g 203 " --> pdb=" O GLU g 199 " (cutoff:3.500A) Processing helix chain 'g' and resid 225 through 239 removed outlier: 3.585A pdb=" N VAL g 229 " --> pdb=" O GLY g 225 " (cutoff:3.500A) Processing helix chain 'g' and resid 248 through 253 removed outlier: 5.149A pdb=" N THR g 253 " --> pdb=" O LEU g 249 " (cutoff:3.500A) Processing helix chain 'g' and resid 255 through 265 removed outlier: 5.211A pdb=" N ARG g 262 " --> pdb=" O ALA g 258 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA g 263 " --> pdb=" O LEU g 259 " (cutoff:3.500A) Processing helix chain 'g' and resid 285 through 295 Processing helix chain 'g' and resid 330 through 343 Processing helix chain 'g' and resid 351 through 357 Proline residue: g 355 - end of helix No H-bonds generated for 'chain 'g' and resid 351 through 357' Processing helix chain 'g' and resid 358 through 363 removed outlier: 3.902A pdb=" N LEU g 363 " --> pdb=" O LYS g 359 " (cutoff:3.500A) Processing helix chain 'g' and resid 370 through 383 removed outlier: 3.745A pdb=" N SER g 382 " --> pdb=" O ALA g 378 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N MET g 383 " --> pdb=" O ILE g 379 " (cutoff:3.500A) Processing helix chain 'g' and resid 384 through 391 Proline residue: g 391 - end of helix Processing helix chain 'g' and resid 395 through 407 removed outlier: 3.813A pdb=" N ILE g 402 " --> pdb=" O ARG g 398 " (cutoff:3.500A) Processing helix chain 'g' and resid 409 through 431 removed outlier: 5.888A pdb=" N VAL g 413 " --> pdb=" O SER g 409 " (cutoff:3.500A) Processing helix chain 'h' and resid 12 through 26 Proline residue: h 23 - end of helix Processing helix chain 'p' and resid 4 through 21 removed outlier: 3.929A pdb=" N LYS p 8 " --> pdb=" O ALA p 4 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS p 20 " --> pdb=" O ALA p 16 " (cutoff:3.500A) Processing helix chain 'p' and resid 33 through 48 Processing helix chain 'p' and resid 59 through 70 removed outlier: 3.506A pdb=" N VAL p 64 " --> pdb=" O THR p 60 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU p 65 " --> pdb=" O ARG p 61 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU p 69 " --> pdb=" O GLU p 65 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN p 70 " --> pdb=" O GLN p 66 " (cutoff:3.500A) Processing helix chain 'p' and resid 74 through 79 Proline residue: p 79 - end of helix Processing helix chain 'p' and resid 92 through 106 removed outlier: 5.457A pdb=" N LEU p 96 " --> pdb=" O PRO p 92 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU p 106 " --> pdb=" O ASN p 102 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 32 removed outlier: 4.669A pdb=" N LEU q 28 " --> pdb=" O VAL q 24 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA q 31 " --> pdb=" O ALA q 27 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLY q 32 " --> pdb=" O LEU q 28 " (cutoff:3.500A) Processing helix chain 'q' and resid 34 through 50 removed outlier: 4.020A pdb=" N PHE q 38 " --> pdb=" O ASN q 34 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS q 39 " --> pdb=" O ILE q 35 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYS q 40 " --> pdb=" O MET q 36 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N GLU q 41 " --> pdb=" O GLY q 37 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP q 48 " --> pdb=" O ALA q 44 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN q 49 " --> pdb=" O ARG q 45 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 84 removed outlier: 3.768A pdb=" N LYS q 80 " --> pdb=" O ALA q 76 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS q 81 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 113 removed outlier: 3.574A pdb=" N LYS q 112 " --> pdb=" O ILE q 108 " (cutoff:3.500A) Processing helix chain 'q' and resid 120 through 136 removed outlier: 4.304A pdb=" N SER q 134 " --> pdb=" O GLY q 130 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N MET q 135 " --> pdb=" O THR q 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 15 removed outlier: 3.618A pdb=" N ARG Z 14 " --> pdb=" O SER Z 10 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLY Z 15 " --> pdb=" O ASN Z 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 10 through 15' Processing helix chain 'Z' and resid 131 through 136 Proline residue: Z 136 - end of helix Processing helix chain 'Z' and resid 207 through 215 removed outlier: 3.996A pdb=" N SER Z 211 " --> pdb=" O LYS Z 207 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS Z 214 " --> pdb=" O ARG Z 210 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY Z 215 " --> pdb=" O SER Z 211 " (cutoff:3.500A) Processing helix chain 'Z' and resid 221 through 226 removed outlier: 4.084A pdb=" N MET Z 225 " --> pdb=" O ARG Z 221 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASN Z 226 " --> pdb=" O GLY Z 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 221 through 226' Processing helix chain 'Z' and resid 266 through 271 removed outlier: 3.935A pdb=" N ILE Z 270 " --> pdb=" O SER Z 266 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL Z 271 " --> pdb=" O ASP Z 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 266 through 271' Processing helix chain 'a' and resid 57 through 62 removed outlier: 5.195A pdb=" N ASN a 62 " --> pdb=" O GLU a 58 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 71 Processing helix chain 'a' and resid 87 through 92 removed outlier: 4.854A pdb=" N TYR a 91 " --> pdb=" O GLU a 87 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU a 92 " --> pdb=" O MET a 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 87 through 92' Processing helix chain 'a' and resid 98 through 103 removed outlier: 4.772A pdb=" N PHE a 102 " --> pdb=" O LYS a 98 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER a 103 " --> pdb=" O VAL a 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 98 through 103' Processing helix chain 'a' and resid 40 through 45 removed outlier: 4.002A pdb=" N GLY a 45 " --> pdb=" O THR a 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 40 through 45' Processing helix chain 'b' and resid 29 through 45 removed outlier: 3.882A pdb=" N ARG b 45 " --> pdb=" O ARG b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 121 Processing helix chain 'b' and resid 135 through 147 removed outlier: 4.150A pdb=" N MET b 139 " --> pdb=" O LYS b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 160 through 168 removed outlier: 4.396A pdb=" N ALA b 167 " --> pdb=" O VAL b 163 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG b 168 " --> pdb=" O ALA b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 182 through 190 removed outlier: 4.222A pdb=" N VAL b 186 " --> pdb=" O ASN b 182 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU b 190 " --> pdb=" O VAL b 186 " (cutoff:3.500A) Processing helix chain 'b' and resid 195 through 206 Processing helix chain 'b' and resid 20 through 26 Processing helix chain 'c' and resid 2 through 21 Proline residue: c 14 - end of helix Processing helix chain 'c' and resid 48 through 61 removed outlier: 4.532A pdb=" N SER c 52 " --> pdb=" O LYS c 48 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA c 53 " --> pdb=" O ALA c 49 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU c 56 " --> pdb=" O SER c 52 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 111 removed outlier: 4.371A pdb=" N TYR c 97 " --> pdb=" O GLY c 93 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL c 106 " --> pdb=" O LYS c 102 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER c 107 " --> pdb=" O LEU c 103 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU c 108 " --> pdb=" O ILE c 104 " (cutoff:3.500A) Proline residue: c 109 - end of helix Processing helix chain 'c' and resid 162 through 174 removed outlier: 3.642A pdb=" N ALA c 166 " --> pdb=" O THR c 162 " (cutoff:3.500A) Processing helix chain 'c' and resid 40 through 45 removed outlier: 4.435A pdb=" N ALA c 43 " --> pdb=" O VAL c 40 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL c 44 " --> pdb=" O GLY c 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 8 removed outlier: 4.668A pdb=" N LYS d 7 " --> pdb=" O ARG d 3 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU d 8 " --> pdb=" O VAL d 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 3 through 8' Processing helix chain 'd' and resid 59 through 82 removed outlier: 3.808A pdb=" N ALA d 64 " --> pdb=" O LYS d 60 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG d 70 " --> pdb=" O HIS d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 138 through 154 removed outlier: 3.685A pdb=" N VAL d 152 " --> pdb=" O ASN d 148 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG d 153 " --> pdb=" O ILE d 149 " (cutoff:3.500A) Processing helix chain 'e' and resid 25 through 39 removed outlier: 3.873A pdb=" N GLU e 32 " --> pdb=" O ARG e 28 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG e 38 " --> pdb=" O ALA e 34 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY e 39 " --> pdb=" O ALA e 35 " (cutoff:3.500A) Processing helix chain 'e' and resid 89 through 97 Processing helix chain 'e' and resid 98 through 111 Proline residue: e 111 - end of helix Processing helix chain 'e' and resid 113 through 124 removed outlier: 3.968A pdb=" N LYS e 122 " --> pdb=" O GLN e 118 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU e 123 " --> pdb=" O MET e 119 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ASN e 124 " --> pdb=" O PHE e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 104 through 110 removed outlier: 4.072A pdb=" N GLU f 108 " --> pdb=" O ARG f 104 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN f 109 " --> pdb=" O GLU f 105 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN f 110 " --> pdb=" O LEU f 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 104 through 110' Processing helix chain 'f' and resid 111 through 119 Proline residue: f 119 - end of helix Processing helix chain 'i' and resid 56 through 62 Proline residue: i 62 - end of helix Processing helix chain 'i' and resid 78 through 85 removed outlier: 6.243A pdb=" N LEU i 82 " --> pdb=" O ASN i 78 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN i 83 " --> pdb=" O LEU i 79 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY i 84 " --> pdb=" O ASP i 80 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE i 85 " --> pdb=" O LYS i 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 78 through 85' Processing helix chain 'i' and resid 92 through 100 Processing helix chain 'i' and resid 129 through 140 removed outlier: 4.068A pdb=" N GLU i 134 " --> pdb=" O ALA i 130 " (cutoff:3.500A) Processing helix chain 'j' and resid 43 through 59 Processing helix chain 'j' and resid 110 through 126 removed outlier: 4.353A pdb=" N LYS j 124 " --> pdb=" O LEU j 120 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU j 125 " --> pdb=" O ALA j 121 " (cutoff:3.500A) Proline residue: j 126 - end of helix Processing helix chain 'k' and resid 9 through 28 Processing helix chain 'k' and resid 34 through 54 removed outlier: 4.428A pdb=" N SER k 42 " --> pdb=" O LYS k 38 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL k 43 " --> pdb=" O GLU k 39 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ARG k 53 " --> pdb=" O THR k 49 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY k 54 " --> pdb=" O LEU k 50 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 66 Processing helix chain 'k' and resid 78 through 92 Processing helix chain 'l' and resid 6 through 22 removed outlier: 3.745A pdb=" N ALA l 10 " --> pdb=" O SER l 6 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS l 21 " --> pdb=" O ARG l 17 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU l 22 " --> pdb=" O VAL l 18 " (cutoff:3.500A) Processing helix chain 'l' and resid 70 through 89 Processing helix chain 'l' and resid 104 through 117 Processing helix chain 'm' and resid 1 through 13 removed outlier: 4.542A pdb=" N GLU m 11 " --> pdb=" O ASP m 7 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLN m 12 " --> pdb=" O ILE m 8 " (cutoff:3.500A) Processing helix chain 'm' and resid 98 through 104 removed outlier: 4.663A pdb=" N GLU m 102 " --> pdb=" O TYR m 98 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG m 104 " --> pdb=" O LEU m 100 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 22 removed outlier: 3.668A pdb=" N LEU n 20 " --> pdb=" O LYS n 16 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA n 21 " --> pdb=" O VAL n 17 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS n 22 " --> pdb=" O LEU n 18 " (cutoff:3.500A) Processing helix chain 'n' and resid 25 through 31 removed outlier: 4.403A pdb=" N HIS n 29 " --> pdb=" O PHE n 25 " (cutoff:3.500A) Processing helix chain 'n' and resid 32 through 37 Processing helix chain 'n' and resid 39 through 54 removed outlier: 3.571A pdb=" N ARG n 51 " --> pdb=" O PHE n 47 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS n 54 " --> pdb=" O ARG n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 73 Processing helix chain 'n' and resid 75 through 87 removed outlier: 3.702A pdb=" N GLY n 87 " --> pdb=" O LEU n 83 " (cutoff:3.500A) Processing helix chain 'n' and resid 92 through 103 Processing helix chain 'n' and resid 104 through 118 removed outlier: 4.622A pdb=" N GLN n 108 " --> pdb=" O THR n 104 " (cutoff:3.500A) Processing helix chain 'r' and resid 13 through 25 Processing helix chain 'r' and resid 28 through 40 Proline residue: r 40 - end of helix Processing helix chain 'r' and resid 43 through 61 Processing helix chain 's' and resid 3 through 9 removed outlier: 4.037A pdb=" N VAL s 7 " --> pdb=" O ASP s 3 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU s 8 " --> pdb=" O PRO s 4 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LYS s 9 " --> pdb=" O ARG s 5 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 3 through 9' Processing helix chain 's' and resid 14 through 24 Processing helix chain 's' and resid 35 through 47 Processing helix chain 't' and resid 64 through 69 removed outlier: 4.470A pdb=" N VAL t 68 " --> pdb=" O HIS t 64 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N MET t 69 " --> pdb=" O VAL t 65 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 64 through 69' Processing helix chain 'v' and resid 50 through 55 removed outlier: 4.050A pdb=" N LYS v 55 " --> pdb=" O ALA v 51 " (cutoff:3.500A) Processing helix chain 'w' and resid 1 through 9 removed outlier: 5.532A pdb=" N LEU w 9 " --> pdb=" O GLU w 5 " (cutoff:3.500A) Processing helix chain 'w' and resid 12 through 35 Processing helix chain 'w' and resid 40 through 65 removed outlier: 4.134A pdb=" N ARG w 44 " --> pdb=" O THR w 40 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE w 57 " --> pdb=" O MET w 53 " (cutoff:3.500A) Processing helix chain 'x' and resid 16 through 27 removed outlier: 3.661A pdb=" N GLY x 27 " --> pdb=" O VAL x 23 " (cutoff:3.500A) Processing helix chain 'x' and resid 40 through 51 Processing helix chain '0' and resid 9 through 19 removed outlier: 5.079A pdb=" N HIS 0 19 " --> pdb=" O LEU 0 15 " (cutoff:3.500A) Processing helix chain '1' and resid 22 through 27 Proline residue: 1 27 - end of helix Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.518A pdb=" N SER 2 24 " --> pdb=" O SER 2 20 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 removed outlier: 3.723A pdb=" N GLY 2 38 " --> pdb=" O ARG 2 34 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 14 Processing helix chain '3' and resid 32 through 37 removed outlier: 4.977A pdb=" N LYS 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N SER 3 37 " --> pdb=" O PHE 3 33 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 32 through 37' Processing helix chain '3' and resid 38 through 46 removed outlier: 4.572A pdb=" N LYS 3 46 " --> pdb=" O ARG 3 42 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 63 removed outlier: 5.946A pdb=" N GLN 3 60 " --> pdb=" O LYS 3 56 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N MET 3 61 " --> pdb=" O ARG 3 57 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU 3 62 " --> pdb=" O ILE 3 58 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA 3 63 " --> pdb=" O LYS 3 59 " (cutoff:3.500A) Processing helix chain '6' and resid 36 through 41 Proline residue: 6 41 - end of helix Processing helix chain '6' and resid 47 through 55 removed outlier: 4.260A pdb=" N SER 6 51 " --> pdb=" O GLN 6 47 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA 6 52 " --> pdb=" O LYS 6 48 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG 6 55 " --> pdb=" O SER 6 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 64 Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 105 through 123 removed outlier: 4.400A pdb=" N GLU B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 149 removed outlier: 4.609A pdb=" N VAL B 134 " --> pdb=" O PRO B 130 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 206 through 226 removed outlier: 4.476A pdb=" N GLN B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 12 Processing helix chain 'C' and resid 27 through 47 Processing helix chain 'C' and resid 71 through 76 removed outlier: 5.011A pdb=" N VAL C 75 " --> pdb=" O LYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.998A pdb=" N ALA C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'D' and resid 7 through 16 removed outlier: 6.895A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 62 Processing helix chain 'D' and resid 64 through 79 removed outlier: 4.915A pdb=" N ALA D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 94 through 102 Processing helix chain 'D' and resid 106 through 116 Processing helix chain 'D' and resid 148 through 158 removed outlier: 5.326A pdb=" N ASN D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 187 removed outlier: 3.948A pdb=" N ALA D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) Proline residue: D 187 - end of helix Processing helix chain 'D' and resid 191 through 200 removed outlier: 7.235A pdb=" N VAL D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 4.153A pdb=" N LEU E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 119 Processing helix chain 'E' and resid 132 through 147 removed outlier: 3.692A pdb=" N LEU E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 166 Processing helix chain 'F' and resid 15 through 33 removed outlier: 4.201A pdb=" N ASN F 33 " --> pdb=" O VAL F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 82 removed outlier: 5.383A pdb=" N GLN F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 28 Processing helix chain 'G' and resid 36 through 55 removed outlier: 4.996A pdb=" N GLY G 55 " --> pdb=" O LYS G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.419A pdb=" N VAL G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 111 Processing helix chain 'G' and resid 115 through 130 removed outlier: 4.986A pdb=" N ASN G 130 " --> pdb=" O ASP G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 149 Processing helix chain 'H' and resid 5 through 21 removed outlier: 4.183A pdb=" N ASP H 9 " --> pdb=" O ASP H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 114 through 122 Processing helix chain 'I' and resid 41 through 56 removed outlier: 4.161A pdb=" N ILE I 45 " --> pdb=" O SER I 41 " (cutoff:3.500A) Proline residue: I 51 - end of helix removed outlier: 4.612A pdb=" N GLU I 56 " --> pdb=" O LEU I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 91 Processing helix chain 'I' and resid 92 through 102 removed outlier: 4.662A pdb=" N THR I 96 " --> pdb=" O PRO I 92 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N THR I 97 " --> pdb=" O GLU I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 39 removed outlier: 3.993A pdb=" N ILE I 39 " --> pdb=" O GLU I 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 34 through 39' Processing helix chain 'J' and resid 14 through 33 Processing helix chain 'J' and resid 80 through 91 removed outlier: 5.810A pdb=" N ASP J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 53 Processing helix chain 'K' and resid 57 through 62 removed outlier: 3.932A pdb=" N THR K 61 " --> pdb=" O SER K 57 " (cutoff:3.500A) Proline residue: K 62 - end of helix No H-bonds generated for 'chain 'K' and resid 57 through 62' Processing helix chain 'K' and resid 63 through 80 Processing helix chain 'K' and resid 95 through 106 removed outlier: 4.776A pdb=" N GLY K 106 " --> pdb=" O LEU K 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 27 removed outlier: 4.096A pdb=" N ASN L 25 " --> pdb=" O SER L 21 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS L 26 " --> pdb=" O PRO L 22 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLY L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 21 through 27' Processing helix chain 'L' and resid 126 through 131 removed outlier: 4.923A pdb=" N TYR L 130 " --> pdb=" O GLY L 126 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY L 131 " --> pdb=" O ARG L 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 126 through 131' Processing helix chain 'M' and resid 14 through 22 removed outlier: 4.842A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE M 22 " --> pdb=" O SER M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 removed outlier: 3.935A pdb=" N GLU M 36 " --> pdb=" O GLN M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 64 removed outlier: 4.969A pdb=" N LYS M 64 " --> pdb=" O ILE M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 84 Processing helix chain 'M' and resid 85 through 94 removed outlier: 5.423A pdb=" N ILE M 89 " --> pdb=" O SER M 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 13 removed outlier: 5.412A pdb=" N MET N 6 " --> pdb=" O ALA N 2 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N THR N 13 " --> pdb=" O LYS N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 51 Processing helix chain 'O' and resid 5 through 16 removed outlier: 5.192A pdb=" N ASN O 9 " --> pdb=" O GLN O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 47 removed outlier: 4.364A pdb=" N GLN O 28 " --> pdb=" O SER O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 4.349A pdb=" N ARG O 53 " --> pdb=" O ASP O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'P' and resid 52 through 63 removed outlier: 6.572A pdb=" N ALA P 56 " --> pdb=" O ASP P 52 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU P 57 " --> pdb=" O GLU P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 67 through 78 Processing helix chain 'P' and resid 79 through 89 Processing helix chain 'R' and resid 16 through 22 Processing helix chain 'R' and resid 30 through 39 removed outlier: 5.479A pdb=" N SER R 39 " --> pdb=" O LYS R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 51 Processing helix chain 'R' and resid 53 through 71 Processing helix chain 'S' and resid 12 through 26 removed outlier: 3.929A pdb=" N THR S 25 " --> pdb=" O LYS S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 75 removed outlier: 4.280A pdb=" N GLU S 73 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA S 75 " --> pdb=" O GLY S 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 6 through 42 removed outlier: 5.006A pdb=" N ARG T 10 " --> pdb=" O SER T 6 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASN T 42 " --> pdb=" O SER T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 65 Processing helix chain 'T' and resid 68 through 86 removed outlier: 4.622A pdb=" N LEU T 86 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'g' and resid 157 through 160 removed outlier: 3.826A pdb=" N TYR g 185 " --> pdb=" O LYS g 130 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLY g 106 " --> pdb=" O THR g 190 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'g' and resid 271 through 274 removed outlier: 6.468A pdb=" N ALA g 280 " --> pdb=" O LEU g 274 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'p' and resid 23 through 29 removed outlier: 4.161A pdb=" N THR p 25 " --> pdb=" O SER p 85 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER p 85 " --> pdb=" O THR p 25 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE p 27 " --> pdb=" O ALA p 83 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA p 81 " --> pdb=" O ASP p 29 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'q' and resid 8 through 15 removed outlier: 6.825A pdb=" N LEU q 52 " --> pdb=" O ALA q 15 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE q 53 " --> pdb=" O PRO q 73 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER q 65 " --> pdb=" O TYR q 61 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'Z' and resid 2 through 6 removed outlier: 8.528A pdb=" N ALA Z 2 " --> pdb=" O ASP Z 20 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N MET Z 16 " --> pdb=" O TYR Z 6 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'Z' and resid 33 through 36 No H-bonds generated for sheet with id= 6 Processing sheet with id= 7, first strand: chain 'Z' and resid 80 through 83 removed outlier: 6.633A pdb=" N LEU Z 93 " --> pdb=" O ALA Z 79 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE Z 74 " --> pdb=" O SER Z 118 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER Z 118 " --> pdb=" O ILE Z 74 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR Z 114 " --> pdb=" O VAL Z 78 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'Z' and resid 162 through 165 removed outlier: 5.727A pdb=" N LEU Z 173 " --> pdb=" O LEU Z 165 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LYS Z 170 " --> pdb=" O SER Z 186 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'Z' and resid 91 through 96 removed outlier: 4.334A pdb=" N GLU Z 100 " --> pdb=" O TYR Z 96 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'a' and resid 33 through 36 removed outlier: 6.855A pdb=" N GLN a 50 " --> pdb=" O LEU a 36 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'a' and resid 166 through 172 removed outlier: 5.002A pdb=" N GLU a 167 " --> pdb=" O SER a 114 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU a 106 " --> pdb=" O ILE a 176 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'a' and resid 184 through 188 removed outlier: 5.404A pdb=" N ASN a 184 " --> pdb=" O ALA a 30 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL a 27 " --> pdb=" O ILE a 10 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER a 198 " --> pdb=" O LYS a 9 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'a' and resid 108 through 112 Processing sheet with id= 14, first strand: chain 'b' and resid 122 through 125 removed outlier: 3.963A pdb=" N LYS b 191 " --> pdb=" O LYS b 151 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'c' and resid 65 through 68 removed outlier: 5.350A pdb=" N GLY c 86 " --> pdb=" O THR c 68 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA c 87 " --> pdb=" O MET c 38 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLY c 39 " --> pdb=" O GLY c 151 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLY c 151 " --> pdb=" O GLY c 39 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'd' and resid 16 through 19 removed outlier: 5.271A pdb=" N ASN d 23 " --> pdb=" O PHE d 38 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'd' and resid 42 through 46 Processing sheet with id= 18, first strand: chain 'd' and resid 95 through 100 Processing sheet with id= 19, first strand: chain 'd' and resid 122 through 126 removed outlier: 5.753A pdb=" N THR d 130 " --> pdb=" O LEU d 90 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU d 90 " --> pdb=" O THR d 130 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLY d 87 " --> pdb=" O GLU d 166 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU d 166 " --> pdb=" O GLY d 87 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'e' and resid 75 through 79 removed outlier: 4.528A pdb=" N GLY e 84 " --> pdb=" O THR e 79 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'f' and resid 6 through 9 removed outlier: 4.513A pdb=" N THR f 6 " --> pdb=" O THR f 21 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'f' and resid 63 through 66 removed outlier: 4.743A pdb=" N LYS f 66 " --> pdb=" O GLU f 81 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU f 81 " --> pdb=" O LYS f 66 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'f' and resid 68 through 71 removed outlier: 4.682A pdb=" N SER f 75 " --> pdb=" O ARG f 71 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'i' and resid 74 through 77 Processing sheet with id= 25, first strand: chain 'i' and resid 87 through 91 removed outlier: 6.886A pdb=" N LYS i 120 " --> pdb=" O GLU i 87 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR i 89 " --> pdb=" O LYS i 120 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'j' and resid 103 through 107 removed outlier: 4.065A pdb=" N PHE j 104 " --> pdb=" O ILE j 34 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLU j 31 " --> pdb=" O ARG j 134 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS j 128 " --> pdb=" O LEU j 37 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'k' and resid 29 through 33 Processing sheet with id= 28, first strand: chain 'l' and resid 54 through 58 removed outlier: 4.097A pdb=" N ALA l 54 " --> pdb=" O ILE l 44 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE l 40 " --> pdb=" O THR l 58 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL l 33 " --> pdb=" O ASP l 96 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'm' and resid 37 through 45 removed outlier: 5.517A pdb=" N ARG m 37 " --> pdb=" O GLU m 34 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU m 34 " --> pdb=" O ARG m 37 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG m 39 " --> pdb=" O VAL m 32 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS m 83 " --> pdb=" O HIS m 29 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'm' and resid 49 through 52 removed outlier: 3.941A pdb=" N LYS m 49 " --> pdb=" O THR m 60 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N GLU m 57 " --> pdb=" O VAL m 76 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'o' and resid 2 through 6 Processing sheet with id= 32, first strand: chain 'o' and resid 18 through 23 removed outlier: 3.825A pdb=" N GLN o 18 " --> pdb=" O ILE o 97 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS o 94 " --> pdb=" O GLU o 63 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR o 59 " --> pdb=" O GLU o 98 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU o 31 " --> pdb=" O VAL o 62 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'o' and resid 64 through 67 removed outlier: 3.607A pdb=" N LYS o 64 " --> pdb=" O LYS o 94 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'o' and resid 70 through 77 removed outlier: 4.575A pdb=" N VAL o 82 " --> pdb=" O LYS o 77 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'r' and resid 2 through 8 removed outlier: 5.874A pdb=" N ILE r 103 " --> pdb=" O ALA r 7 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL r 106 " --> pdb=" O SER r 72 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'r' and resid 73 through 79 removed outlier: 4.982A pdb=" N THR r 100 " --> pdb=" O GLY r 79 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'r' and resid 81 through 88 removed outlier: 5.826A pdb=" N ARG r 88 " --> pdb=" O ARG r 92 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG r 92 " --> pdb=" O ARG r 88 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 's' and resid 25 through 30 removed outlier: 3.938A pdb=" N ARG s 77 " --> pdb=" O VAL s 30 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS s 62 " --> pdb=" O THR s 73 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ARG s 75 " --> pdb=" O LYS s 60 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LYS s 60 " --> pdb=" O ARG s 75 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG s 77 " --> pdb=" O ASN s 58 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASN s 58 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA s 79 " --> pdb=" O ILE s 56 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE s 56 " --> pdb=" O ALA s 79 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL s 81 " --> pdb=" O VAL s 54 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL s 54 " --> pdb=" O VAL s 81 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 't' and resid 25 through 28 removed outlier: 3.660A pdb=" N ALA t 25 " --> pdb=" O LEU t 34 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 't' and resid 39 through 44 removed outlier: 4.930A pdb=" N ASN t 39 " --> pdb=" O ALA t 61 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 't' and resid 80 through 83 removed outlier: 5.916A pdb=" N ARG t 80 " --> pdb=" O LYS t 95 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'u' and resid 59 through 62 removed outlier: 3.891A pdb=" N PHE u 68 " --> pdb=" O GLY u 60 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR u 66 " --> pdb=" O GLY u 62 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'u' and resid 73 through 79 removed outlier: 4.647A pdb=" N LYS u 86 " --> pdb=" O GLU u 78 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'v' and resid 12 through 19 removed outlier: 3.659A pdb=" N SER v 19 " --> pdb=" O ASN v 23 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN v 23 " --> pdb=" O SER v 19 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'x' and resid 34 through 38 removed outlier: 6.632A pdb=" N LYS x 3 " --> pdb=" O GLN x 59 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU x 53 " --> pdb=" O LYS x 9 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '1' and resid 3 through 7 removed outlier: 4.605A pdb=" N TYR 1 17 " --> pdb=" O LEU 1 7 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '1' and resid 30 through 35 removed outlier: 5.664A pdb=" N VAL 1 30 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '3' and resid 22 through 25 removed outlier: 5.557A pdb=" N LEU 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '4' and resid 1 through 5 removed outlier: 3.618A pdb=" N LYS 4 35 " --> pdb=" O LYS 4 2 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG 4 4 " --> pdb=" O LYS 4 35 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY 4 37 " --> pdb=" O ARG 4 4 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '4' and resid 14 through 19 removed outlier: 3.660A pdb=" N ARG 4 19 " --> pdb=" O LYS 4 22 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain '6' and resid 21 through 24 Processing sheet with id= 52, first strand: chain 'B' and resid 67 through 71 removed outlier: 3.665A pdb=" N LEU B 68 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU B 161 " --> pdb=" O PRO B 182 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 53 through 58 removed outlier: 3.866A pdb=" N LYS C 53 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 163 through 170 removed outlier: 3.819A pdb=" N GLY C 154 " --> pdb=" O ARG C 163 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'D' and resid 165 through 168 removed outlier: 3.703A pdb=" N GLU D 173 " --> pdb=" O ASP D 168 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'E' and resid 17 through 25 removed outlier: 4.061A pdb=" N HIS E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'E' and resid 84 through 88 removed outlier: 5.006A pdb=" N ASN E 93 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE E 123 " --> pdb=" O GLY E 104 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'F' and resid 39 through 43 removed outlier: 6.224A pdb=" N TYR F 60 " --> pdb=" O TRP F 43 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LYS F 3 " --> pdb=" O GLU F 93 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'F' and resid 44 through 48 removed outlier: 3.773A pdb=" N GLY F 44 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG F 56 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'G' and resid 73 through 79 No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain 'H' and resid 23 through 27 removed outlier: 6.942A pdb=" N GLU H 23 " --> pdb=" O LEU H 64 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'H' and resid 76 through 79 removed outlier: 5.098A pdb=" N GLY H 76 " --> pdb=" O TRP H 132 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE H 105 " --> pdb=" O LEU H 128 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'I' and resid 5 through 11 removed outlier: 6.009A pdb=" N TYR I 61 " --> pdb=" O GLU I 25 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG I 27 " --> pdb=" O TYR I 61 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'J' and resid 6 through 13 Processing sheet with id= 65, first strand: chain 'K' and resid 32 through 37 removed outlier: 7.214A pdb=" N VAL K 86 " --> pdb=" O THR K 110 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'K' and resid 85 through 90 removed outlier: 4.623A pdb=" N GLY K 90 " --> pdb=" O VAL K 115 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'L' and resid 42 through 45 removed outlier: 5.094A pdb=" N LEU L 94 " --> pdb=" O VAL L 111 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'L' and resid 49 through 52 removed outlier: 3.789A pdb=" N GLY L 51 " --> pdb=" O TYR L 65 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR L 65 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LYS L 64 " --> pdb=" O ILE L 80 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE L 80 " --> pdb=" O LYS L 64 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'P' and resid 5 through 11 removed outlier: 4.085A pdb=" N GLY P 38 " --> pdb=" O ILE P 20 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Q' and resid 8 through 13 removed outlier: 5.219A pdb=" N LYS Q 8 " --> pdb=" O GLU Q 65 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LYS Q 62 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Q' and resid 21 through 28 removed outlier: 4.694A pdb=" N LYS Q 21 " --> pdb=" O ASP Q 50 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE Q 23 " --> pdb=" O ALA Q 48 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'S' and resid 30 through 33 removed outlier: 4.238A pdb=" N HIS S 47 " --> pdb=" O ILE S 62 " (cutoff:3.500A) 1960 hydrogen bonds defined for protein. 5805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3993 hydrogen bonds 6546 hydrogen bond angles 0 basepair planarities 1560 basepair parallelities 2414 stacking parallelities Total time for adding SS restraints: 249.77 Time building geometry restraints manager: 65.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 12199 1.27 - 1.41: 55417 1.41 - 1.55: 85696 1.55 - 1.69: 9986 1.69 - 1.82: 253 Bond restraints: 163551 Sorted by residual: bond pdb=" C ARG w 29 " pdb=" O ARG w 29 " ideal model delta sigma weight residual 1.237 1.135 0.102 1.19e-02 7.06e+03 7.32e+01 bond pdb=" CA ARG w 29 " pdb=" C ARG w 29 " ideal model delta sigma weight residual 1.524 1.450 0.073 1.29e-02 6.01e+03 3.21e+01 bond pdb=" C ARG w 29 " pdb=" N PHE w 30 " ideal model delta sigma weight residual 1.335 1.280 0.055 1.30e-02 5.92e+03 1.82e+01 bond pdb=" O3C G4P g 501 " pdb=" PC G4P g 501 " ideal model delta sigma weight residual 1.712 1.640 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" O3' G4P g 501 " pdb=" PC G4P g 501 " ideal model delta sigma weight residual 1.713 1.650 0.063 2.00e-02 2.50e+03 9.84e+00 ... (remaining 163546 not shown) Histogram of bond angle deviations from ideal: 92.51 - 101.64: 2874 101.64 - 110.77: 88935 110.77 - 119.90: 87545 119.90 - 129.03: 61400 129.03 - 138.16: 4248 Bond angle restraints: 245002 Sorted by residual: angle pdb=" C PHE u 77 " pdb=" N GLU u 78 " pdb=" CA GLU u 78 " ideal model delta sigma weight residual 122.44 111.27 11.17 1.19e+00 7.06e-01 8.81e+01 angle pdb=" N GLU d 78 " pdb=" CA GLU d 78 " pdb=" CB GLU d 78 " ideal model delta sigma weight residual 110.40 121.59 -11.19 1.63e+00 3.76e-01 4.71e+01 angle pdb=" C VAL p 89 " pdb=" N VAL p 90 " pdb=" CA VAL p 90 " ideal model delta sigma weight residual 121.97 134.17 -12.20 1.80e+00 3.09e-01 4.60e+01 angle pdb=" CA GLU E 13 " pdb=" CB GLU E 13 " pdb=" CG GLU E 13 " ideal model delta sigma weight residual 114.10 127.41 -13.31 2.00e+00 2.50e-01 4.43e+01 angle pdb=" CG1 ILE B 151 " pdb=" CB ILE B 151 " pdb=" CG2 ILE B 151 " ideal model delta sigma weight residual 110.70 92.51 18.19 3.00e+00 1.11e-01 3.68e+01 ... (remaining 244997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 91598 35.85 - 71.71: 11755 71.71 - 107.56: 1354 107.56 - 143.41: 21 143.41 - 179.26: 55 Dihedral angle restraints: 104783 sinusoidal: 87914 harmonic: 16869 Sorted by residual: dihedral pdb=" O4' C A1472 " pdb=" C1' C A1472 " pdb=" N1 C A1472 " pdb=" C2 C A1472 " ideal model delta sinusoidal sigma weight residual 200.00 24.65 175.35 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U X2906 " pdb=" C1' U X2906 " pdb=" N1 U X2906 " pdb=" C2 U X2906 " ideal model delta sinusoidal sigma weight residual 200.00 35.60 164.40 1 1.50e+01 4.44e-03 8.38e+01 dihedral pdb=" O4' U A 199 " pdb=" C1' U A 199 " pdb=" N1 U A 199 " pdb=" C2 U A 199 " ideal model delta sinusoidal sigma weight residual 200.00 38.64 161.36 1 1.50e+01 4.44e-03 8.31e+01 ... (remaining 104780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 30693 0.137 - 0.274: 624 0.274 - 0.412: 37 0.412 - 0.549: 6 0.549 - 0.686: 2 Chirality restraints: 31362 Sorted by residual: chirality pdb=" C1' G A1013 " pdb=" O4' G A1013 " pdb=" C2' G A1013 " pdb=" N9 G A1013 " both_signs ideal model delta sigma weight residual False 2.46 1.77 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" CB ILE H 74 " pdb=" CA ILE H 74 " pdb=" CG1 ILE H 74 " pdb=" CG2 ILE H 74 " both_signs ideal model delta sigma weight residual False 2.64 2.03 0.61 2.00e-01 2.50e+01 9.31e+00 chirality pdb=" C3' A X2468 " pdb=" C4' A X2468 " pdb=" O3' A X2468 " pdb=" C2' A X2468 " both_signs ideal model delta sigma weight residual False -2.74 -2.28 -0.46 2.00e-01 2.50e+01 5.32e+00 ... (remaining 31359 not shown) Planarity restraints: 12913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR r 39 " -0.120 5.00e-02 4.00e+02 1.86e-01 5.52e+01 pdb=" N PRO r 40 " 0.321 5.00e-02 4.00e+02 pdb=" CA PRO r 40 " -0.114 5.00e-02 4.00e+02 pdb=" CD PRO r 40 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 103 " 0.032 2.00e-02 2.50e+03 3.40e-02 2.89e+01 pdb=" CG TRP G 103 " -0.090 2.00e-02 2.50e+03 pdb=" CD1 TRP G 103 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP G 103 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 103 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP G 103 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 103 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 103 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 103 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP G 103 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 260 " -0.065 2.00e-02 2.50e+03 3.19e-02 2.28e+01 pdb=" N1 U A 260 " 0.061 2.00e-02 2.50e+03 pdb=" C2 U A 260 " 0.012 2.00e-02 2.50e+03 pdb=" O2 U A 260 " 0.010 2.00e-02 2.50e+03 pdb=" N3 U A 260 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U A 260 " -0.009 2.00e-02 2.50e+03 pdb=" O4 U A 260 " -0.025 2.00e-02 2.50e+03 pdb=" C5 U A 260 " 0.014 2.00e-02 2.50e+03 pdb=" C6 U A 260 " 0.007 2.00e-02 2.50e+03 ... (remaining 12910 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 18062 2.73 - 3.27: 125816 3.27 - 3.81: 305776 3.81 - 4.36: 362107 4.36 - 4.90: 500961 Nonbonded interactions: 1312722 Sorted by model distance: nonbonded pdb=" OG1 THR c 68 " pdb=" O ILE c 85 " model vdw 2.186 2.440 nonbonded pdb=" O2 C X2841 " pdb=" O2' A X2908 " model vdw 2.196 2.440 nonbonded pdb=" OP1 G X 822 " pdb=" O2' G X 824 " model vdw 2.215 2.440 nonbonded pdb=" OP1 A X 774 " pdb=" O2' A X1477 " model vdw 2.222 2.440 nonbonded pdb=" O2' G A 412 " pdb=" O2 U A 448 " model vdw 2.228 2.440 ... (remaining 1312717 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 15.540 Check model and map are aligned: 1.650 Set scattering table: 1.090 Process input model: 541.320 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.400 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: 0.020 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 569.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 163551 Z= 0.393 Angle : 0.979 23.221 245002 Z= 0.483 Chirality : 0.050 0.686 31362 Planarity : 0.008 0.186 12913 Dihedral : 23.965 179.263 93992 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.10 % Favored : 97.74 % Rotamer: Outliers : 0.15 % Allowed : 0.77 % Favored : 99.08 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.02 % Twisted Proline : 0.91 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.09), residues: 5897 helix: -1.57 (0.10), residues: 2022 sheet: -0.70 (0.16), residues: 989 loop : -2.22 (0.10), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.003 TRP G 103 HIS 0.025 0.002 HIS M 91 PHE 0.064 0.003 PHE c 99 TYR 0.065 0.003 TYR J 58 ARG 0.019 0.001 ARG G 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1879 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1872 time to evaluate : 6.451 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: c 161 ASN cc_start: 0.8882 (p0) cc_final: 0.8673 (t0) REVERT: e 50 ASP cc_start: 0.7176 (t70) cc_final: 0.6791 (t70) REVERT: f 96 THR cc_start: 0.8681 (m) cc_final: 0.8375 (p) REVERT: j 74 TYR cc_start: 0.8101 (p90) cc_final: 0.7801 (p90) REVERT: j 113 VAL cc_start: 0.8802 (m) cc_final: 0.8316 (p) REVERT: k 23 ASP cc_start: 0.6862 (m-30) cc_final: 0.6388 (m-30) REVERT: l 31 LEU cc_start: 0.9282 (tt) cc_final: 0.9006 (tp) REVERT: l 32 ASN cc_start: 0.8627 (t0) cc_final: 0.8175 (t0) REVERT: l 49 ASN cc_start: 0.8172 (p0) cc_final: 0.7821 (p0) REVERT: l 70 ASP cc_start: 0.8804 (t0) cc_final: 0.8560 (t0) REVERT: m 3 LYS cc_start: 0.7864 (mttt) cc_final: 0.7507 (mttt) REVERT: m 5 ILE cc_start: 0.9415 (mm) cc_final: 0.8933 (mm) REVERT: m 8 ILE cc_start: 0.9120 (mm) cc_final: 0.8657 (mm) REVERT: n 102 ASP cc_start: 0.7286 (t0) cc_final: 0.7005 (t0) REVERT: r 19 LEU cc_start: 0.8616 (mt) cc_final: 0.8072 (mt) REVERT: r 100 THR cc_start: 0.7553 (m) cc_final: 0.7236 (p) REVERT: r 103 ILE cc_start: 0.8673 (mt) cc_final: 0.8380 (mt) REVERT: u 23 ASP cc_start: 0.8651 (t0) cc_final: 0.8438 (t0) REVERT: u 32 LYS cc_start: 0.8019 (mmtm) cc_final: 0.7742 (mmmt) REVERT: u 85 LYS cc_start: 0.7750 (mmtt) cc_final: 0.7490 (mmtt) REVERT: w 26 PHE cc_start: 0.8151 (t80) cc_final: 0.7932 (t80) REVERT: x 29 LYS cc_start: 0.8907 (mppt) cc_final: 0.8397 (mtmm) REVERT: 0 36 MET cc_start: 0.8501 (tpt) cc_final: 0.8254 (tpp) REVERT: 1 23 LYS cc_start: 0.8818 (pttm) cc_final: 0.7869 (ptpp) REVERT: 6 14 VAL cc_start: 0.9050 (t) cc_final: 0.8828 (t) REVERT: B 59 ASN cc_start: 0.9348 (m110) cc_final: 0.9085 (m110) REVERT: B 89 MET cc_start: 0.5066 (pmm) cc_final: 0.3906 (pmm) REVERT: B 108 GLN cc_start: 0.9330 (pt0) cc_final: 0.8911 (pp30) REVERT: B 119 LYS cc_start: 0.9164 (mmpt) cc_final: 0.8511 (tptp) REVERT: C 125 ASN cc_start: 0.8495 (t0) cc_final: 0.8215 (t0) REVERT: C 129 PHE cc_start: 0.8664 (p90) cc_final: 0.8457 (p90) REVERT: D 96 ASN cc_start: 0.9148 (t0) cc_final: 0.8746 (t0) REVERT: D 175 THR cc_start: 0.8795 (m) cc_final: 0.8340 (p) REVERT: E 142 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7439 (tm-30) REVERT: F 11 ARG cc_start: 0.8575 (ptt90) cc_final: 0.7768 (ptt90) REVERT: F 13 ASN cc_start: 0.8848 (m-40) cc_final: 0.8139 (m110) REVERT: F 73 GLN cc_start: 0.8460 (pm20) cc_final: 0.8154 (pm20) REVERT: G 148 ASN cc_start: 0.8837 (m-40) cc_final: 0.8527 (p0) REVERT: H 51 PHE cc_start: 0.7745 (p90) cc_final: 0.7523 (p90) REVERT: J 24 LYS cc_start: 0.9013 (ptpt) cc_final: 0.8421 (ptmm) REVERT: J 73 LEU cc_start: 0.8571 (tp) cc_final: 0.8343 (tp) REVERT: K 70 GLU cc_start: 0.8875 (tp30) cc_final: 0.8584 (mm-30) REVERT: L 25 ASN cc_start: 0.8471 (m-40) cc_final: 0.8056 (m110) REVERT: L 48 THR cc_start: 0.9059 (p) cc_final: 0.8803 (p) REVERT: L 83 ILE cc_start: 0.8798 (mm) cc_final: 0.8577 (mm) REVERT: M 31 GLN cc_start: 0.8944 (tp40) cc_final: 0.8287 (tp-100) REVERT: M 64 LYS cc_start: 0.7880 (mmpt) cc_final: 0.7123 (mmtt) REVERT: M 69 LEU cc_start: 0.9164 (tt) cc_final: 0.8778 (mt) REVERT: M 75 LEU cc_start: 0.9368 (tt) cc_final: 0.9142 (mm) REVERT: M 78 LYS cc_start: 0.9046 (pptt) cc_final: 0.8763 (mtmm) REVERT: N 7 ILE cc_start: 0.9415 (mm) cc_final: 0.9126 (tp) REVERT: N 37 PHE cc_start: 0.8465 (m-10) cc_final: 0.8109 (m-10) REVERT: N 41 ARG cc_start: 0.8354 (mtm110) cc_final: 0.7991 (mtm110) REVERT: O 12 ILE cc_start: 0.9155 (mt) cc_final: 0.8921 (mt) REVERT: O 16 LYS cc_start: 0.8771 (ttpt) cc_final: 0.8559 (ptmm) REVERT: P 8 LYS cc_start: 0.9002 (tttm) cc_final: 0.8796 (tttp) REVERT: Q 63 ILE cc_start: 0.9191 (pt) cc_final: 0.8864 (mm) REVERT: R 59 LYS cc_start: 0.9245 (mttt) cc_final: 0.9003 (mtmm) REVERT: S 22 LEU cc_start: 0.8974 (tt) cc_final: 0.8398 (tt) REVERT: S 53 ASP cc_start: 0.8664 (p0) cc_final: 0.8323 (p0) REVERT: S 61 PHE cc_start: 0.8483 (t80) cc_final: 0.8048 (t80) outliers start: 7 outliers final: 2 residues processed: 1873 average time/residue: 1.3163 time to fit residues: 4251.5978 Evaluate side-chains 1361 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1359 time to evaluate : 6.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain w residue 24 GLU Chi-restraints excluded: chain w residue 28 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 896 optimal weight: 20.0000 chunk 804 optimal weight: 40.0000 chunk 446 optimal weight: 6.9990 chunk 274 optimal weight: 20.0000 chunk 542 optimal weight: 4.9990 chunk 430 optimal weight: 4.9990 chunk 832 optimal weight: 20.0000 chunk 322 optimal weight: 20.0000 chunk 506 optimal weight: 7.9990 chunk 619 optimal weight: 5.9990 chunk 964 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 86 ASN a 19 ASN ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 ASN b 40 GLN ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 3 GLN f 82 ASN ** f 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 61 GLN ** k 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 12 GLN ** m 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 GLN ** t 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 9 ASN B 18 HIS B 203 ASN C 101 ASN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN D 85 ASN G 84 ASN ** G 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS K 121 ASN L 122 ASN M 31 GLN O 9 ASN P 41 ASN P 72 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 163551 Z= 0.236 Angle : 0.662 16.782 245002 Z= 0.341 Chirality : 0.037 0.572 31362 Planarity : 0.005 0.089 12913 Dihedral : 24.639 179.967 82792 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.63 % Favored : 95.25 % Rotamer: Outliers : 3.37 % Allowed : 17.87 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.02 % Twisted Proline : 0.45 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.10), residues: 5897 helix: -0.10 (0.11), residues: 2065 sheet: -0.63 (0.16), residues: 1046 loop : -2.10 (0.10), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP G 103 HIS 0.015 0.002 HIS j 28 PHE 0.040 0.002 PHE n 47 TYR 0.025 0.002 TYR I 61 ARG 0.014 0.001 ARG v 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1622 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1465 time to evaluate : 6.420 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: h 86 ASP cc_start: 0.6326 (t0) cc_final: 0.6105 (t0) REVERT: p 31 ARG cc_start: 0.7608 (pmt170) cc_final: 0.6786 (ttp80) REVERT: q 113 MET cc_start: 0.7836 (mmm) cc_final: 0.7570 (mmm) REVERT: q 135 MET cc_start: 0.8183 (pmm) cc_final: 0.5906 (mmt) REVERT: a 55 ASP cc_start: 0.7923 (m-30) cc_final: 0.7590 (m-30) REVERT: c 97 TYR cc_start: 0.8234 (m-10) cc_final: 0.7982 (m-10) REVERT: c 101 ASP cc_start: 0.7834 (m-30) cc_final: 0.7484 (m-30) REVERT: c 164 GLU cc_start: 0.9013 (mp0) cc_final: 0.8740 (mp0) REVERT: d 108 VAL cc_start: 0.8910 (OUTLIER) cc_final: 0.8703 (p) REVERT: e 141 TYR cc_start: 0.8356 (t80) cc_final: 0.7951 (t80) REVERT: f 96 THR cc_start: 0.8571 (m) cc_final: 0.8366 (p) REVERT: l 70 ASP cc_start: 0.8850 (t0) cc_final: 0.8479 (t0) REVERT: m 4 LEU cc_start: 0.8989 (mm) cc_final: 0.8700 (mm) REVERT: m 80 LYS cc_start: 0.7772 (ttmt) cc_final: 0.7496 (ttmt) REVERT: u 64 ASP cc_start: 0.6563 (t70) cc_final: 0.6360 (t0) REVERT: v 34 GLN cc_start: 0.8284 (mp10) cc_final: 0.8083 (mp10) REVERT: v 39 LEU cc_start: 0.8648 (mp) cc_final: 0.8319 (mt) REVERT: w 47 ARG cc_start: 0.7936 (mtm110) cc_final: 0.7681 (mtm110) REVERT: x 29 LYS cc_start: 0.8952 (mppt) cc_final: 0.8388 (mtmm) REVERT: B 69 PHE cc_start: 0.8433 (m-10) cc_final: 0.8048 (m-80) REVERT: B 108 GLN cc_start: 0.9401 (pt0) cc_final: 0.9176 (pt0) REVERT: B 119 LYS cc_start: 0.9070 (mmpt) cc_final: 0.8370 (tptp) REVERT: C 113 GLN cc_start: 0.8762 (tp-100) cc_final: 0.8425 (tp-100) REVERT: C 146 GLN cc_start: 0.7854 (tt0) cc_final: 0.7015 (tt0) REVERT: C 202 TYR cc_start: 0.7369 (t80) cc_final: 0.6454 (t80) REVERT: D 96 ASN cc_start: 0.9237 (t0) cc_final: 0.8748 (t0) REVERT: E 31 PHE cc_start: 0.7886 (m-80) cc_final: 0.7665 (m-80) REVERT: F 5 GLU cc_start: 0.7933 (mp0) cc_final: 0.7691 (mp0) REVERT: F 20 LYS cc_start: 0.9006 (ptpp) cc_final: 0.8540 (ptpp) REVERT: F 25 ARG cc_start: 0.8210 (tpm170) cc_final: 0.7980 (tpm170) REVERT: G 103 TRP cc_start: 0.8940 (m-90) cc_final: 0.8674 (m-90) REVERT: H 19 MET cc_start: 0.8099 (ttp) cc_final: 0.7659 (tmm) REVERT: J 24 LYS cc_start: 0.9099 (ptpt) cc_final: 0.8497 (pttt) REVERT: K 20 SER cc_start: 0.7917 (p) cc_final: 0.7677 (m) REVERT: K 70 GLU cc_start: 0.8861 (tp30) cc_final: 0.8591 (mm-30) REVERT: L 25 ASN cc_start: 0.8536 (m-40) cc_final: 0.8266 (m110) REVERT: M 31 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8160 (tp-100) REVERT: M 71 ARG cc_start: 0.8937 (ptp-110) cc_final: 0.8665 (ptp-110) REVERT: M 75 LEU cc_start: 0.9393 (tt) cc_final: 0.8887 (mm) REVERT: M 78 LYS cc_start: 0.8916 (pptt) cc_final: 0.8422 (pptt) REVERT: N 58 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8224 (mmtt) REVERT: P 57 LEU cc_start: 0.9381 (tt) cc_final: 0.9023 (tp) REVERT: P 61 GLN cc_start: 0.9016 (mm-40) cc_final: 0.8809 (mm110) REVERT: P 71 ARG cc_start: 0.8898 (tpt-90) cc_final: 0.8686 (tpt90) REVERT: Q 75 PHE cc_start: 0.8004 (m-80) cc_final: 0.7794 (m-80) REVERT: Q 82 GLU cc_start: 0.8446 (tp30) cc_final: 0.8148 (tp30) REVERT: R 59 LYS cc_start: 0.9274 (mttt) cc_final: 0.9034 (mtmm) REVERT: S 20 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8471 (pt0) REVERT: S 61 PHE cc_start: 0.8377 (t80) cc_final: 0.7950 (t80) outliers start: 157 outliers final: 93 residues processed: 1511 average time/residue: 1.2930 time to fit residues: 3436.9098 Evaluate side-chains 1413 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1319 time to evaluate : 6.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 17 SER Chi-restraints excluded: chain q residue 54 ILE Chi-restraints excluded: chain Z residue 135 ILE Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 78 ILE Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 132 ASP Chi-restraints excluded: chain b residue 195 THR Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain d residue 62 HIS Chi-restraints excluded: chain d residue 108 VAL Chi-restraints excluded: chain d residue 138 ASP Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 44 ASN Chi-restraints excluded: chain j residue 52 ILE Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 129 THR Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 117 ILE Chi-restraints excluded: chain l residue 25 THR Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 63 THR Chi-restraints excluded: chain n residue 90 VAL Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 111 ASP Chi-restraints excluded: chain o residue 25 LEU Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 33 VAL Chi-restraints excluded: chain o residue 37 ASP Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain s residue 8 LEU Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 54 VAL Chi-restraints excluded: chain s residue 70 THR Chi-restraints excluded: chain t residue 10 MET Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 45 SER Chi-restraints excluded: chain u residue 44 ILE Chi-restraints excluded: chain u residue 51 THR Chi-restraints excluded: chain v residue 28 THR Chi-restraints excluded: chain v residue 33 LEU Chi-restraints excluded: chain w residue 4 ASN Chi-restraints excluded: chain w residue 24 GLU Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain 1 residue 16 ASN Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 43 THR Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain R residue 25 HIS Chi-restraints excluded: chain R residue 32 ASP Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 66 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 535 optimal weight: 7.9990 chunk 299 optimal weight: 10.0000 chunk 802 optimal weight: 30.0000 chunk 656 optimal weight: 5.9990 chunk 266 optimal weight: 20.0000 chunk 966 optimal weight: 10.0000 chunk 1043 optimal weight: 9.9990 chunk 860 optimal weight: 10.0000 chunk 958 optimal weight: 20.0000 chunk 329 optimal weight: 20.0000 chunk 775 optimal weight: 30.0000 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: p 66 GLN ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 140 HIS ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 189 HIS ** c 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 HIS f 3 GLN i 35 HIS i 59 GLN ** i 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 36 ASN ** t 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 GLN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 51 HIS P 41 ASN P 61 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 163551 Z= 0.305 Angle : 0.669 14.744 245002 Z= 0.344 Chirality : 0.037 0.522 31362 Planarity : 0.005 0.085 12913 Dihedral : 24.690 179.097 82790 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.31 % Favored : 93.54 % Rotamer: Outliers : 4.55 % Allowed : 21.43 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.02 % Twisted Proline : 0.45 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.10), residues: 5897 helix: 0.43 (0.12), residues: 2038 sheet: -0.64 (0.16), residues: 1021 loop : -1.95 (0.11), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP b 83 HIS 0.013 0.002 HIS j 28 PHE 0.033 0.002 PHE i 58 TYR 0.027 0.002 TYR I 116 ARG 0.016 0.001 ARG a 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1595 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1383 time to evaluate : 6.424 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: p 20 LYS cc_start: 0.8306 (pptt) cc_final: 0.8083 (tptp) REVERT: p 80 ASN cc_start: 0.7083 (t0) cc_final: 0.6476 (p0) REVERT: q 57 GLU cc_start: 0.8096 (mp0) cc_final: 0.7564 (mp0) REVERT: q 71 LYS cc_start: 0.9264 (mmmm) cc_final: 0.8989 (mtmm) REVERT: q 127 MET cc_start: 0.4687 (mmp) cc_final: 0.4396 (mmp) REVERT: c 17 MET cc_start: 0.8131 (ppp) cc_final: 0.7865 (ppp) REVERT: c 59 PHE cc_start: 0.9043 (m-80) cc_final: 0.8767 (m-80) REVERT: c 97 TYR cc_start: 0.8320 (m-10) cc_final: 0.7951 (m-10) REVERT: c 101 ASP cc_start: 0.7967 (m-30) cc_final: 0.7505 (m-30) REVERT: c 164 GLU cc_start: 0.8983 (mp0) cc_final: 0.8753 (mp0) REVERT: c 175 MET cc_start: 0.8457 (mmp) cc_final: 0.8149 (mmp) REVERT: d 95 TYR cc_start: 0.7966 (m-80) cc_final: 0.7551 (m-80) REVERT: e 30 SER cc_start: 0.8694 (t) cc_final: 0.8165 (t) REVERT: e 141 TYR cc_start: 0.8162 (t80) cc_final: 0.7939 (t80) REVERT: j 17 MET cc_start: 0.7123 (ptp) cc_final: 0.6863 (ptp) REVERT: m 1 MET cc_start: 0.6593 (tmm) cc_final: 0.6195 (tmm) REVERT: m 3 LYS cc_start: 0.8106 (mttt) cc_final: 0.7480 (mptt) REVERT: o 16 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7917 (tm-30) REVERT: s 29 GLU cc_start: 0.6771 (tp30) cc_final: 0.6504 (tp30) REVERT: s 41 ASP cc_start: 0.7100 (t0) cc_final: 0.6471 (t0) REVERT: u 64 ASP cc_start: 0.6607 (t70) cc_final: 0.6239 (t70) REVERT: v 39 LEU cc_start: 0.8801 (mp) cc_final: 0.8419 (mt) REVERT: x 29 LYS cc_start: 0.9012 (mppt) cc_final: 0.8452 (mtmt) REVERT: 2 37 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8211 (tttm) REVERT: B 51 GLU cc_start: 0.8949 (tp30) cc_final: 0.8500 (tp30) REVERT: B 69 PHE cc_start: 0.8515 (m-10) cc_final: 0.7767 (m-10) REVERT: B 89 MET cc_start: 0.5184 (pmm) cc_final: 0.4798 (pmm) REVERT: B 108 GLN cc_start: 0.9412 (pt0) cc_final: 0.9209 (pt0) REVERT: B 119 LYS cc_start: 0.9147 (mmpt) cc_final: 0.8408 (tptp) REVERT: B 136 GLN cc_start: 0.9035 (mm110) cc_final: 0.8825 (mm110) REVERT: B 177 ARG cc_start: 0.8739 (tpp80) cc_final: 0.8212 (mmt90) REVERT: C 23 TYR cc_start: 0.7963 (t80) cc_final: 0.7683 (t80) REVERT: C 113 GLN cc_start: 0.8822 (tp-100) cc_final: 0.8471 (tp-100) REVERT: D 50 GLN cc_start: 0.8345 (mt0) cc_final: 0.7854 (mp10) REVERT: D 96 ASN cc_start: 0.9164 (t0) cc_final: 0.8829 (t0) REVERT: F 25 ARG cc_start: 0.8293 (tpm170) cc_final: 0.8051 (tpm170) REVERT: G 70 MET cc_start: 0.8810 (tpp) cc_final: 0.8590 (tpp) REVERT: G 123 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8308 (mm-30) REVERT: G 146 GLU cc_start: 0.8195 (pm20) cc_final: 0.7720 (pm20) REVERT: I 115 LYS cc_start: 0.9235 (mmtp) cc_final: 0.8846 (mmtp) REVERT: J 24 LYS cc_start: 0.8981 (ptpt) cc_final: 0.8767 (ptmm) REVERT: J 63 GLU cc_start: 0.6340 (tt0) cc_final: 0.6112 (tt0) REVERT: L 25 ASN cc_start: 0.8662 (m-40) cc_final: 0.8366 (m110) REVERT: L 60 SER cc_start: 0.7573 (t) cc_final: 0.7280 (p) REVERT: L 88 GLN cc_start: 0.8270 (mm-40) cc_final: 0.7920 (mm-40) REVERT: M 31 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8376 (tp-100) REVERT: M 60 ILE cc_start: 0.8948 (mp) cc_final: 0.8497 (tp) REVERT: M 69 LEU cc_start: 0.8992 (mp) cc_final: 0.8507 (mt) REVERT: M 72 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8249 (mp0) REVERT: M 75 LEU cc_start: 0.9417 (tt) cc_final: 0.8900 (mm) REVERT: M 78 LYS cc_start: 0.8959 (pptt) cc_final: 0.8709 (pptt) REVERT: N 58 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8267 (mmtt) REVERT: O 58 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8254 (mttm) REVERT: P 65 LYS cc_start: 0.8666 (mptt) cc_final: 0.8346 (mmtm) REVERT: P 71 ARG cc_start: 0.8820 (tpt-90) cc_final: 0.8565 (tpt90) REVERT: P 80 MET cc_start: 0.7997 (ppp) cc_final: 0.7626 (ppp) REVERT: Q 64 MET cc_start: 0.8140 (tmm) cc_final: 0.7931 (tmm) REVERT: Q 75 PHE cc_start: 0.7955 (m-80) cc_final: 0.6924 (m-80) REVERT: Q 82 GLU cc_start: 0.8576 (tp30) cc_final: 0.8266 (tp30) REVERT: R 59 LYS cc_start: 0.9324 (mttt) cc_final: 0.9066 (mtmm) REVERT: R 70 MET cc_start: 0.7926 (tpt) cc_final: 0.7614 (tpt) REVERT: S 16 MET cc_start: 0.8215 (tpp) cc_final: 0.7851 (tpp) REVERT: S 61 PHE cc_start: 0.8498 (t80) cc_final: 0.8182 (t80) outliers start: 212 outliers final: 144 residues processed: 1471 average time/residue: 1.2760 time to fit residues: 3283.8249 Evaluate side-chains 1439 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1294 time to evaluate : 6.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 17 SER Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain Z residue 135 ILE Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 10 ILE Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 36 LEU Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain a residue 134 SER Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 132 ASP Chi-restraints excluded: chain b residue 195 THR Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain d residue 62 HIS Chi-restraints excluded: chain d residue 138 ASP Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 36 ILE Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain e residue 58 ILE Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 73 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain i residue 23 ILE Chi-restraints excluded: chain i residue 27 ASN Chi-restraints excluded: chain i residue 30 THR Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 44 ASN Chi-restraints excluded: chain j residue 52 ILE Chi-restraints excluded: chain j residue 79 LEU Chi-restraints excluded: chain j residue 106 ILE Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain j residue 127 ILE Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 76 ASN Chi-restraints excluded: chain l residue 25 THR Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain n residue 90 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 111 ASP Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 33 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain r residue 33 VAL Chi-restraints excluded: chain r residue 53 SER Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 7 ASP Chi-restraints excluded: chain t residue 10 MET Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 35 VAL Chi-restraints excluded: chain t residue 45 SER Chi-restraints excluded: chain u residue 39 VAL Chi-restraints excluded: chain u residue 51 THR Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 13 THR Chi-restraints excluded: chain v residue 28 THR Chi-restraints excluded: chain v residue 33 LEU Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 4 ASN Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain w residue 43 ILE Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 27 MET Chi-restraints excluded: chain 1 residue 16 ASN Chi-restraints excluded: chain 1 residue 19 SER Chi-restraints excluded: chain 1 residue 39 ASP Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 22 LEU Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 6 residue 23 GLU Chi-restraints excluded: chain 6 residue 27 VAL Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 166 TYR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 49 ILE Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain R residue 25 HIS Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 ASP Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 58 ILE Chi-restraints excluded: chain T residue 66 LEU Chi-restraints excluded: chain T residue 79 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 954 optimal weight: 20.0000 chunk 726 optimal weight: 20.0000 chunk 501 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 461 optimal weight: 20.0000 chunk 648 optimal weight: 7.9990 chunk 969 optimal weight: 9.9990 chunk 1026 optimal weight: 6.9990 chunk 506 optimal weight: 20.0000 chunk 918 optimal weight: 6.9990 chunk 276 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 46 GLN a 14 GLN ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 28 HIS ** k 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 67 ASN v 16 ASN ** w 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 HIS ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 163551 Z= 0.265 Angle : 0.637 13.163 245002 Z= 0.328 Chirality : 0.036 0.522 31362 Planarity : 0.005 0.080 12913 Dihedral : 24.700 179.588 82787 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.46 % Favored : 93.42 % Rotamer: Outliers : 5.18 % Allowed : 23.73 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.02 % Twisted Proline : 0.45 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.11), residues: 5897 helix: 0.55 (0.12), residues: 2055 sheet: -0.59 (0.16), residues: 1014 loop : -1.89 (0.11), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP b 83 HIS 0.009 0.001 HIS j 28 PHE 0.034 0.002 PHE a 53 TYR 0.025 0.002 TYR I 116 ARG 0.014 0.001 ARG I 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1597 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1356 time to evaluate : 6.427 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: q 125 MET cc_start: 0.6132 (tpp) cc_final: 0.5652 (tpp) REVERT: q 135 MET cc_start: 0.8011 (pmm) cc_final: 0.5414 (mmt) REVERT: Z 236 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6157 (mm-30) REVERT: c 17 MET cc_start: 0.8265 (ppp) cc_final: 0.7943 (ppp) REVERT: c 59 PHE cc_start: 0.9090 (m-80) cc_final: 0.8809 (m-80) REVERT: c 69 ARG cc_start: 0.7997 (tpm170) cc_final: 0.7336 (tpm170) REVERT: c 97 TYR cc_start: 0.8303 (m-10) cc_final: 0.7818 (m-10) REVERT: c 101 ASP cc_start: 0.7976 (m-30) cc_final: 0.7505 (m-30) REVERT: c 175 MET cc_start: 0.8591 (mmp) cc_final: 0.8237 (mmp) REVERT: d 95 TYR cc_start: 0.7975 (m-80) cc_final: 0.7590 (m-80) REVERT: e 30 SER cc_start: 0.8741 (t) cc_final: 0.7970 (t) REVERT: e 80 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7376 (mm-40) REVERT: e 109 MET cc_start: 0.7338 (mtt) cc_final: 0.6573 (mtt) REVERT: m 1 MET cc_start: 0.6572 (tmm) cc_final: 0.6295 (tmm) REVERT: m 3 LYS cc_start: 0.7974 (mttt) cc_final: 0.7671 (mttt) REVERT: m 85 GLU cc_start: 0.7252 (mt-10) cc_final: 0.7009 (mt-10) REVERT: v 39 LEU cc_start: 0.8830 (mp) cc_final: 0.8461 (mt) REVERT: w 21 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8802 (tt) REVERT: x 29 LYS cc_start: 0.8995 (mppt) cc_final: 0.8400 (mtmt) REVERT: 1 31 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7139 (mm-30) REVERT: 1 43 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.9146 (p) REVERT: 2 37 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8269 (tttm) REVERT: B 51 GLU cc_start: 0.8892 (tp30) cc_final: 0.8497 (tp30) REVERT: B 69 PHE cc_start: 0.8503 (m-10) cc_final: 0.7904 (m-10) REVERT: B 89 MET cc_start: 0.4981 (pmm) cc_final: 0.4773 (pmm) REVERT: B 119 LYS cc_start: 0.9169 (mmpt) cc_final: 0.8431 (tptp) REVERT: B 136 GLN cc_start: 0.9094 (mm110) cc_final: 0.8844 (mm110) REVERT: B 147 PHE cc_start: 0.8037 (m-10) cc_final: 0.7539 (m-80) REVERT: C 113 GLN cc_start: 0.8859 (tp-100) cc_final: 0.8495 (tp-100) REVERT: D 96 ASN cc_start: 0.9171 (t0) cc_final: 0.8822 (t0) REVERT: F 25 ARG cc_start: 0.8307 (tpm170) cc_final: 0.8058 (tpm170) REVERT: G 70 MET cc_start: 0.8866 (tpp) cc_final: 0.8604 (tpp) REVERT: G 103 TRP cc_start: 0.9115 (m-10) cc_final: 0.8666 (m-90) REVERT: J 24 LYS cc_start: 0.9011 (ptpt) cc_final: 0.8776 (pttm) REVERT: K 19 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7219 (tm-30) REVERT: K 70 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8378 (mm-30) REVERT: L 25 ASN cc_start: 0.8668 (m-40) cc_final: 0.8352 (m110) REVERT: L 60 SER cc_start: 0.7602 (t) cc_final: 0.7346 (p) REVERT: L 65 TYR cc_start: 0.8216 (t80) cc_final: 0.7917 (t80) REVERT: L 88 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7887 (mm-40) REVERT: M 21 TYR cc_start: 0.7801 (m-80) cc_final: 0.7268 (m-80) REVERT: M 31 GLN cc_start: 0.9060 (tp-100) cc_final: 0.8281 (tp-100) REVERT: M 60 ILE cc_start: 0.9084 (mp) cc_final: 0.8726 (tp) REVERT: M 75 LEU cc_start: 0.9417 (tt) cc_final: 0.8839 (mm) REVERT: N 7 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9171 (tp) REVERT: O 58 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8306 (mttp) REVERT: P 57 LEU cc_start: 0.9428 (tt) cc_final: 0.9118 (tp) REVERT: P 61 GLN cc_start: 0.9126 (mm110) cc_final: 0.8895 (mm110) REVERT: P 65 LYS cc_start: 0.8637 (mptt) cc_final: 0.8312 (mmtm) REVERT: R 59 LYS cc_start: 0.9307 (mttt) cc_final: 0.9054 (mtmm) REVERT: S 15 LEU cc_start: 0.7977 (pp) cc_final: 0.7720 (pp) REVERT: S 16 MET cc_start: 0.8497 (tpp) cc_final: 0.7636 (tpp) REVERT: S 18 LYS cc_start: 0.8678 (mttt) cc_final: 0.8336 (mmtt) REVERT: S 20 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8228 (mp0) REVERT: S 61 PHE cc_start: 0.8552 (t80) cc_final: 0.8241 (t80) outliers start: 241 outliers final: 163 residues processed: 1457 average time/residue: 1.2622 time to fit residues: 3237.5563 Evaluate side-chains 1439 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1272 time to evaluate : 6.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain Z residue 135 ILE Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 198 GLU Chi-restraints excluded: chain Z residue 259 THR Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 36 LEU Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain a residue 137 SER Chi-restraints excluded: chain a residue 140 HIS Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 132 ASP Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain d residue 62 HIS Chi-restraints excluded: chain d residue 138 ASP Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain f residue 6 THR Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 42 THR Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 73 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain i residue 23 ILE Chi-restraints excluded: chain i residue 27 ASN Chi-restraints excluded: chain i residue 39 ASN Chi-restraints excluded: chain i residue 59 GLN Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 44 ASN Chi-restraints excluded: chain j residue 52 ILE Chi-restraints excluded: chain j residue 79 LEU Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 106 ILE Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain j residue 127 ILE Chi-restraints excluded: chain j residue 129 THR Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 76 ASN Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain l residue 25 THR Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain n residue 90 VAL Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 111 ASP Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 33 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain r residue 39 THR Chi-restraints excluded: chain s residue 27 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 86 ASP Chi-restraints excluded: chain t residue 7 ASP Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 35 VAL Chi-restraints excluded: chain t residue 45 SER Chi-restraints excluded: chain u residue 51 THR Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 13 THR Chi-restraints excluded: chain v residue 28 THR Chi-restraints excluded: chain v residue 33 LEU Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 4 ASN Chi-restraints excluded: chain w residue 21 LEU Chi-restraints excluded: chain w residue 23 GLU Chi-restraints excluded: chain w residue 43 ILE Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 58 GLU Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 1 residue 16 ASN Chi-restraints excluded: chain 1 residue 19 SER Chi-restraints excluded: chain 1 residue 39 ASP Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 22 LEU Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 27 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 58 TYR Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 7 ILE Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain R residue 25 HIS Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 32 ASP Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 58 ILE Chi-restraints excluded: chain T residue 66 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 854 optimal weight: 9.9990 chunk 582 optimal weight: 7.9990 chunk 14 optimal weight: 40.0000 chunk 764 optimal weight: 20.0000 chunk 423 optimal weight: 10.0000 chunk 875 optimal weight: 20.0000 chunk 709 optimal weight: 30.0000 chunk 1 optimal weight: 40.0000 chunk 524 optimal weight: 8.9990 chunk 921 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 28 HIS ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 12 GLN w 27 ASN ** 2 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 40 GLN B 55 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 163551 Z= 0.311 Angle : 0.672 13.245 245002 Z= 0.345 Chirality : 0.037 0.497 31362 Planarity : 0.005 0.082 12913 Dihedral : 24.751 179.528 82787 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.39 % Favored : 92.47 % Rotamer: Outliers : 5.63 % Allowed : 25.21 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.02 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.11), residues: 5897 helix: 0.54 (0.12), residues: 2059 sheet: -0.58 (0.16), residues: 1037 loop : -1.88 (0.11), residues: 2801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP b 83 HIS 0.009 0.001 HIS j 28 PHE 0.037 0.002 PHE i 58 TYR 0.030 0.002 TYR I 116 ARG 0.013 0.001 ARG x 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1592 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1330 time to evaluate : 6.416 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: q 43 ASN cc_start: 0.8249 (t0) cc_final: 0.7860 (t0) REVERT: q 125 MET cc_start: 0.6601 (tpp) cc_final: 0.6289 (tpp) REVERT: q 135 MET cc_start: 0.8373 (pmm) cc_final: 0.5937 (mmt) REVERT: c 17 MET cc_start: 0.8529 (ppp) cc_final: 0.8070 (ppp) REVERT: c 59 PHE cc_start: 0.9119 (m-10) cc_final: 0.8799 (m-80) REVERT: c 69 ARG cc_start: 0.8187 (tpm170) cc_final: 0.7636 (tpm170) REVERT: c 97 TYR cc_start: 0.8397 (m-10) cc_final: 0.8153 (m-10) REVERT: c 101 ASP cc_start: 0.8077 (m-30) cc_final: 0.7579 (m-30) REVERT: c 175 MET cc_start: 0.8612 (mmp) cc_final: 0.8256 (mmp) REVERT: d 95 TYR cc_start: 0.8137 (m-80) cc_final: 0.7707 (m-80) REVERT: e 30 SER cc_start: 0.8786 (t) cc_final: 0.8026 (t) REVERT: e 76 TYR cc_start: 0.7657 (m-10) cc_final: 0.7435 (m-10) REVERT: e 97 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7722 (p90) REVERT: e 109 MET cc_start: 0.7366 (mtt) cc_final: 0.6665 (mtt) REVERT: f 44 LYS cc_start: 0.8849 (tppt) cc_final: 0.8446 (tppt) REVERT: f 54 LYS cc_start: 0.8497 (ttmm) cc_final: 0.8281 (ttmm) REVERT: k 45 GLU cc_start: 0.6372 (mt-10) cc_final: 0.6123 (mt-10) REVERT: m 1 MET cc_start: 0.6568 (tmm) cc_final: 0.6257 (tmm) REVERT: m 7 ASP cc_start: 0.7892 (p0) cc_final: 0.7624 (p0) REVERT: n 38 GLN cc_start: 0.7856 (tp40) cc_final: 0.7595 (tp40) REVERT: o 75 ARG cc_start: 0.8516 (tpp80) cc_final: 0.8175 (tpp80) REVERT: r 28 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7504 (tm-30) REVERT: w 21 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8859 (tt) REVERT: x 29 LYS cc_start: 0.8998 (mppt) cc_final: 0.8460 (mtmt) REVERT: 2 37 LYS cc_start: 0.8650 (ttpt) cc_final: 0.8314 (tttm) REVERT: B 21 ARG cc_start: 0.5569 (mmp80) cc_final: 0.5139 (mmp80) REVERT: B 54 TYR cc_start: 0.8396 (m-80) cc_final: 0.8183 (m-80) REVERT: B 69 PHE cc_start: 0.8539 (m-10) cc_final: 0.7678 (m-10) REVERT: B 89 MET cc_start: 0.4652 (pmm) cc_final: 0.4328 (pmm) REVERT: B 119 LYS cc_start: 0.9263 (mmpt) cc_final: 0.8499 (tptp) REVERT: B 136 GLN cc_start: 0.9044 (mm110) cc_final: 0.8770 (mm110) REVERT: B 167 ARG cc_start: 0.8684 (ttm170) cc_final: 0.8143 (tmm160) REVERT: C 113 GLN cc_start: 0.8893 (tp-100) cc_final: 0.8526 (tp-100) REVERT: D 96 ASN cc_start: 0.9157 (t0) cc_final: 0.8797 (t0) REVERT: F 25 ARG cc_start: 0.8259 (tpm170) cc_final: 0.8034 (tpm170) REVERT: F 64 ASN cc_start: 0.8147 (m-40) cc_final: 0.7764 (m-40) REVERT: G 123 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8348 (mm-30) REVERT: J 24 LYS cc_start: 0.9035 (ptpt) cc_final: 0.8775 (pttm) REVERT: K 70 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8435 (mm-30) REVERT: L 25 ASN cc_start: 0.8701 (m-40) cc_final: 0.8380 (m110) REVERT: L 60 SER cc_start: 0.7253 (t) cc_final: 0.7030 (p) REVERT: L 88 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7950 (mm-40) REVERT: M 31 GLN cc_start: 0.9115 (tp-100) cc_final: 0.8487 (tp-100) REVERT: M 71 ARG cc_start: 0.9085 (ptp-110) cc_final: 0.8792 (ptp-110) REVERT: M 103 LYS cc_start: 0.8367 (ptmt) cc_final: 0.8145 (ttpt) REVERT: O 58 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8394 (mttp) REVERT: P 57 LEU cc_start: 0.9457 (tt) cc_final: 0.9128 (tp) REVERT: P 61 GLN cc_start: 0.9178 (mm110) cc_final: 0.8926 (mm110) REVERT: P 65 LYS cc_start: 0.8638 (mptt) cc_final: 0.8333 (mmtm) REVERT: R 70 MET cc_start: 0.7884 (tpt) cc_final: 0.7468 (tpt) REVERT: S 16 MET cc_start: 0.8534 (tpp) cc_final: 0.8148 (tpp) REVERT: S 20 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8799 (mp0) outliers start: 262 outliers final: 194 residues processed: 1446 average time/residue: 1.2904 time to fit residues: 3274.6202 Evaluate side-chains 1441 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1243 time to evaluate : 6.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain q residue 127 MET Chi-restraints excluded: chain Z residue 5 LYS Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 95 ASN Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 198 GLU Chi-restraints excluded: chain Z residue 241 ILE Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 36 LEU Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain a residue 134 SER Chi-restraints excluded: chain a residue 137 SER Chi-restraints excluded: chain a residue 140 HIS Chi-restraints excluded: chain a residue 179 VAL Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 132 ASP Chi-restraints excluded: chain b residue 195 THR Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain c residue 144 ASP Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain d residue 62 HIS Chi-restraints excluded: chain d residue 138 ASP Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain e residue 97 TYR Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 73 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain i residue 23 ILE Chi-restraints excluded: chain i residue 27 ASN Chi-restraints excluded: chain i residue 59 GLN Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 44 ASN Chi-restraints excluded: chain j residue 52 ILE Chi-restraints excluded: chain j residue 79 LEU Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 106 ILE Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain j residue 129 THR Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 40 LEU Chi-restraints excluded: chain k residue 76 ASN Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain l residue 25 THR Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 90 VAL Chi-restraints excluded: chain n residue 92 ARG Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 111 ASP Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 33 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain r residue 39 THR Chi-restraints excluded: chain s residue 27 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 70 THR Chi-restraints excluded: chain s residue 86 ASP Chi-restraints excluded: chain t residue 7 ASP Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain t residue 35 VAL Chi-restraints excluded: chain t residue 45 SER Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain u residue 51 THR Chi-restraints excluded: chain v residue 3 ARG Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 13 THR Chi-restraints excluded: chain v residue 33 LEU Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 4 ASN Chi-restraints excluded: chain w residue 21 LEU Chi-restraints excluded: chain w residue 23 GLU Chi-restraints excluded: chain w residue 43 ILE Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 46 MET Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain x residue 58 GLU Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 18 THR Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 1 residue 16 ASN Chi-restraints excluded: chain 1 residue 19 SER Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 22 LEU Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 23 GLU Chi-restraints excluded: chain 6 residue 27 VAL Chi-restraints excluded: chain 6 residue 56 VAL Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 116 ASP Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 41 ASN Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain R residue 25 HIS Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 32 ASP Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 17 THR Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 58 ILE Chi-restraints excluded: chain T residue 66 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 345 optimal weight: 10.0000 chunk 924 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 602 optimal weight: 20.0000 chunk 253 optimal weight: 20.0000 chunk 1027 optimal weight: 0.7980 chunk 852 optimal weight: 20.0000 chunk 475 optimal weight: 40.0000 chunk 85 optimal weight: 2.9990 chunk 339 optimal weight: 20.0000 chunk 539 optimal weight: 2.9990 overall best weight: 7.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 2 ASN ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 28 HIS ** k 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 81 ASN ** w 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 40 GLN D 67 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 163551 Z= 0.257 Angle : 0.645 13.989 245002 Z= 0.330 Chirality : 0.036 0.511 31362 Planarity : 0.005 0.079 12913 Dihedral : 24.738 179.772 82787 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.19 % Favored : 92.69 % Rotamer: Outliers : 5.39 % Allowed : 27.47 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.02 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.11), residues: 5897 helix: 0.58 (0.12), residues: 2049 sheet: -0.60 (0.16), residues: 1039 loop : -1.85 (0.11), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP b 83 HIS 0.007 0.001 HIS a 126 PHE 0.036 0.002 PHE S 61 TYR 0.029 0.002 TYR I 116 ARG 0.016 0.001 ARG x 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1565 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1314 time to evaluate : 6.459 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: q 125 MET cc_start: 0.6762 (tpp) cc_final: 0.5439 (tmm) REVERT: q 135 MET cc_start: 0.8472 (pmm) cc_final: 0.6195 (mmt) REVERT: c 17 MET cc_start: 0.8591 (ppp) cc_final: 0.8113 (ppp) REVERT: c 59 PHE cc_start: 0.9118 (m-10) cc_final: 0.8794 (m-80) REVERT: c 83 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7632 (ppp) REVERT: c 101 ASP cc_start: 0.8054 (m-30) cc_final: 0.7526 (m-30) REVERT: c 175 MET cc_start: 0.8688 (mmp) cc_final: 0.8282 (mmp) REVERT: d 95 TYR cc_start: 0.8213 (m-80) cc_final: 0.7774 (m-80) REVERT: e 30 SER cc_start: 0.8758 (t) cc_final: 0.8045 (t) REVERT: e 92 GLU cc_start: 0.7536 (pp20) cc_final: 0.7207 (pp20) REVERT: e 109 MET cc_start: 0.7373 (mtt) cc_final: 0.6672 (mtt) REVERT: k 45 GLU cc_start: 0.6344 (mt-10) cc_final: 0.6093 (mt-10) REVERT: l 52 THR cc_start: 0.8932 (m) cc_final: 0.8602 (p) REVERT: r 31 GLU cc_start: 0.7801 (pm20) cc_final: 0.7509 (pm20) REVERT: x 29 LYS cc_start: 0.9006 (mppt) cc_final: 0.8489 (mtmt) REVERT: 2 37 LYS cc_start: 0.8566 (ttpt) cc_final: 0.8289 (tttm) REVERT: B 54 TYR cc_start: 0.8447 (m-80) cc_final: 0.8244 (m-80) REVERT: B 69 PHE cc_start: 0.8460 (m-10) cc_final: 0.7599 (m-10) REVERT: B 89 MET cc_start: 0.5096 (OUTLIER) cc_final: 0.4738 (pmm) REVERT: B 119 LYS cc_start: 0.9263 (mmpt) cc_final: 0.8527 (tptp) REVERT: B 136 GLN cc_start: 0.9004 (mm110) cc_final: 0.8753 (mm110) REVERT: B 167 ARG cc_start: 0.8712 (ttm170) cc_final: 0.8168 (tmm160) REVERT: C 113 GLN cc_start: 0.8855 (tp-100) cc_final: 0.8457 (tp-100) REVERT: D 96 ASN cc_start: 0.9115 (t0) cc_final: 0.8767 (t0) REVERT: D 182 ARG cc_start: 0.7687 (tpm170) cc_final: 0.7364 (tpm170) REVERT: F 16 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8778 (mm-30) REVERT: G 70 MET cc_start: 0.8918 (tpp) cc_final: 0.8590 (tpp) REVERT: G 103 TRP cc_start: 0.9133 (m-10) cc_final: 0.8508 (m-90) REVERT: G 123 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8341 (mm-30) REVERT: H 32 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8837 (tp) REVERT: J 24 LYS cc_start: 0.9051 (ptpt) cc_final: 0.8786 (pttm) REVERT: L 25 ASN cc_start: 0.8677 (m-40) cc_final: 0.8321 (m110) REVERT: M 21 TYR cc_start: 0.7730 (m-80) cc_final: 0.7257 (m-80) REVERT: M 31 GLN cc_start: 0.9141 (tp-100) cc_final: 0.8510 (tp-100) REVERT: M 103 LYS cc_start: 0.8503 (ptmt) cc_final: 0.8287 (ttpt) REVERT: N 9 LYS cc_start: 0.9536 (OUTLIER) cc_final: 0.9316 (mttt) REVERT: N 26 ARG cc_start: 0.8680 (tmt-80) cc_final: 0.8226 (ttp80) REVERT: O 58 LYS cc_start: 0.8609 (ttmt) cc_final: 0.8325 (mttm) REVERT: P 65 LYS cc_start: 0.8638 (mptt) cc_final: 0.8260 (mmtm) REVERT: Q 75 PHE cc_start: 0.8277 (m-80) cc_final: 0.7997 (m-80) REVERT: S 15 LEU cc_start: 0.8139 (pp) cc_final: 0.7896 (mm) REVERT: S 16 MET cc_start: 0.8574 (tpp) cc_final: 0.7895 (tpp) REVERT: S 20 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8747 (mp0) outliers start: 251 outliers final: 186 residues processed: 1423 average time/residue: 1.2815 time to fit residues: 3206.0848 Evaluate side-chains 1434 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1242 time to evaluate : 6.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain q residue 110 GLU Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain q residue 127 MET Chi-restraints excluded: chain Z residue 5 LYS Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 200 HIS Chi-restraints excluded: chain Z residue 241 ILE Chi-restraints excluded: chain Z residue 259 THR Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 36 LEU Chi-restraints excluded: chain a residue 55 ASP Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain a residue 134 SER Chi-restraints excluded: chain a residue 137 SER Chi-restraints excluded: chain a residue 140 HIS Chi-restraints excluded: chain a residue 179 VAL Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 132 ASP Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain c residue 83 MET Chi-restraints excluded: chain c residue 144 ASP Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain d residue 138 ASP Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain e residue 97 TYR Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain f residue 6 THR Chi-restraints excluded: chain f residue 12 ASP Chi-restraints excluded: chain f residue 59 LYS Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 73 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 87 ILE Chi-restraints excluded: chain i residue 27 ASN Chi-restraints excluded: chain i residue 59 GLN Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 44 ASN Chi-restraints excluded: chain j residue 52 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 79 LEU Chi-restraints excluded: chain j residue 106 ILE Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain j residue 129 THR Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 40 LEU Chi-restraints excluded: chain k residue 76 ASN Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain l residue 25 THR Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 30 VAL Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain m residue 102 GLU Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 90 VAL Chi-restraints excluded: chain n residue 92 ARG Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 111 ASP Chi-restraints excluded: chain o residue 25 LEU Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 33 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 27 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 81 VAL Chi-restraints excluded: chain s residue 86 ASP Chi-restraints excluded: chain t residue 7 ASP Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain t residue 45 SER Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain u residue 51 THR Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 13 THR Chi-restraints excluded: chain v residue 33 LEU Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 23 GLU Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 46 MET Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain x residue 58 GLU Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 1 residue 16 ASN Chi-restraints excluded: chain 1 residue 19 SER Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 3 residue 22 LEU Chi-restraints excluded: chain 3 residue 45 ARG Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 27 VAL Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 41 ASN Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain R residue 25 HIS Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 32 ASP Chi-restraints excluded: chain R residue 53 ASN Chi-restraints excluded: chain R residue 75 TYR Chi-restraints excluded: chain S residue 7 LYS Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 58 ILE Chi-restraints excluded: chain T residue 66 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 990 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 585 optimal weight: 2.9990 chunk 750 optimal weight: 20.0000 chunk 581 optimal weight: 4.9990 chunk 864 optimal weight: 20.0000 chunk 573 optimal weight: 0.9980 chunk 1023 optimal weight: 5.9990 chunk 640 optimal weight: 30.0000 chunk 624 optimal weight: 8.9990 chunk 472 optimal weight: 30.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 12 GLN o 11 GLN ** r 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 GLN ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 163551 Z= 0.194 Angle : 0.617 12.566 245002 Z= 0.315 Chirality : 0.034 0.526 31362 Planarity : 0.004 0.079 12913 Dihedral : 24.679 179.560 82787 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.04 % Favored : 92.79 % Rotamer: Outliers : 4.79 % Allowed : 28.93 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.02 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.11), residues: 5897 helix: 0.61 (0.12), residues: 2052 sheet: -0.55 (0.16), residues: 1024 loop : -1.76 (0.11), residues: 2821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP b 83 HIS 0.007 0.001 HIS j 28 PHE 0.039 0.002 PHE i 58 TYR 0.031 0.002 TYR I 116 ARG 0.015 0.001 ARG O 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1560 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1337 time to evaluate : 6.370 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: q 125 MET cc_start: 0.6831 (tpp) cc_final: 0.5528 (tmm) REVERT: q 135 MET cc_start: 0.8590 (pmm) cc_final: 0.6522 (mmt) REVERT: c 17 MET cc_start: 0.8509 (ppp) cc_final: 0.8056 (ppp) REVERT: c 59 PHE cc_start: 0.9106 (m-10) cc_final: 0.8796 (m-80) REVERT: c 83 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7563 (ppp) REVERT: c 101 ASP cc_start: 0.8161 (m-30) cc_final: 0.7597 (m-30) REVERT: c 175 MET cc_start: 0.8667 (mmp) cc_final: 0.8192 (mmp) REVERT: d 42 MET cc_start: 0.7990 (tpt) cc_final: 0.7694 (tpt) REVERT: d 95 TYR cc_start: 0.8222 (m-80) cc_final: 0.7726 (m-80) REVERT: e 30 SER cc_start: 0.8719 (t) cc_final: 0.7995 (t) REVERT: e 92 GLU cc_start: 0.7505 (pp20) cc_final: 0.7160 (pp20) REVERT: e 109 MET cc_start: 0.7348 (mtt) cc_final: 0.6697 (mtt) REVERT: l 52 THR cc_start: 0.8902 (m) cc_final: 0.8573 (p) REVERT: x 20 ARG cc_start: 0.7602 (mtm110) cc_final: 0.7383 (mtm110) REVERT: x 29 LYS cc_start: 0.8987 (mppt) cc_final: 0.8428 (mtmt) REVERT: B 51 GLU cc_start: 0.9189 (pt0) cc_final: 0.8930 (tp30) REVERT: B 54 TYR cc_start: 0.8489 (m-80) cc_final: 0.8110 (m-80) REVERT: B 69 PHE cc_start: 0.8483 (m-10) cc_final: 0.7555 (m-10) REVERT: B 89 MET cc_start: 0.5224 (OUTLIER) cc_final: 0.4725 (pmm) REVERT: B 136 GLN cc_start: 0.9055 (mm110) cc_final: 0.8802 (mm110) REVERT: B 167 ARG cc_start: 0.8680 (ttm170) cc_final: 0.8313 (tmm160) REVERT: B 170 ARG cc_start: 0.8362 (tpp-160) cc_final: 0.7821 (tpp-160) REVERT: C 113 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8440 (tp-100) REVERT: C 138 GLN cc_start: 0.9266 (tp40) cc_final: 0.9031 (tp40) REVERT: D 96 ASN cc_start: 0.9059 (t0) cc_final: 0.8729 (t0) REVERT: F 16 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8744 (mm-30) REVERT: G 30 MET cc_start: 0.0369 (ptm) cc_final: -0.0193 (tmm) REVERT: G 70 MET cc_start: 0.8964 (tpp) cc_final: 0.8643 (tpp) REVERT: G 103 TRP cc_start: 0.9077 (m-10) cc_final: 0.8429 (m-90) REVERT: G 123 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8370 (mm-30) REVERT: J 24 LYS cc_start: 0.9128 (ptpt) cc_final: 0.8807 (pttt) REVERT: J 27 GLU cc_start: 0.8740 (pp20) cc_final: 0.8429 (pp20) REVERT: L 25 ASN cc_start: 0.8658 (m-40) cc_final: 0.8293 (m110) REVERT: M 31 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8462 (tp-100) REVERT: M 103 LYS cc_start: 0.8516 (ptmt) cc_final: 0.8262 (ttpt) REVERT: N 9 LYS cc_start: 0.9529 (OUTLIER) cc_final: 0.9326 (mttt) REVERT: O 53 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7760 (ttm110) REVERT: O 58 LYS cc_start: 0.8562 (ttmt) cc_final: 0.8294 (mttm) REVERT: P 57 LEU cc_start: 0.9402 (tt) cc_final: 0.9075 (tp) REVERT: P 61 GLN cc_start: 0.9145 (mm110) cc_final: 0.8831 (mm110) REVERT: P 65 LYS cc_start: 0.8631 (mptt) cc_final: 0.8426 (mptt) REVERT: S 16 MET cc_start: 0.8513 (tpp) cc_final: 0.7839 (tpp) REVERT: S 20 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8657 (mp0) outliers start: 223 outliers final: 164 residues processed: 1435 average time/residue: 1.3624 time to fit residues: 3453.0647 Evaluate side-chains 1430 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1261 time to evaluate : 6.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain q residue 110 GLU Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain q residue 127 MET Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 198 GLU Chi-restraints excluded: chain Z residue 241 ILE Chi-restraints excluded: chain Z residue 259 THR Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 36 LEU Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain a residue 140 HIS Chi-restraints excluded: chain a residue 179 VAL Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 132 ASP Chi-restraints excluded: chain b residue 193 LEU Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain c residue 83 MET Chi-restraints excluded: chain c residue 144 ASP Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain d residue 116 ILE Chi-restraints excluded: chain d residue 138 ASP Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain e residue 97 TYR Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain e residue 142 GLU Chi-restraints excluded: chain f residue 73 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain i residue 27 ASN Chi-restraints excluded: chain i residue 59 GLN Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 44 ASN Chi-restraints excluded: chain j residue 52 ILE Chi-restraints excluded: chain j residue 79 LEU Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain j residue 129 THR Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 76 ASN Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain l residue 25 THR Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 63 LEU Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 30 VAL Chi-restraints excluded: chain m residue 36 ASN Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain n residue 90 VAL Chi-restraints excluded: chain n residue 92 ARG Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 111 ASP Chi-restraints excluded: chain o residue 25 LEU Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 33 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain r residue 53 SER Chi-restraints excluded: chain s residue 27 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 86 ASP Chi-restraints excluded: chain t residue 7 ASP Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain t residue 45 SER Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain u residue 51 THR Chi-restraints excluded: chain v residue 3 ARG Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 13 THR Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 4 ASN Chi-restraints excluded: chain w residue 23 GLU Chi-restraints excluded: chain w residue 30 PHE Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 46 MET Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain x residue 58 GLU Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 0 residue 38 LEU Chi-restraints excluded: chain 1 residue 16 ASN Chi-restraints excluded: chain 1 residue 19 SER Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 56 VAL Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 41 ASN Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain R residue 25 HIS Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 32 ASP Chi-restraints excluded: chain R residue 75 TYR Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 58 ILE Chi-restraints excluded: chain T residue 66 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 633 optimal weight: 20.0000 chunk 408 optimal weight: 4.9990 chunk 611 optimal weight: 20.0000 chunk 308 optimal weight: 20.0000 chunk 201 optimal weight: 20.0000 chunk 198 optimal weight: 20.0000 chunk 650 optimal weight: 30.0000 chunk 697 optimal weight: 30.0000 chunk 506 optimal weight: 8.9990 chunk 95 optimal weight: 30.0000 chunk 804 optimal weight: 40.0000 overall best weight: 14.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 43 GLN ** m 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 101 ASN o 81 ASN ** t 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.130 163551 Z= 0.486 Angle : 0.820 13.088 245002 Z= 0.416 Chirality : 0.044 0.443 31362 Planarity : 0.006 0.080 12913 Dihedral : 24.876 179.492 82787 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 27.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.00 % Favored : 90.89 % Rotamer: Outliers : 5.67 % Allowed : 29.51 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.02 % Twisted Proline : 0.45 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.11), residues: 5897 helix: 0.21 (0.11), residues: 2064 sheet: -0.78 (0.16), residues: 1031 loop : -1.97 (0.11), residues: 2802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP b 83 HIS 0.013 0.002 HIS S 57 PHE 0.076 0.003 PHE G 47 TYR 0.032 0.003 TYR Z 83 ARG 0.013 0.001 ARG O 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1496 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1232 time to evaluate : 6.457 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: q 125 MET cc_start: 0.6882 (tpp) cc_final: 0.5519 (tmm) REVERT: q 135 MET cc_start: 0.8704 (pmm) cc_final: 0.6658 (mmt) REVERT: c 17 MET cc_start: 0.8806 (ppp) cc_final: 0.8294 (ppp) REVERT: c 59 PHE cc_start: 0.9195 (m-10) cc_final: 0.8953 (m-80) REVERT: c 101 ASP cc_start: 0.8212 (m-30) cc_final: 0.7840 (m-30) REVERT: d 42 MET cc_start: 0.7887 (tpt) cc_final: 0.7557 (tpt) REVERT: d 95 TYR cc_start: 0.8472 (m-80) cc_final: 0.7965 (m-80) REVERT: e 30 SER cc_start: 0.8877 (t) cc_final: 0.8287 (t) REVERT: e 109 MET cc_start: 0.7499 (mtt) cc_final: 0.6895 (mtt) REVERT: k 45 GLU cc_start: 0.6669 (mm-30) cc_final: 0.6261 (mt-10) REVERT: l 52 THR cc_start: 0.8909 (m) cc_final: 0.8621 (p) REVERT: n 85 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8781 (tt) REVERT: r 28 GLN cc_start: 0.7812 (pp30) cc_final: 0.7040 (pp30) REVERT: r 31 GLU cc_start: 0.7923 (pm20) cc_final: 0.7229 (pm20) REVERT: x 29 LYS cc_start: 0.9064 (mppt) cc_final: 0.8544 (mtmt) REVERT: B 69 PHE cc_start: 0.8645 (m-10) cc_final: 0.8000 (m-10) REVERT: B 77 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7161 (mp10) REVERT: B 89 MET cc_start: 0.5448 (OUTLIER) cc_final: 0.5162 (pmm) REVERT: B 96 TRP cc_start: 0.7652 (t60) cc_final: 0.6643 (t60) REVERT: B 136 GLN cc_start: 0.9026 (mm110) cc_final: 0.8757 (mm110) REVERT: C 74 MET cc_start: 0.7790 (ppp) cc_final: 0.6893 (ppp) REVERT: C 113 GLN cc_start: 0.8993 (tp-100) cc_final: 0.8593 (tp-100) REVERT: D 67 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8197 (mm-40) REVERT: D 96 ASN cc_start: 0.9126 (t0) cc_final: 0.8788 (t0) REVERT: D 175 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8706 (p) REVERT: D 182 ARG cc_start: 0.7972 (tpm170) cc_final: 0.7352 (tpm170) REVERT: G 31 MET cc_start: 0.0440 (tmm) cc_final: -0.1636 (mmm) REVERT: G 59 MET cc_start: 0.4176 (tpp) cc_final: 0.3568 (tpp) REVERT: G 103 TRP cc_start: 0.9196 (m-10) cc_final: 0.8511 (m-90) REVERT: H 92 ASN cc_start: 0.9317 (p0) cc_final: 0.8946 (p0) REVERT: J 24 LYS cc_start: 0.9134 (ptpt) cc_final: 0.8921 (pttt) REVERT: J 25 ILE cc_start: 0.9572 (mm) cc_final: 0.9358 (tp) REVERT: K 55 ARG cc_start: 0.7374 (mmm-85) cc_final: 0.7028 (mmm-85) REVERT: L 25 ASN cc_start: 0.8830 (m-40) cc_final: 0.8526 (m110) REVERT: M 31 GLN cc_start: 0.9114 (tp-100) cc_final: 0.8481 (tp-100) REVERT: M 55 LYS cc_start: 0.8795 (pptt) cc_final: 0.8543 (pptt) REVERT: N 9 LYS cc_start: 0.9549 (OUTLIER) cc_final: 0.9061 (mptt) REVERT: N 26 ARG cc_start: 0.8742 (tmt-80) cc_final: 0.8330 (ttp80) REVERT: P 57 LEU cc_start: 0.9432 (tt) cc_final: 0.9100 (tp) REVERT: P 61 GLN cc_start: 0.9251 (mm110) cc_final: 0.8929 (mm110) REVERT: P 65 LYS cc_start: 0.8773 (mptt) cc_final: 0.8450 (mmtm) REVERT: S 15 LEU cc_start: 0.8401 (pp) cc_final: 0.8177 (mm) REVERT: S 16 MET cc_start: 0.8764 (tpp) cc_final: 0.7585 (tpp) REVERT: S 20 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: S 28 LYS cc_start: 0.8314 (ptpp) cc_final: 0.8102 (ptpp) outliers start: 264 outliers final: 207 residues processed: 1360 average time/residue: 1.3394 time to fit residues: 3220.2166 Evaluate side-chains 1402 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1189 time to evaluate : 6.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain p residue 124 LYS Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain q residue 127 MET Chi-restraints excluded: chain Z residue 18 THR Chi-restraints excluded: chain Z residue 135 ILE Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 241 ILE Chi-restraints excluded: chain Z residue 259 THR Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 36 LEU Chi-restraints excluded: chain a residue 55 ASP Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 103 SER Chi-restraints excluded: chain a residue 134 SER Chi-restraints excluded: chain a residue 137 SER Chi-restraints excluded: chain a residue 140 HIS Chi-restraints excluded: chain a residue 179 VAL Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 132 ASP Chi-restraints excluded: chain b residue 193 LEU Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 144 ASP Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain d residue 116 ILE Chi-restraints excluded: chain d residue 138 ASP Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain e residue 97 TYR Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain e residue 142 GLU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 57 VAL Chi-restraints excluded: chain f residue 73 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain i residue 4 HIS Chi-restraints excluded: chain i residue 27 ASN Chi-restraints excluded: chain i residue 59 GLN Chi-restraints excluded: chain j residue 17 MET Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 44 ASN Chi-restraints excluded: chain j residue 52 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 79 LEU Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 106 ILE Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain j residue 129 THR Chi-restraints excluded: chain k residue 16 MET Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain k residue 117 ILE Chi-restraints excluded: chain l residue 25 THR Chi-restraints excluded: chain l residue 27 GLU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain m residue 4 LEU Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 30 VAL Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 106 LYS Chi-restraints excluded: chain n residue 85 LEU Chi-restraints excluded: chain n residue 90 VAL Chi-restraints excluded: chain n residue 92 ARG Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 111 ASP Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 33 VAL Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain o residue 45 ASN Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain s residue 27 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 81 VAL Chi-restraints excluded: chain s residue 86 ASP Chi-restraints excluded: chain t residue 7 ASP Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain t residue 45 SER Chi-restraints excluded: chain t residue 46 LYS Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain u residue 51 THR Chi-restraints excluded: chain u residue 65 ASP Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 13 THR Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 4 ASN Chi-restraints excluded: chain w residue 23 GLU Chi-restraints excluded: chain w residue 30 PHE Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 39 ASP Chi-restraints excluded: chain x residue 58 GLU Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 1 residue 16 ASN Chi-restraints excluded: chain 1 residue 19 SER Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 22 LEU Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 45 ARG Chi-restraints excluded: chain 3 residue 51 SER Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain 6 residue 56 VAL Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain M residue 102 SER Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 82 ILE Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 30 ASP Chi-restraints excluded: chain P residue 41 ASN Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 52 ASP Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain R residue 25 HIS Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 32 ASP Chi-restraints excluded: chain R residue 75 TYR Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 32 LYS Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain T residue 58 ILE Chi-restraints excluded: chain T residue 66 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 931 optimal weight: 4.9990 chunk 980 optimal weight: 5.9990 chunk 894 optimal weight: 6.9990 chunk 953 optimal weight: 0.6980 chunk 574 optimal weight: 6.9990 chunk 415 optimal weight: 0.0040 chunk 749 optimal weight: 10.0000 chunk 292 optimal weight: 20.0000 chunk 861 optimal weight: 4.9990 chunk 902 optimal weight: 10.0000 chunk 950 optimal weight: 6.9990 overall best weight: 3.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 200 HIS ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 43 GLN ** m 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN C 101 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 163551 Z= 0.177 Angle : 0.648 16.187 245002 Z= 0.329 Chirality : 0.035 0.530 31362 Planarity : 0.004 0.078 12913 Dihedral : 24.774 179.733 82787 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.94 % Favored : 92.93 % Rotamer: Outliers : 3.87 % Allowed : 31.81 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.02 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.11), residues: 5897 helix: 0.40 (0.12), residues: 2049 sheet: -0.63 (0.16), residues: 1039 loop : -1.81 (0.11), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP b 83 HIS 0.009 0.001 HIS D 116 PHE 0.039 0.002 PHE q 42 TYR 0.025 0.002 TYR I 116 ARG 0.012 0.001 ARG N 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1503 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1323 time to evaluate : 6.366 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: p 124 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8217 (tmtt) REVERT: q 125 MET cc_start: 0.7139 (tpp) cc_final: 0.5743 (tmm) REVERT: q 135 MET cc_start: 0.8757 (pmm) cc_final: 0.6690 (mmt) REVERT: q 140 GLU cc_start: 0.7674 (tt0) cc_final: 0.7379 (mp0) REVERT: c 59 PHE cc_start: 0.9131 (m-10) cc_final: 0.8909 (m-80) REVERT: d 42 MET cc_start: 0.7724 (tpt) cc_final: 0.7497 (tpt) REVERT: d 95 TYR cc_start: 0.8236 (m-80) cc_final: 0.7676 (m-80) REVERT: e 30 SER cc_start: 0.8675 (t) cc_final: 0.7957 (t) REVERT: e 36 ILE cc_start: 0.9095 (tp) cc_final: 0.8834 (tp) REVERT: e 109 MET cc_start: 0.7274 (mtt) cc_final: 0.6594 (mtt) REVERT: f 91 LYS cc_start: 0.8000 (mmmm) cc_final: 0.7640 (tptm) REVERT: k 45 GLU cc_start: 0.6468 (mm-30) cc_final: 0.6060 (mt-10) REVERT: l 52 THR cc_start: 0.8867 (m) cc_final: 0.8534 (p) REVERT: m 7 ASP cc_start: 0.7814 (p0) cc_final: 0.7358 (p0) REVERT: m 106 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8054 (ttpp) REVERT: n 85 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8581 (tt) REVERT: r 28 GLN cc_start: 0.7659 (pp30) cc_final: 0.7033 (pp30) REVERT: r 31 GLU cc_start: 0.7757 (pm20) cc_final: 0.6853 (pm20) REVERT: x 29 LYS cc_start: 0.8993 (mppt) cc_final: 0.8486 (mtmt) REVERT: 4 18 ARG cc_start: 0.8298 (tpt90) cc_final: 0.7963 (tpm170) REVERT: B 69 PHE cc_start: 0.8472 (m-10) cc_final: 0.7643 (m-80) REVERT: B 77 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7356 (mp10) REVERT: B 89 MET cc_start: 0.5217 (OUTLIER) cc_final: 0.4657 (pmm) REVERT: B 96 TRP cc_start: 0.7396 (t60) cc_final: 0.6707 (t60) REVERT: B 136 GLN cc_start: 0.9052 (mm110) cc_final: 0.8815 (mm110) REVERT: B 147 PHE cc_start: 0.8346 (m-10) cc_final: 0.8109 (m-80) REVERT: C 113 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8416 (tp-100) REVERT: C 138 GLN cc_start: 0.9289 (tp40) cc_final: 0.9065 (tp40) REVERT: C 183 TYR cc_start: 0.8150 (t80) cc_final: 0.7932 (t80) REVERT: D 96 ASN cc_start: 0.8905 (t0) cc_final: 0.8684 (t0) REVERT: D 175 THR cc_start: 0.9003 (OUTLIER) cc_final: 0.8757 (p) REVERT: D 182 ARG cc_start: 0.7782 (tpm170) cc_final: 0.7331 (tpm170) REVERT: G 59 MET cc_start: 0.3290 (tpp) cc_final: 0.3008 (tpp) REVERT: G 70 MET cc_start: 0.9005 (tpp) cc_final: 0.8687 (tpp) REVERT: G 103 TRP cc_start: 0.9048 (m-10) cc_final: 0.8415 (m-90) REVERT: I 93 GLU cc_start: 0.8685 (mp0) cc_final: 0.8475 (pm20) REVERT: J 24 LYS cc_start: 0.9238 (ptpt) cc_final: 0.8651 (pttm) REVERT: K 55 ARG cc_start: 0.7280 (mmm-85) cc_final: 0.6934 (mmm-85) REVERT: L 25 ASN cc_start: 0.8637 (m-40) cc_final: 0.8295 (m110) REVERT: M 31 GLN cc_start: 0.9061 (tp-100) cc_final: 0.8401 (tp-100) REVERT: M 55 LYS cc_start: 0.8735 (pptt) cc_final: 0.8470 (pptt) REVERT: M 75 LEU cc_start: 0.9436 (tp) cc_final: 0.9199 (pp) REVERT: N 26 ARG cc_start: 0.8606 (tmt-80) cc_final: 0.8324 (ttp80) REVERT: N 58 LYS cc_start: 0.8333 (mmtt) cc_final: 0.8097 (mmtt) REVERT: O 58 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8137 (mttm) REVERT: P 65 LYS cc_start: 0.8599 (mptt) cc_final: 0.8239 (mmtm) REVERT: S 16 MET cc_start: 0.8610 (tpp) cc_final: 0.7710 (tpp) REVERT: S 20 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8589 (mp0) REVERT: S 28 LYS cc_start: 0.7999 (ptpp) cc_final: 0.7798 (ptpp) outliers start: 180 outliers final: 145 residues processed: 1401 average time/residue: 1.3169 time to fit residues: 3225.8353 Evaluate side-chains 1408 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1256 time to evaluate : 6.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain p residue 124 LYS Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain q residue 127 MET Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 259 THR Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 36 LEU Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 140 HIS Chi-restraints excluded: chain a residue 179 VAL Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 132 ASP Chi-restraints excluded: chain b residue 193 LEU Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 51 ASP Chi-restraints excluded: chain c residue 144 ASP Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain d residue 116 ILE Chi-restraints excluded: chain d residue 138 ASP Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain e residue 57 ILE Chi-restraints excluded: chain e residue 97 TYR Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain e residue 142 GLU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 42 THR Chi-restraints excluded: chain f residue 73 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain i residue 4 HIS Chi-restraints excluded: chain i residue 27 ASN Chi-restraints excluded: chain i residue 59 GLN Chi-restraints excluded: chain i residue 106 ASN Chi-restraints excluded: chain j residue 40 SER Chi-restraints excluded: chain j residue 52 ILE Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 79 LEU Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain j residue 129 THR Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 30 VAL Chi-restraints excluded: chain m residue 55 ILE Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 73 THR Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 106 LYS Chi-restraints excluded: chain n residue 85 LEU Chi-restraints excluded: chain n residue 90 VAL Chi-restraints excluded: chain n residue 92 ARG Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 111 ASP Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain s residue 81 VAL Chi-restraints excluded: chain s residue 86 ASP Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain t residue 46 LYS Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain u residue 51 THR Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 23 GLU Chi-restraints excluded: chain w residue 30 PHE Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 39 ASP Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain x residue 58 GLU Chi-restraints excluded: chain 0 residue 10 LYS Chi-restraints excluded: chain 1 residue 16 ASN Chi-restraints excluded: chain 1 residue 19 SER Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 45 ARG Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 6 residue 9 PHE Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 41 ASN Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 5 ASN Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain R residue 25 HIS Chi-restraints excluded: chain R residue 32 ASP Chi-restraints excluded: chain R residue 75 TYR Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 32 LYS Chi-restraints excluded: chain T residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 626 optimal weight: 20.0000 chunk 1008 optimal weight: 10.0000 chunk 615 optimal weight: 3.9990 chunk 478 optimal weight: 0.8980 chunk 701 optimal weight: 20.0000 chunk 1058 optimal weight: 3.9990 chunk 973 optimal weight: 2.9990 chunk 842 optimal weight: 20.0000 chunk 87 optimal weight: 40.0000 chunk 650 optimal weight: 3.9990 chunk 516 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 131 HIS f 82 ASN ** i 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 GLN ** t 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 ASN ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 163551 Z= 0.176 Angle : 0.629 20.100 245002 Z= 0.320 Chirality : 0.034 0.520 31362 Planarity : 0.004 0.079 12913 Dihedral : 24.627 179.958 82787 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.68 % Favored : 92.22 % Rotamer: Outliers : 3.26 % Allowed : 32.60 % Favored : 64.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.02 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.11), residues: 5897 helix: 0.47 (0.12), residues: 2049 sheet: -0.50 (0.16), residues: 1039 loop : -1.78 (0.11), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP b 83 HIS 0.017 0.001 HIS S 14 PHE 0.040 0.002 PHE q 42 TYR 0.032 0.002 TYR Z 83 ARG 0.022 0.001 ARG j 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11794 Ramachandran restraints generated. 5897 Oldfield, 0 Emsley, 5897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1475 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1323 time to evaluate : 6.392 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: p 124 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8138 (tmtt) REVERT: q 112 LYS cc_start: 0.8916 (pptt) cc_final: 0.8638 (pptt) REVERT: q 135 MET cc_start: 0.8758 (pmm) cc_final: 0.6723 (mmt) REVERT: q 140 GLU cc_start: 0.7650 (tt0) cc_final: 0.7400 (mp0) REVERT: a 191 ASN cc_start: 0.8206 (p0) cc_final: 0.7886 (p0) REVERT: c 59 PHE cc_start: 0.9101 (m-10) cc_final: 0.8869 (m-80) REVERT: c 83 MET cc_start: 0.7916 (ptt) cc_final: 0.7638 (ppp) REVERT: c 101 ASP cc_start: 0.8104 (m-30) cc_final: 0.7716 (m-30) REVERT: d 95 TYR cc_start: 0.8191 (m-80) cc_final: 0.7663 (m-80) REVERT: e 92 GLU cc_start: 0.7567 (pp20) cc_final: 0.7257 (pp20) REVERT: f 96 THR cc_start: 0.8635 (m) cc_final: 0.8431 (p) REVERT: k 45 GLU cc_start: 0.6426 (mm-30) cc_final: 0.5995 (mt-10) REVERT: l 52 THR cc_start: 0.8855 (m) cc_final: 0.8496 (p) REVERT: m 7 ASP cc_start: 0.7891 (p0) cc_final: 0.7537 (p0) REVERT: m 106 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8005 (ttpp) REVERT: n 85 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8605 (tt) REVERT: u 52 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8780 (ttmm) REVERT: x 29 LYS cc_start: 0.8987 (mppt) cc_final: 0.8533 (mtmt) REVERT: x 49 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8314 (mtmt) REVERT: 0 16 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7818 (ttp80) REVERT: 3 30 SER cc_start: 0.8533 (t) cc_final: 0.8213 (m) REVERT: 4 18 ARG cc_start: 0.8292 (tpt90) cc_final: 0.7966 (tpm170) REVERT: B 51 GLU cc_start: 0.9136 (pt0) cc_final: 0.8912 (tp30) REVERT: B 69 PHE cc_start: 0.8422 (m-10) cc_final: 0.7592 (m-80) REVERT: B 77 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7294 (mp10) REVERT: B 89 MET cc_start: 0.5103 (OUTLIER) cc_final: 0.4511 (pmm) REVERT: B 96 TRP cc_start: 0.7404 (t60) cc_final: 0.6918 (t60) REVERT: B 136 GLN cc_start: 0.9000 (mm110) cc_final: 0.8737 (mm110) REVERT: B 144 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8219 (pp) REVERT: B 147 PHE cc_start: 0.8129 (m-10) cc_final: 0.7877 (m-10) REVERT: B 177 ARG cc_start: 0.8908 (mmm-85) cc_final: 0.8660 (mmm-85) REVERT: B 203 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.7873 (m-40) REVERT: C 113 GLN cc_start: 0.8891 (tp-100) cc_final: 0.8492 (tp-100) REVERT: D 96 ASN cc_start: 0.8866 (t0) cc_final: 0.8654 (t0) REVERT: D 175 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8745 (p) REVERT: D 178 ARG cc_start: 0.8134 (pmt170) cc_final: 0.7238 (pmt170) REVERT: D 182 ARG cc_start: 0.7788 (tpm170) cc_final: 0.7276 (tpm170) REVERT: D 189 ILE cc_start: 0.8723 (tp) cc_final: 0.8515 (mm) REVERT: G 31 MET cc_start: -0.0003 (tmm) cc_final: -0.2114 (mmp) REVERT: G 49 ILE cc_start: 0.8897 (mm) cc_final: 0.8657 (mm) REVERT: G 70 MET cc_start: 0.9050 (tpp) cc_final: 0.8723 (tpp) REVERT: G 123 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8421 (mm-30) REVERT: H 32 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8789 (tp) REVERT: I 93 GLU cc_start: 0.8686 (mp0) cc_final: 0.8440 (pm20) REVERT: J 24 LYS cc_start: 0.9057 (ptpt) cc_final: 0.8811 (pttt) REVERT: J 66 GLU cc_start: 0.7344 (tt0) cc_final: 0.6849 (pt0) REVERT: K 70 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8352 (mm-30) REVERT: L 25 ASN cc_start: 0.8630 (m-40) cc_final: 0.8368 (m-40) REVERT: M 31 GLN cc_start: 0.9050 (tp-100) cc_final: 0.8447 (tp-100) REVERT: M 75 LEU cc_start: 0.9448 (tp) cc_final: 0.9148 (pp) REVERT: M 103 LYS cc_start: 0.9020 (ttpt) cc_final: 0.8815 (tttt) REVERT: N 26 ARG cc_start: 0.8463 (tmt-80) cc_final: 0.8167 (ttp80) REVERT: O 58 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8130 (mttm) REVERT: P 65 LYS cc_start: 0.8523 (mptt) cc_final: 0.8176 (mmtm) REVERT: Q 75 PHE cc_start: 0.8165 (m-80) cc_final: 0.7926 (m-10) REVERT: S 16 MET cc_start: 0.8521 (tpp) cc_final: 0.7743 (tpp) REVERT: S 20 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8492 (mp0) outliers start: 152 outliers final: 124 residues processed: 1397 average time/residue: 1.3149 time to fit residues: 3208.8196 Evaluate side-chains 1419 residues out of total 5031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1284 time to evaluate : 6.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 90 VAL Chi-restraints excluded: chain p residue 124 LYS Chi-restraints excluded: chain q residue 71 LYS Chi-restraints excluded: chain q residue 116 LEU Chi-restraints excluded: chain q residue 127 MET Chi-restraints excluded: chain Z residue 46 GLN Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 259 THR Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 36 LEU Chi-restraints excluded: chain a residue 61 SER Chi-restraints excluded: chain a residue 110 VAL Chi-restraints excluded: chain a residue 140 HIS Chi-restraints excluded: chain a residue 179 VAL Chi-restraints excluded: chain a residue 186 LEU Chi-restraints excluded: chain a residue 201 THR Chi-restraints excluded: chain b residue 16 ASP Chi-restraints excluded: chain b residue 93 THR Chi-restraints excluded: chain b residue 132 ASP Chi-restraints excluded: chain b residue 193 LEU Chi-restraints excluded: chain c residue 16 LEU Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 144 ASP Chi-restraints excluded: chain d residue 44 ILE Chi-restraints excluded: chain d residue 138 ASP Chi-restraints excluded: chain d residue 154 SER Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 46 THR Chi-restraints excluded: chain e residue 97 TYR Chi-restraints excluded: chain e residue 124 ASN Chi-restraints excluded: chain e residue 142 GLU Chi-restraints excluded: chain f residue 18 GLU Chi-restraints excluded: chain f residue 73 ASP Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain i residue 4 HIS Chi-restraints excluded: chain i residue 27 ASN Chi-restraints excluded: chain j residue 52 ILE Chi-restraints excluded: chain j residue 79 LEU Chi-restraints excluded: chain j residue 85 SER Chi-restraints excluded: chain j residue 110 SER Chi-restraints excluded: chain j residue 113 VAL Chi-restraints excluded: chain j residue 129 THR Chi-restraints excluded: chain k residue 76 ASN Chi-restraints excluded: chain k residue 104 LEU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 30 VAL Chi-restraints excluded: chain m residue 55 ILE Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 102 GLU Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 106 LYS Chi-restraints excluded: chain n residue 85 LEU Chi-restraints excluded: chain n residue 90 VAL Chi-restraints excluded: chain n residue 92 ARG Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain n residue 111 ASP Chi-restraints excluded: chain o residue 31 GLU Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain r residue 81 THR Chi-restraints excluded: chain s residue 81 VAL Chi-restraints excluded: chain s residue 86 ASP Chi-restraints excluded: chain t residue 24 LEU Chi-restraints excluded: chain t residue 31 ASP Chi-restraints excluded: chain t residue 46 LYS Chi-restraints excluded: chain t residue 48 THR Chi-restraints excluded: chain u residue 51 THR Chi-restraints excluded: chain v residue 8 THR Chi-restraints excluded: chain v residue 40 VAL Chi-restraints excluded: chain w residue 23 GLU Chi-restraints excluded: chain w residue 30 PHE Chi-restraints excluded: chain x residue 8 LEU Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 39 ASP Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain x residue 58 GLU Chi-restraints excluded: chain 1 residue 19 SER Chi-restraints excluded: chain 1 residue 47 GLU Chi-restraints excluded: chain 3 residue 45 ARG Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain B residue 77 GLN Chi-restraints excluded: chain B residue 89 MET Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 50 GLN Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain G residue 48 ASP Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 123 GLU Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 38 ASP Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 86 TYR Chi-restraints excluded: chain N residue 11 GLN Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 41 ASN Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 30 TYR Chi-restraints excluded: chain R residue 25 HIS Chi-restraints excluded: chain R residue 32 ASP Chi-restraints excluded: chain R residue 75 TYR Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 32 LYS Chi-restraints excluded: chain T residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1062 random chunks: chunk 669 optimal weight: 10.0000 chunk 897 optimal weight: 20.0000 chunk 258 optimal weight: 20.0000 chunk 776 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 234 optimal weight: 20.0000 chunk 843 optimal weight: 20.0000 chunk 353 optimal weight: 20.0000 chunk 866 optimal weight: 0.9980 chunk 106 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 overall best weight: 14.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 GLN ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 131 HIS f 82 ASN ** i 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 43 GLN ** m 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 36 ASN ** o 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 57 ASN ** t 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN ** K 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 HIS ** P 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.046306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034523 restraints weight = 1048682.880| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.98 r_work: 0.2706 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.128 163551 Z= 0.479 Angle : 0.813 19.892 245002 Z= 0.412 Chirality : 0.042 0.449 31362 Planarity : 0.006 0.090 12913 Dihedral : 24.798 179.375 82787 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 26.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.21 % Favored : 90.67 % Rotamer: Outliers : 3.84 % Allowed : 32.67 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.45 % Cis-general : 0.02 % Twisted Proline : 0.45 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.11), residues: 5897 helix: 0.23 (0.11), residues: 2035 sheet: -0.68 (0.16), residues: 1072 loop : -1.98 (0.11), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP b 83 HIS 0.010 0.002 HIS S 57 PHE 0.050 0.003 PHE w 26 TYR 0.033 0.003 TYR Z 83 ARG 0.032 0.001 ARG i 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47855.29 seconds wall clock time: 835 minutes 22.30 seconds (50122.30 seconds total)