Starting phenix.real_space_refine on Fri Mar 1 05:12:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fr8_29397/03_2024/8fr8_29397.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fr8_29397/03_2024/8fr8_29397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fr8_29397/03_2024/8fr8_29397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fr8_29397/03_2024/8fr8_29397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fr8_29397/03_2024/8fr8_29397.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fr8_29397/03_2024/8fr8_29397.pdb" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 4842 5.49 5 S 94 5.16 5 C 76792 2.51 5 N 28556 2.21 5 O 42536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c ASP 40": "OD1" <-> "OD2" Residue "y GLU 75": "OE1" <-> "OE2" Residue "d PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 16": "OE1" <-> "OE2" Residue "j ASP 50": "OD1" <-> "OD2" Residue "j TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 77": "OD1" <-> "OD2" Residue "N ASP 31": "OD1" <-> "OD2" Residue "N TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 48": "OE1" <-> "OE2" Residue "N TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L ASP 113": "OD1" <-> "OD2" Residue "M PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 101": "OD1" <-> "OD2" Residue "O ASP 120": "OD1" <-> "OD2" Residue "O ASP 149": "OD1" <-> "OD2" Residue "O GLU 186": "OE1" <-> "OE2" Residue "P ASP 36": "OD1" <-> "OD2" Residue "P ASP 48": "OD1" <-> "OD2" Residue "P PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 20": "OE1" <-> "OE2" Residue "Q TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 5": "OD1" <-> "OD2" Residue "R GLU 15": "OE1" <-> "OE2" Residue "R TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 71": "OE1" <-> "OE2" Residue "R PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 88": "OD1" <-> "OD2" Residue "R ASP 99": "OD1" <-> "OD2" Residue "S PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S GLU 93": "OE1" <-> "OE2" Residue "S ASP 105": "OD1" <-> "OD2" Residue "S ASP 117": "OD1" <-> "OD2" Residue "T ASP 19": "OD1" <-> "OD2" Residue "T ASP 52": "OD1" <-> "OD2" Residue "T PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 129": "OD1" <-> "OD2" Residue "U PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D ASP 69": "OD1" <-> "OD2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 91": "OD1" <-> "OD2" Residue "W GLU 97": "OE1" <-> "OE2" Residue "X TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 28": "OD1" <-> "OD2" Residue "X ASP 44": "OD1" <-> "OD2" Residue "X ASP 53": "OD1" <-> "OD2" Residue "Z ASP 26": "OD1" <-> "OD2" Residue "Z ASP 51": "OD1" <-> "OD2" Residue "1 TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 90": "OE1" <-> "OE2" Residue "2 GLU 115": "OE1" <-> "OE2" Residue "2 GLU 132": "OE1" <-> "OE2" Residue "2 GLU 149": "OE1" <-> "OE2" Residue "2 GLU 152": "OE1" <-> "OE2" Residue "6 ASP 20": "OD1" <-> "OD2" Residue "7 ASP 39": "OD1" <-> "OD2" Residue "G TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 66": "OD1" <-> "OD2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G GLU 104": "OE1" <-> "OE2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 192": "OE1" <-> "OE2" Residue "f GLU 90": "OE1" <-> "OE2" Residue "f GLU 187": "OE1" <-> "OE2" Residue "g TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 33": "OD1" <-> "OD2" Residue "h ASP 67": "OD1" <-> "OD2" Residue "h TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 5": "OD1" <-> "OD2" Residue "i ASP 23": "OD1" <-> "OD2" Residue "i GLU 43": "OE1" <-> "OE2" Residue "i TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 53": "OD1" <-> "OD2" Residue "i TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 76": "OD1" <-> "OD2" Residue "k ASP 82": "OD1" <-> "OD2" Residue "k GLU 113": "OE1" <-> "OE2" Residue "k ASP 114": "OD1" <-> "OD2" Residue "k TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 14": "OD1" <-> "OD2" Residue "l ASP 19": "OD1" <-> "OD2" Residue "m ASP 45": "OD1" <-> "OD2" Residue "m GLU 77": "OE1" <-> "OE2" Residue "m GLU 103": "OE1" <-> "OE2" Residue "p ASP 19": "OD1" <-> "OD2" Residue "q TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 43": "OD1" <-> "OD2" Residue "t ASP 45": "OD1" <-> "OD2" Residue "u ASP 11": "OD1" <-> "OD2" Residue "u PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 82": "OE1" <-> "OE2" Residue "u PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 127": "OE1" <-> "OE2" Residue "u ASP 165": "OD1" <-> "OD2" Residue "I PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 691": "OD1" <-> "OD2" Residue "I GLU 707": "OE1" <-> "OE2" Residue "I PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 33": "OD1" <-> "OD2" Residue "9 GLU 26": "OE1" <-> "OE2" Residue "9 ASP 33": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 152820 Number of models: 1 Model: "" Number of chains: 58 Chain: "c" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 423 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "y" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 605 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "E" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1642 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 11, 'rna3p_pur': 30, 'rna3p_pyr': 28} Link IDs: {'rna2p': 18, 'rna3p': 58} Chain: "d" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 662 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "B" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2522 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 12, 'rna3p_pur': 54, 'rna3p_pyr': 42} Link IDs: {'rna2p': 22, 'rna3p': 95} Chain: "j" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "N" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "3" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "A" Number of atoms: 66981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3119, 66981 Classifications: {'RNA': 3119} Modifications used: {'rna2p_pur': 304, 'rna2p_pyr': 152, 'rna3p_pur': 1479, 'rna3p_pyr': 1184} Link IDs: {'rna2p': 456, 'rna3p': 2662} Chain: "K" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2110 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 19, 'TRANS': 255} Chain: "L" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "M" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1569 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "O" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1445 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain: "P" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1348 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "Q" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1018 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 147} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "R" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 918 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain: "S" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 990 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "T" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "U" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "V" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "J" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "D" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "C" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "W" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "X" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "Y" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "Z" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 756 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "1" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 732 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain breaks: 1 Chain: "2" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1347 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 8, 'TRANS': 171} Chain: "4" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 586 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "6" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "7" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 474 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "8" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "0" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "x" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "F" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "a" Number of atoms: 32439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1511, 32439 Classifications: {'RNA': 1511} Modifications used: {'rna2p_pur': 120, 'rna2p_pyr': 91, 'rna3p_pur': 729, 'rna3p_pyr': 571} Link IDs: {'rna2p': 211, 'rna3p': 1299} Chain: "b" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 280 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "G" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1660 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain: "e" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1641 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "f" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1296 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 8, 'TRANS': 171} Chain: "g" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "h" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1232 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "i" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "k" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "l" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 788 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "m" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 855 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "n" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "p" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "q" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "r" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 748 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "t" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 660 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1793 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "v" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "I" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1126 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 142} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 593 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "o" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 543 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "9" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 819 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 93} Time building chain proxies: 56.84, per 1000 atoms: 0.37 Number of scatterers: 152820 At special positions: 0 Unit cell: (264.401, 253.385, 234.741, 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 94 16.00 P 4842 15.00 O 42536 8.00 N 28556 7.00 C 76792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 67.58 Conformation dependent library (CDL) restraints added in 6.9 seconds 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11500 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 74 sheets defined 36.9% alpha, 19.5% beta 1644 base pairs and 2604 stacking pairs defined. Time for finding SS restraints: 55.42 Creating SS restraints... Processing helix chain 'y' and resid 52 through 61 Processing helix chain 'y' and resid 61 through 74 removed outlier: 4.212A pdb=" N ALA y 65 " --> pdb=" O ASP y 61 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL y 66 " --> pdb=" O GLY y 62 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 8 Processing helix chain 'd' and resid 12 through 25 removed outlier: 3.928A pdb=" N VAL d 21 " --> pdb=" O LYS d 17 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN d 22 " --> pdb=" O LYS d 18 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 67 removed outlier: 3.726A pdb=" N MET d 66 " --> pdb=" O THR d 63 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL d 67 " --> pdb=" O GLU d 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 63 through 67' Processing helix chain 'd' and resid 70 through 75 Processing helix chain 'j' and resid 14 through 19 Processing helix chain 'j' and resid 26 through 37 Processing helix chain 'j' and resid 50 through 64 Processing helix chain 'j' and resid 66 through 83 Processing helix chain 'j' and resid 86 through 94 Processing helix chain 'j' and resid 107 through 112 Processing helix chain 'N' and resid 44 through 58 Processing helix chain 'N' and resid 110 through 125 Processing helix chain '3' and resid 3 through 11 Processing helix chain 'K' and resid 10 through 14 removed outlier: 3.808A pdb=" N ARG K 14 " --> pdb=" O PRO K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 198 through 204 removed outlier: 3.764A pdb=" N SER K 202 " --> pdb=" O ALA K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 215 removed outlier: 3.801A pdb=" N MET K 212 " --> pdb=" O LYS K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 226 Processing helix chain 'K' and resid 262 through 266 removed outlier: 3.547A pdb=" N LYS K 266 " --> pdb=" O PRO K 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 74 Processing helix chain 'L' and resid 88 through 93 Processing helix chain 'L' and resid 102 through 106 Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'M' and resid 21 through 26 Processing helix chain 'M' and resid 30 through 46 Processing helix chain 'M' and resid 103 through 121 Processing helix chain 'M' and resid 137 through 149 Processing helix chain 'M' and resid 162 through 171 removed outlier: 4.520A pdb=" N ASN M 171 " --> pdb=" O LYS M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 183 Processing helix chain 'M' and resid 184 through 191 Processing helix chain 'M' and resid 198 through 210 removed outlier: 4.301A pdb=" N LYS M 210 " --> pdb=" O SER M 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 27 removed outlier: 5.810A pdb=" N ARG O 20 " --> pdb=" O ARG O 16 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N GLU O 21 " --> pdb=" O GLU O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 35 Processing helix chain 'O' and resid 47 through 51 removed outlier: 3.541A pdb=" N ALA O 51 " --> pdb=" O GLY O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 69 removed outlier: 4.189A pdb=" N GLY O 59 " --> pdb=" O LYS O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 113 removed outlier: 3.737A pdb=" N MET O 103 " --> pdb=" O ARG O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 118 Processing helix chain 'O' and resid 149 through 153 Processing helix chain 'O' and resid 169 through 181 Processing helix chain 'P' and resid 59 through 82 removed outlier: 3.811A pdb=" N GLY P 67 " --> pdb=" O ARG P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 138 through 151 Processing helix chain 'Q' and resid 22 through 29 removed outlier: 3.596A pdb=" N TYR Q 29 " --> pdb=" O TYR Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 59 removed outlier: 4.831A pdb=" N ILE Q 50 " --> pdb=" O GLN Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 73 removed outlier: 3.912A pdb=" N ALA Q 71 " --> pdb=" O GLU Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 108 Processing helix chain 'Q' and resid 113 through 115 No H-bonds generated for 'chain 'Q' and resid 113 through 115' Processing helix chain 'Q' and resid 119 through 123 removed outlier: 4.323A pdb=" N HIS Q 123 " --> pdb=" O ALA Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 20 Processing helix chain 'R' and resid 32 through 44 removed outlier: 3.695A pdb=" N GLU R 38 " --> pdb=" O ALA R 34 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA R 42 " --> pdb=" O GLU R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 63 Processing helix chain 'R' and resid 87 through 101 Processing helix chain 'R' and resid 119 through 126 Processing helix chain 'S' and resid 26 through 32 Processing helix chain 'S' and resid 38 through 49 removed outlier: 4.132A pdb=" N LYS S 42 " --> pdb=" O MET S 38 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA S 47 " --> pdb=" O ALA S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 85 Processing helix chain 'S' and resid 103 through 115 Processing helix chain 'S' and resid 122 through 138 Processing helix chain 'T' and resid 24 through 38 Processing helix chain 'T' and resid 58 through 62 Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 89 through 96 Processing helix chain 'T' and resid 97 through 109 removed outlier: 4.468A pdb=" N VAL T 101 " --> pdb=" O PRO T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 112 through 120 removed outlier: 3.776A pdb=" N LYS T 120 " --> pdb=" O ARG T 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 109 removed outlier: 3.963A pdb=" N GLU U 108 " --> pdb=" O ARG U 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 118 Processing helix chain 'V' and resid 5 through 9 Processing helix chain 'V' and resid 39 through 43 Processing helix chain 'V' and resid 56 through 61 removed outlier: 3.620A pdb=" N LEU V 61 " --> pdb=" O ILE V 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 80 through 87 Processing helix chain 'V' and resid 94 through 101 Processing helix chain 'V' and resid 130 through 141 Processing helix chain 'J' and resid 13 through 32 Processing helix chain 'J' and resid 38 through 57 Proline residue: J 46 - end of helix Processing helix chain 'J' and resid 59 through 68 Processing helix chain 'J' and resid 72 through 83 removed outlier: 3.637A pdb=" N ILE J 83 " --> pdb=" O LEU J 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 27 Processing helix chain 'D' and resid 67 through 72 Processing helix chain 'D' and resid 76 through 96 Processing helix chain 'D' and resid 111 through 124 Processing helix chain 'C' and resid 4 through 12 removed outlier: 4.541A pdb=" N ALA C 10 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER C 11 " --> pdb=" O VAL C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 55 Processing helix chain 'C' and resid 96 through 102 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'W' and resid 6 through 21 removed outlier: 4.390A pdb=" N LYS W 12 " --> pdb=" O LEU W 8 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS W 13 " --> pdb=" O ASN W 9 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG W 14 " --> pdb=" O ALA W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 31 removed outlier: 3.691A pdb=" N ARG W 30 " --> pdb=" O GLY W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 72 removed outlier: 3.719A pdb=" N GLU W 37 " --> pdb=" O ARG W 33 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG W 51 " --> pdb=" O TYR W 47 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS W 54 " --> pdb=" O ARG W 50 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY W 55 " --> pdb=" O ARG W 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 75 through 87 Processing helix chain 'W' and resid 91 through 102 Processing helix chain 'W' and resid 102 through 117 Processing helix chain 'X' and resid 51 through 57 Processing helix chain 'Y' and resid 20 through 32 removed outlier: 4.362A pdb=" N VAL Y 27 " --> pdb=" O LYS Y 23 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU Y 30 " --> pdb=" O ARG Y 26 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL Y 31 " --> pdb=" O VAL Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 45 Processing helix chain 'Y' and resid 50 through 68 Processing helix chain 'Y' and resid 72 through 76 removed outlier: 3.571A pdb=" N LEU Y 76 " --> pdb=" O PRO Y 73 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 98 No H-bonds generated for 'chain 'Y' and resid 96 through 98' Processing helix chain 'Z' and resid 6 through 9 Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 38 through 51 Processing helix chain '2' and resid 20 through 30 Processing helix chain '2' and resid 51 through 62 Processing helix chain '6' and resid 6 through 11 Processing helix chain '6' and resid 14 through 39 Processing helix chain '6' and resid 45 through 67 Processing helix chain '7' and resid 16 through 27 Processing helix chain '7' and resid 40 through 50 Processing helix chain '8' and resid 9 through 18 Processing helix chain '8' and resid 43 through 50 Processing helix chain '0' and resid 11 through 20 Processing helix chain '0' and resid 20 through 27 removed outlier: 3.767A pdb=" N THR 0 27 " --> pdb=" O LEU 0 23 " (cutoff:3.500A) Processing helix chain '0' and resid 27 through 41 Processing helix chain 'x' and resid 7 through 13 Processing helix chain 'x' and resid 37 through 44 Processing helix chain 'x' and resid 51 through 64 removed outlier: 4.420A pdb=" N SER x 56 " --> pdb=" O ALA x 52 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG x 57 " --> pdb=" O ALA x 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 32 Processing helix chain 'b' and resid 4 through 24 removed outlier: 3.672A pdb=" N LYS b 10 " --> pdb=" O LYS b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 33 Processing helix chain 'G' and resid 6 through 11 Processing helix chain 'G' and resid 27 through 45 Processing helix chain 'G' and resid 71 through 76 Processing helix chain 'G' and resid 80 through 93 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.725A pdb=" N SER G 124 " --> pdb=" O ALA G 120 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN G 125 " --> pdb=" O GLU G 121 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG G 126 " --> pdb=" O GLN G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 143 Processing helix chain 'G' and resid 156 through 160 Processing helix chain 'e' and resid 8 through 15 removed outlier: 3.677A pdb=" N SER e 12 " --> pdb=" O ALA e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 24 through 29 Processing helix chain 'e' and resid 44 through 60 Processing helix chain 'e' and resid 63 through 77 removed outlier: 4.145A pdb=" N ARG e 69 " --> pdb=" O LYS e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 80 through 91 Processing helix chain 'e' and resid 92 through 101 Processing helix chain 'e' and resid 105 through 116 Processing helix chain 'e' and resid 141 through 147 removed outlier: 4.102A pdb=" N ASN e 146 " --> pdb=" O GLU e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 147 through 156 Processing helix chain 'e' and resid 182 through 187 removed outlier: 4.366A pdb=" N ASP e 187 " --> pdb=" O ARG e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 192 through 201 removed outlier: 3.998A pdb=" N VAL e 196 " --> pdb=" O GLU e 192 " (cutoff:3.500A) Processing helix chain 'f' and resid 80 through 95 Processing helix chain 'f' and resid 133 through 144 Processing helix chain 'f' and resid 157 through 172 Processing helix chain 'f' and resid 174 through 183 Processing helix chain 'f' and resid 191 through 207 Processing helix chain 'f' and resid 209 through 214 Processing helix chain 'g' and resid 15 through 17 No H-bonds generated for 'chain 'g' and resid 15 through 17' Processing helix chain 'g' and resid 18 through 28 removed outlier: 3.617A pdb=" N SER g 22 " --> pdb=" O THR g 18 " (cutoff:3.500A) Processing helix chain 'g' and resid 29 through 33 removed outlier: 4.096A pdb=" N ASP g 33 " --> pdb=" O ILE g 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 82 Processing helix chain 'h' and resid 20 through 31 Processing helix chain 'h' and resid 35 through 55 Processing helix chain 'h' and resid 57 through 70 Processing helix chain 'h' and resid 92 through 111 Processing helix chain 'h' and resid 115 through 130 Processing helix chain 'h' and resid 132 through 148 Processing helix chain 'h' and resid 149 through 155 removed outlier: 3.859A pdb=" N HIS h 153 " --> pdb=" O ALA h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 20 Processing helix chain 'i' and resid 30 through 43 Processing helix chain 'i' and resid 96 through 101 removed outlier: 3.891A pdb=" N GLY i 99 " --> pdb=" O ARG i 96 " (cutoff:3.500A) Processing helix chain 'i' and resid 115 through 121 Processing helix chain 'k' and resid 61 through 76 Proline residue: k 71 - end of helix Processing helix chain 'k' and resid 91 through 111 Processing helix chain 'k' and resid 114 through 122 Processing helix chain 'l' and resid 14 through 32 Processing helix chain 'l' and resid 80 through 90 Processing helix chain 'm' and resid 62 through 67 removed outlier: 3.503A pdb=" N ARG m 65 " --> pdb=" O LYS m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 68 through 85 Processing helix chain 'm' and resid 101 through 112 Processing helix chain 'n' and resid 3 through 11 Processing helix chain 'n' and resid 113 through 118 removed outlier: 3.891A pdb=" N GLY n 118 " --> pdb=" O SER n 115 " (cutoff:3.500A) Processing helix chain 'p' and resid 4 through 16 removed outlier: 3.827A pdb=" N GLN p 14 " --> pdb=" O GLU p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 24 through 46 Processing helix chain 'p' and resid 49 through 74 removed outlier: 3.848A pdb=" N GLY p 55 " --> pdb=" O HIS p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 74 through 86 removed outlier: 3.602A pdb=" N TYR p 78 " --> pdb=" O ASP p 74 " (cutoff:3.500A) Processing helix chain 'q' and resid 52 through 62 Processing helix chain 'q' and resid 67 through 77 Processing helix chain 'q' and resid 78 through 85 Processing helix chain 'q' and resid 101 through 113 Processing helix chain 't' and resid 4 through 42 removed outlier: 3.886A pdb=" N ARG t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 Processing helix chain 't' and resid 68 through 86 Processing helix chain 'u' and resid 5 through 11 Processing helix chain 'u' and resid 24 through 29 removed outlier: 3.708A pdb=" N ARG u 29 " --> pdb=" O LYS u 26 " (cutoff:3.500A) Processing helix chain 'u' and resid 42 through 64 Processing helix chain 'u' and resid 73 through 88 removed outlier: 4.815A pdb=" N GLU u 78 " --> pdb=" O LYS u 74 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N SER u 79 " --> pdb=" O GLN u 75 " (cutoff:3.500A) Processing helix chain 'u' and resid 103 through 124 Processing helix chain 'u' and resid 130 through 149 Processing helix chain 'u' and resid 150 through 152 No H-bonds generated for 'chain 'u' and resid 150 through 152' Processing helix chain 'u' and resid 169 through 180 Processing helix chain 'u' and resid 206 through 227 Processing helix chain 'I' and resid 692 through 694 No H-bonds generated for 'chain 'I' and resid 692 through 694' Processing helix chain 'I' and resid 695 through 700 Processing helix chain 'I' and resid 734 through 741 Processing helix chain 'I' and resid 774 through 781 Processing helix chain 'H' and resid 84 through 93 Processing helix chain 'o' and resid 22 through 27 Processing helix chain 'o' and resid 36 through 41 Processing helix chain 'o' and resid 52 through 57 Processing helix chain 'o' and resid 59 through 76 Processing helix chain '9' and resid 3 through 21 Processing helix chain '9' and resid 25 through 33 removed outlier: 4.100A pdb=" N ARG 9 29 " --> pdb=" O ALA 9 25 " (cutoff:3.500A) Processing helix chain '9' and resid 44 through 51 Processing helix chain '9' and resid 52 through 60 Proline residue: 9 57 - end of helix Processing helix chain '9' and resid 80 through 91 Processing sheet with id=AA1, first strand: chain 'c' and resid 8 through 9 removed outlier: 3.616A pdb=" N VAL c 9 " --> pdb=" O ASN c 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 13 through 15 Processing sheet with id=AA3, first strand: chain 'y' and resid 32 through 39 removed outlier: 6.134A pdb=" N GLN y 33 " --> pdb=" O LEU y 48 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU y 48 " --> pdb=" O GLN y 33 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LYS y 35 " --> pdb=" O ILE y 46 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE y 46 " --> pdb=" O LYS y 35 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYR y 37 " --> pdb=" O ARG y 44 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG y 44 " --> pdb=" O TYR y 37 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 48 through 49 Processing sheet with id=AA5, first strand: chain 'N' and resid 63 through 66 removed outlier: 6.613A pdb=" N VAL N 102 " --> pdb=" O ALA N 36 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA N 36 " --> pdb=" O VAL N 102 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE N 104 " --> pdb=" O ILE N 34 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 40 through 43 removed outlier: 5.813A pdb=" N LYS N 76 " --> pdb=" O PRO N 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 3 through 5 Processing sheet with id=AA8, first strand: chain 'K' and resid 34 through 36 Processing sheet with id=AA9, first strand: chain 'K' and resid 102 through 105 removed outlier: 6.381A pdb=" N HIS K 96 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL K 79 " --> pdb=" O HIS K 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 130 through 132 removed outlier: 6.678A pdb=" N ALA K 174 " --> pdb=" O LEU K 166 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS K 168 " --> pdb=" O TYR K 172 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N TYR K 172 " --> pdb=" O LYS K 168 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE K 182 " --> pdb=" O VAL K 269 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 145 through 146 removed outlier: 6.067A pdb=" N VAL K 145 " --> pdb=" O LYS K 154 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 17 removed outlier: 6.705A pdb=" N VAL L 28 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET L 13 " --> pdb=" O VAL L 26 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL L 26 " --> pdb=" O MET L 13 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN L 15 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL L 24 " --> pdb=" O GLN L 15 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL L 191 " --> pdb=" O VAL L 185 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL L 185 " --> pdb=" O VAL L 191 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU L 193 " --> pdb=" O HIS L 183 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS L 181 " --> pdb=" O LYS L 195 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N THR L 176 " --> pdb=" O GLY L 116 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLY L 116 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLN L 178 " --> pdb=" O VAL L 114 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL L 114 " --> pdb=" O GLN L 178 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR L 117 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU L 205 " --> pdb=" O THR L 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 80 through 85 removed outlier: 3.575A pdb=" N ARG L 38 " --> pdb=" O GLN L 51 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA L 53 " --> pdb=" O VAL L 36 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL L 36 " --> pdb=" O ALA L 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 122 through 124 Processing sheet with id=AB6, first strand: chain 'M' and resid 16 through 20 removed outlier: 4.274A pdb=" N GLY M 16 " --> pdb=" O VAL M 7 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU M 3 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ILE M 124 " --> pdb=" O LYS M 4 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP M 6 " --> pdb=" O ILE M 124 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA M 126 " --> pdb=" O ASP M 6 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU M 155 " --> pdb=" O VAL M 195 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N SER M 197 " --> pdb=" O LEU M 155 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL M 157 " --> pdb=" O SER M 197 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL M 154 " --> pdb=" O HIS M 176 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ILE M 178 " --> pdb=" O VAL M 154 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL M 156 " --> pdb=" O ILE M 178 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 73 through 76 removed outlier: 4.080A pdb=" N GLY O 93 " --> pdb=" O ARG O 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 9 through 10 removed outlier: 3.503A pdb=" N VAL P 9 " --> pdb=" O ILE P 51 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA P 50 " --> pdb=" O ALA P 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 16 through 20 removed outlier: 3.859A pdb=" N ASN P 20 " --> pdb=" O ASN P 23 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN P 23 " --> pdb=" O ASN P 20 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 123 through 128 removed outlier: 6.178A pdb=" N LYS P 131 " --> pdb=" O GLU P 127 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 96 through 100 removed outlier: 3.864A pdb=" N ASN P 103 " --> pdb=" O LYS P 100 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Q' and resid 18 through 20 Processing sheet with id=AC4, first strand: chain 'Q' and resid 77 through 81 removed outlier: 3.886A pdb=" N VAL Q 149 " --> pdb=" O LEU Q 80 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR Q 133 " --> pdb=" O GLN Q 118 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 47 through 49 removed outlier: 6.412A pdb=" N GLU R 27 " --> pdb=" O ILE R 105 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE R 105 " --> pdb=" O GLU R 27 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'S' and resid 61 through 62 Processing sheet with id=AC7, first strand: chain 'T' and resid 122 through 124 removed outlier: 6.104A pdb=" N VAL T 54 " --> pdb=" O LYS T 123 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TYR T 16 " --> pdb=" O ILE T 55 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE T 57 " --> pdb=" O TYR T 16 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE T 18 " --> pdb=" O ILE T 57 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TRP T 15 " --> pdb=" O ILE T 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'T' and resid 73 through 77 Processing sheet with id=AC9, first strand: chain 'U' and resid 7 through 10 removed outlier: 6.022A pdb=" N LYS U 17 " --> pdb=" O VAL U 10 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA U 16 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA U 46 " --> pdb=" O ALA U 16 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU U 18 " --> pdb=" O LYS U 44 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL U 40 " --> pdb=" O ILE U 22 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL U 24 " --> pdb=" O VAL U 38 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL U 38 " --> pdb=" O VAL U 24 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS U 59 " --> pdb=" O ILE U 87 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA U 83 " --> pdb=" O VAL U 63 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA U 84 " --> pdb=" O ARG U 7 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LYS U 9 " --> pdb=" O ALA U 84 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE U 86 " --> pdb=" O LYS U 9 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'U' and resid 69 through 70 removed outlier: 6.497A pdb=" N THR C 59 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLU C 63 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N LYS C 43 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THR C 24 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL C 85 " --> pdb=" O THR C 24 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN C 26 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE C 83 " --> pdb=" O ASN C 26 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N HIS C 28 " --> pdb=" O ASP C 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'V' and resid 76 through 79 removed outlier: 6.081A pdb=" N GLN V 76 " --> pdb=" O LYS V 111 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU V 113 " --> pdb=" O GLN V 76 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL V 78 " --> pdb=" O LEU V 113 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 91 through 93 removed outlier: 7.406A pdb=" N GLY V 91 " --> pdb=" O ASP V 123 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR V 125 " --> pdb=" O GLY V 91 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL V 93 " --> pdb=" O THR V 125 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL V 122 " --> pdb=" O SER V 143 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N THR V 145 " --> pdb=" O VAL V 122 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL V 124 " --> pdb=" O THR V 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'J' and resid 33 through 37 removed outlier: 4.191A pdb=" N MET J 110 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 58 through 64 removed outlier: 6.681A pdb=" N LEU D 51 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA D 62 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL D 49 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER D 64 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE D 47 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 89 through 90 removed outlier: 4.382A pdb=" N LYS C 110 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 12 through 16 removed outlier: 6.921A pdb=" N TYR X 4 " --> pdb=" O VAL X 42 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL X 42 " --> pdb=" O TYR X 4 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE X 6 " --> pdb=" O ALA X 40 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN X 47 " --> pdb=" O ASP X 44 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 21 through 25 removed outlier: 3.894A pdb=" N GLU X 66 " --> pdb=" O VAL X 96 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS X 98 " --> pdb=" O VAL X 64 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL X 64 " --> pdb=" O LYS X 98 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR X 100 " --> pdb=" O ALA X 62 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA X 62 " --> pdb=" O THR X 100 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 73 through 78 Processing sheet with id=AE1, first strand: chain 'Y' and resid 9 through 17 removed outlier: 5.898A pdb=" N SER Y 108 " --> pdb=" O TYR Y 16 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE Y 101 " --> pdb=" O ILE Y 92 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE Y 92 " --> pdb=" O PHE Y 101 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE Y 103 " --> pdb=" O LYS Y 90 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS Y 90 " --> pdb=" O ILE Y 103 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS Y 105 " --> pdb=" O THR Y 88 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR Y 88 " --> pdb=" O LYS Y 105 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THR Y 107 " --> pdb=" O GLY Y 86 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU Y 115 " --> pdb=" O VAL Y 78 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL Y 78 " --> pdb=" O GLU Y 115 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Z' and resid 11 through 14 removed outlier: 4.351A pdb=" N LYS Z 80 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Z' and resid 66 through 69 Processing sheet with id=AE4, first strand: chain '1' and resid 65 through 67 removed outlier: 6.281A pdb=" N THR 1 8 " --> pdb=" O VAL 1 74 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL 1 73 " --> pdb=" O THR 1 81 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '1' and resid 40 through 44 Processing sheet with id=AE6, first strand: chain '1' and resid 83 through 85 Processing sheet with id=AE7, first strand: chain '2' and resid 9 through 12 removed outlier: 5.969A pdb=" N ASN 2 9 " --> pdb=" O THR 2 68 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP 2 70 " --> pdb=" O ASN 2 9 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LEU 2 11 " --> pdb=" O ASP 2 70 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ALA 2 78 " --> pdb=" O VAL 2 99 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL 2 99 " --> pdb=" O ALA 2 78 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR 2 80 " --> pdb=" O LEU 2 97 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU 2 97 " --> pdb=" O THR 2 80 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA 2 82 " --> pdb=" O ALA 2 95 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ALA 2 95 " --> pdb=" O ALA 2 82 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP 2 84 " --> pdb=" O GLN 2 93 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N LYS 2 32 " --> pdb=" O GLN 2 93 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N ALA 2 95 " --> pdb=" O LYS 2 32 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU 2 97 " --> pdb=" O PRO 2 34 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL 2 36 " --> pdb=" O LEU 2 97 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL 2 99 " --> pdb=" O VAL 2 36 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR 2 38 " --> pdb=" O VAL 2 99 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '2' and resid 144 through 147 Processing sheet with id=AE9, first strand: chain '2' and resid 123 through 126 Processing sheet with id=AF1, first strand: chain '4' and resid 22 through 23 removed outlier: 6.717A pdb=" N LEU 4 59 " --> pdb=" O LEU 4 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '4' and resid 30 through 31 Processing sheet with id=AF3, first strand: chain '7' and resid 34 through 38 Processing sheet with id=AF4, first strand: chain '8' and resid 27 through 30 Processing sheet with id=AF5, first strand: chain 'x' and resid 14 through 16 Processing sheet with id=AF6, first strand: chain 'F' and resid 2 through 3 removed outlier: 6.271A pdb=" N LYS F 2 " --> pdb=" O ARG F 35 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 20 through 21 removed outlier: 3.751A pdb=" N ARG G 58 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP G 53 " --> pdb=" O HIS G 68 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL G 63 " --> pdb=" O GLN G 99 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 20 through 21 removed outlier: 3.751A pdb=" N ARG G 58 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP G 53 " --> pdb=" O HIS G 68 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 164 through 171 Processing sheet with id=AG1, first strand: chain 'e' and resid 123 through 124 Processing sheet with id=AG2, first strand: chain 'f' and resid 37 through 49 removed outlier: 5.328A pdb=" N GLU f 38 " --> pdb=" O GLY f 65 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY f 65 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL f 40 " --> pdb=" O ILE f 63 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE f 63 " --> pdb=" O VAL f 40 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER f 42 " --> pdb=" O LEU f 61 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'f' and resid 110 through 113 removed outlier: 6.096A pdb=" N VAL f 118 " --> pdb=" O LEU f 153 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA f 150 " --> pdb=" O ILE f 131 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'g' and resid 41 through 52 removed outlier: 5.182A pdb=" N ILE g 42 " --> pdb=" O VAL g 62 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL g 62 " --> pdb=" O ILE g 42 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY g 44 " --> pdb=" O TYR g 60 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TYR g 60 " --> pdb=" O GLY g 44 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA g 56 " --> pdb=" O LEU g 48 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARG g 92 " --> pdb=" O PRO g 3 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLU g 5 " --> pdb=" O VAL g 90 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL g 90 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET g 7 " --> pdb=" O THR g 88 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR g 88 " --> pdb=" O MET g 7 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE g 9 " --> pdb=" O LEU g 86 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'h' and resid 73 through 78 Processing sheet with id=AG6, first strand: chain 'i' and resid 24 through 28 Processing sheet with id=AG7, first strand: chain 'i' and resid 78 through 79 Processing sheet with id=AG8, first strand: chain 'i' and resid 78 through 79 removed outlier: 6.573A pdb=" N ILE i 105 " --> pdb=" O LEU i 128 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'k' and resid 26 through 31 removed outlier: 4.275A pdb=" N ILE k 26 " --> pdb=" O LEU k 41 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ASN k 49 " --> pdb=" O ALA k 85 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'l' and resid 35 through 52 removed outlier: 3.861A pdb=" N SER l 35 " --> pdb=" O LEU l 77 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASP l 75 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU l 73 " --> pdb=" O PRO l 39 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS l 71 " --> pdb=" O PRO l 41 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR l 69 " --> pdb=" O PRO l 43 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLU l 45 " --> pdb=" O MET l 67 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N MET l 67 " --> pdb=" O GLU l 45 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN l 47 " --> pdb=" O PHE l 65 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE l 65 " --> pdb=" O ASN l 47 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR l 49 " --> pdb=" O GLU l 63 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU l 63 " --> pdb=" O TYR l 49 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'l' and resid 35 through 52 removed outlier: 3.861A pdb=" N SER l 35 " --> pdb=" O LEU l 77 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ASP l 75 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU l 73 " --> pdb=" O PRO l 39 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS l 71 " --> pdb=" O PRO l 41 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N THR l 69 " --> pdb=" O PRO l 43 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N GLU l 45 " --> pdb=" O MET l 67 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N MET l 67 " --> pdb=" O GLU l 45 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN l 47 " --> pdb=" O PHE l 65 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE l 65 " --> pdb=" O ASN l 47 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR l 49 " --> pdb=" O GLU l 63 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU l 63 " --> pdb=" O TYR l 49 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'm' and resid 50 through 54 removed outlier: 6.936A pdb=" N ILE m 43 " --> pdb=" O ILE m 51 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TRP m 53 " --> pdb=" O VAL m 41 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL m 41 " --> pdb=" O TRP m 53 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY m 28 " --> pdb=" O ASP m 92 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N PHE m 94 " --> pdb=" O GLY m 28 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA m 30 " --> pdb=" O PHE m 94 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LYS m 96 " --> pdb=" O ALA m 30 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE m 32 " --> pdb=" O LYS m 96 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VAL m 91 " --> pdb=" O VAL m 116 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR m 118 " --> pdb=" O VAL m 91 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'n' and resid 30 through 40 removed outlier: 6.456A pdb=" N ARG n 54 " --> pdb=" O THR n 35 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL n 37 " --> pdb=" O VAL n 52 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL n 52 " --> pdb=" O VAL n 37 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR n 39 " --> pdb=" O ARG n 50 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ARG n 50 " --> pdb=" O THR n 39 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N TYR n 95 " --> pdb=" O THR n 64 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU n 81 " --> pdb=" O ILE n 98 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'q' and resid 3 through 9 removed outlier: 6.867A pdb=" N VAL q 22 " --> pdb=" O VAL q 36 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL q 36 " --> pdb=" O VAL q 22 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'r' and resid 22 through 32 removed outlier: 14.924A pdb=" N THR r 22 " --> pdb=" O ARG r 43 " (cutoff:3.500A) removed outlier: 11.857A pdb=" N ARG r 43 " --> pdb=" O THR r 22 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE r 24 " --> pdb=" O GLU r 41 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N GLU r 41 " --> pdb=" O ILE r 24 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL r 37 " --> pdb=" O VAL r 28 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASP r 30 " --> pdb=" O THR r 35 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR r 35 " --> pdb=" O ASP r 30 " (cutoff:3.500A) removed outlier: 15.740A pdb=" N LYS r 86 " --> pdb=" O THR r 56 " (cutoff:3.500A) removed outlier: 13.593A pdb=" N LYS r 58 " --> pdb=" O LYS r 86 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N TRP r 88 " --> pdb=" O LYS r 58 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS r 60 " --> pdb=" O TRP r 88 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N LEU r 90 " --> pdb=" O LYS r 60 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N HIS r 62 " --> pdb=" O LEU r 90 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N GLU r 92 " --> pdb=" O HIS r 62 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG r 87 " --> pdb=" O THR r 79 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N SER r 75 " --> pdb=" O VAL r 91 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE r 93 " --> pdb=" O ARG r 73 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ARG r 73 " --> pdb=" O ILE r 93 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'u' and resid 16 through 19 removed outlier: 6.540A pdb=" N PHE u 16 " --> pdb=" O ILE u 41 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE u 41 " --> pdb=" O PHE u 16 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N HIS u 18 " --> pdb=" O TYR u 39 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE u 38 " --> pdb=" O ASP u 34 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASP u 34 " --> pdb=" O ILE u 38 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE u 40 " --> pdb=" O PHE u 32 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'u' and resid 91 through 92 removed outlier: 7.867A pdb=" N VAL u 92 " --> pdb=" O VAL u 67 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE u 69 " --> pdb=" O VAL u 92 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU u 68 " --> pdb=" O TRP u 162 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL u 164 " --> pdb=" O LEU u 68 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL u 70 " --> pdb=" O VAL u 164 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL u 161 " --> pdb=" O ILE u 184 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE u 186 " --> pdb=" O VAL u 161 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N VAL u 163 " --> pdb=" O ILE u 186 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL u 183 " --> pdb=" O TYR u 198 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE u 200 " --> pdb=" O VAL u 183 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ALA u 185 " --> pdb=" O ILE u 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'I' and resid 661 through 662 removed outlier: 6.926A pdb=" N LYS I 662 " --> pdb=" O VAL I 687 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N ARG I 689 " --> pdb=" O LYS I 662 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY I 677 " --> pdb=" O ILE I 706 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 752 through 753 Processing sheet with id=AI2, first strand: chain 'H' and resid 22 through 27 removed outlier: 3.841A pdb=" N LYS H 44 " --> pdb=" O SER H 41 " (cutoff:3.500A) 2105 hydrogen bonds defined for protein. 5913 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4194 hydrogen bonds 6582 hydrogen bond angles 0 basepair planarities 1644 basepair parallelities 2604 stacking parallelities Total time for adding SS restraints: 261.44 Time building geometry restraints manager: 72.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 22263 1.32 - 1.45: 68624 1.45 - 1.57: 65231 1.57 - 1.69: 9682 1.69 - 1.82: 170 Bond restraints: 165970 Sorted by residual: bond pdb=" C THR y 24 " pdb=" N PRO y 25 " ideal model delta sigma weight residual 1.330 1.435 -0.105 1.22e-02 6.72e+03 7.35e+01 bond pdb=" N VAL d 51 " pdb=" CA VAL d 51 " ideal model delta sigma weight residual 1.463 1.380 0.083 1.14e-02 7.69e+03 5.35e+01 bond pdb=" C LEU d 71 " pdb=" N GLY d 72 " ideal model delta sigma weight residual 1.333 1.419 -0.086 1.31e-02 5.83e+03 4.35e+01 bond pdb=" C LEU d 15 " pdb=" N LEU d 16 " ideal model delta sigma weight residual 1.334 1.409 -0.075 1.33e-02 5.65e+03 3.19e+01 bond pdb=" N LEU d 71 " pdb=" CA LEU d 71 " ideal model delta sigma weight residual 1.458 1.393 0.066 1.27e-02 6.20e+03 2.68e+01 ... (remaining 165965 not shown) Histogram of bond angle deviations from ideal: 95.87 - 103.59: 16117 103.59 - 111.32: 86070 111.32 - 119.04: 64246 119.04 - 126.76: 68369 126.76 - 134.48: 13532 Bond angle restraints: 248334 Sorted by residual: angle pdb=" N VAL d 51 " pdb=" CA VAL d 51 " pdb=" C VAL d 51 " ideal model delta sigma weight residual 110.23 122.25 -12.02 1.04e+00 9.25e-01 1.34e+02 angle pdb=" N ARG d 37 " pdb=" CA ARG d 37 " pdb=" C ARG d 37 " ideal model delta sigma weight residual 110.80 130.32 -19.52 2.13e+00 2.20e-01 8.40e+01 angle pdb=" C ARG d 37 " pdb=" N SER d 38 " pdb=" CA SER d 38 " ideal model delta sigma weight residual 122.84 133.82 -10.98 1.30e+00 5.92e-01 7.13e+01 angle pdb=" O THR c 23 " pdb=" C THR c 23 " pdb=" N ARG c 24 " ideal model delta sigma weight residual 123.23 113.46 9.77 1.30e+00 5.92e-01 5.65e+01 angle pdb=" C VAL d 58 " pdb=" N PRO d 59 " pdb=" CA PRO d 59 " ideal model delta sigma weight residual 119.92 111.95 7.97 1.07e+00 8.73e-01 5.54e+01 ... (remaining 248329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 93048 35.96 - 71.91: 12434 71.91 - 107.87: 1323 107.87 - 143.82: 34 143.82 - 179.78: 54 Dihedral angle restraints: 106893 sinusoidal: 89013 harmonic: 17880 Sorted by residual: dihedral pdb=" O4' C A3046 " pdb=" C1' C A3046 " pdb=" N1 C A3046 " pdb=" C2 C A3046 " ideal model delta sinusoidal sigma weight residual -160.00 18.70 -178.70 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C E 566 " pdb=" C1' C E 566 " pdb=" N1 C E 566 " pdb=" C2 C E 566 " ideal model delta sinusoidal sigma weight residual 200.00 27.60 172.40 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C A1535 " pdb=" C1' C A1535 " pdb=" N1 C A1535 " pdb=" C2 C A1535 " ideal model delta sinusoidal sigma weight residual -160.00 8.57 -168.57 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 106890 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 30967 0.124 - 0.248: 764 0.248 - 0.372: 15 0.372 - 0.496: 2 0.496 - 0.620: 1 Chirality restraints: 31749 Sorted by residual: chirality pdb=" CA VAL d 51 " pdb=" N VAL d 51 " pdb=" C VAL d 51 " pdb=" CB VAL d 51 " both_signs ideal model delta sigma weight residual False 2.44 1.82 0.62 2.00e-01 2.50e+01 9.61e+00 chirality pdb=" CA LEU c 11 " pdb=" N LEU c 11 " pdb=" C LEU c 11 " pdb=" CB LEU c 11 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA LEU I 719 " pdb=" N LEU I 719 " pdb=" C LEU I 719 " pdb=" CB LEU I 719 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 31746 not shown) Planarity restraints: 13529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS d 70 " -0.023 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C LYS d 70 " 0.076 2.00e-02 2.50e+03 pdb=" O LYS d 70 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU d 71 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY d 54 " 0.020 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C GLY d 54 " -0.072 2.00e-02 2.50e+03 pdb=" O GLY d 54 " 0.028 2.00e-02 2.50e+03 pdb=" N ARG d 55 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET O 45 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C MET O 45 " 0.071 2.00e-02 2.50e+03 pdb=" O MET O 45 " -0.027 2.00e-02 2.50e+03 pdb=" N GLY O 46 " -0.023 2.00e-02 2.50e+03 ... (remaining 13526 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 390 2.32 - 2.96: 70270 2.96 - 3.61: 277037 3.61 - 4.25: 475698 4.25 - 4.90: 643722 Nonbonded interactions: 1467117 Sorted by model distance: nonbonded pdb=" O ILE d 45 " pdb=" O VAL d 62 " model vdw 1.674 3.040 nonbonded pdb=" C5 C E 503 " pdb=" C4 U E 572 " model vdw 1.948 3.560 nonbonded pdb=" O2' U a 91 " pdb=" O5' A a 92 " model vdw 1.963 2.440 nonbonded pdb=" OG SER e 25 " pdb=" OH TYR e 31 " model vdw 1.987 2.440 nonbonded pdb=" O HIS d 52 " pdb=" O LYS d 56 " model vdw 1.988 3.040 ... (remaining 1467112 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: 6.770 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: 0.120 Extract box with map and model: 29.570 Check model and map are aligned: 1.650 Set scattering table: 1.010 Process input model: 546.980 Find NCS groups from input model: 3.600 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 601.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.135 165970 Z= 0.679 Angle : 0.893 19.524 248334 Z= 0.453 Chirality : 0.055 0.620 31749 Planarity : 0.006 0.087 13529 Dihedral : 24.004 179.777 95393 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.48 % Favored : 92.45 % Rotamer: Outliers : 0.23 % Allowed : 3.77 % Favored : 96.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.90 (0.09), residues: 6188 helix: -1.22 (0.10), residues: 2043 sheet: -2.13 (0.14), residues: 1086 loop : -2.32 (0.10), residues: 3059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP d 34 HIS 0.022 0.002 HIS J 16 PHE 0.028 0.002 PHE I 764 TYR 0.025 0.002 TYR o 34 ARG 0.017 0.001 ARG 0 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 966 time to evaluate : 6.674 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 TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 16 LEU cc_start: 0.8779 (tp) cc_final: 0.8485 (tp) REVERT: j 73 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8061 (tm-30) REVERT: N 31 ASP cc_start: 0.8031 (m-30) cc_final: 0.7620 (m-30) REVERT: Q 4 ILE cc_start: 0.8779 (mt) cc_final: 0.8521 (mp) REVERT: R 83 LYS cc_start: 0.3616 (pttt) cc_final: 0.3028 (mptt) REVERT: D 53 ASN cc_start: 0.8185 (t0) cc_final: 0.7933 (t0) REVERT: X 80 ASN cc_start: 0.8378 (p0) cc_final: 0.8082 (p0) REVERT: Z 21 TYR cc_start: 0.7861 (m-10) cc_final: 0.7642 (m-10) REVERT: Z 26 ASP cc_start: 0.7838 (t0) cc_final: 0.7469 (t0) REVERT: G 68 HIS cc_start: 0.8285 (m90) cc_final: 0.8077 (m90) REVERT: k 88 ASP cc_start: 0.7226 (m-30) cc_final: 0.6857 (m-30) REVERT: k 111 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7555 (tm-30) REVERT: p 34 LYS cc_start: 0.8434 (tptp) cc_final: 0.8162 (tptt) outliers start: 12 outliers final: 5 residues processed: 974 average time/residue: 2.2704 time to fit residues: 3162.0708 Evaluate side-chains 773 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 768 time to evaluate : 5.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain e residue 94 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 917 optimal weight: 3.9990 chunk 823 optimal weight: 10.0000 chunk 456 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 555 optimal weight: 1.9990 chunk 439 optimal weight: 0.0370 chunk 851 optimal weight: 3.9990 chunk 329 optimal weight: 0.7980 chunk 517 optimal weight: 5.9990 chunk 633 optimal weight: 5.9990 chunk 986 optimal weight: 6.9990 overall best weight: 2.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 52 HIS N 14 HIS ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 ASN K 109 GLN K 164 GLN L 21 ASN L 99 GLN M 151 ASN M 208 ASN O 34 GLN O 62 ASN P 103 ASN Q 118 GLN ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 136 GLN V 76 GLN J 17 GLN W 94 ASN X 13 GLN Z 63 GLN 2 61 HIS 2 94 HIS 2 143 GLN 2 156 GLN 6 31 ASN x 59 ASN G 143 GLN e 54 GLN h 25 GLN h 49 GLN k 27 GLN k 57 ASN k 66 GLN n 77 HIS ** q 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 107 ASN r 33 GLN t 3 ASN u 24 ASN u 45 GLN u 93 ASN u 94 GLN u 203 ASN I 701 GLN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 12 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 165970 Z= 0.176 Angle : 0.573 12.474 248334 Z= 0.295 Chirality : 0.034 0.269 31749 Planarity : 0.005 0.064 13529 Dihedral : 24.497 179.703 83232 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 1.89 % Allowed : 12.71 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -1.38 (0.10), residues: 6188 helix: 0.39 (0.11), residues: 2031 sheet: -1.44 (0.14), residues: 1119 loop : -1.61 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 34 HIS 0.013 0.001 HIS d 14 PHE 0.023 0.002 PHE d 74 TYR 0.020 0.001 TYR j 59 ARG 0.008 0.001 ARG g 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 878 time to evaluate : 6.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: c 24 ARG cc_start: 0.6482 (OUTLIER) cc_final: 0.4170 (tpm170) REVERT: d 36 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7435 (ptm-80) REVERT: d 64 GLU cc_start: 0.7455 (tp30) cc_final: 0.7235 (tp30) REVERT: j 5 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7807 (t) REVERT: j 73 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8145 (tm-30) REVERT: N 31 ASP cc_start: 0.7843 (m-30) cc_final: 0.7642 (m-30) REVERT: P 23 ASN cc_start: 0.7673 (t0) cc_final: 0.7451 (t0) REVERT: Q 4 ILE cc_start: 0.8798 (mt) cc_final: 0.8552 (mp) REVERT: Q 27 ARG cc_start: 0.8357 (ttp-110) cc_final: 0.8112 (ttp-110) REVERT: Q 121 LYS cc_start: 0.5733 (mppt) cc_final: 0.5348 (mttt) REVERT: X 63 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: x 34 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7188 (tm-30) REVERT: G 23 TYR cc_start: 0.8560 (t80) cc_final: 0.8332 (t80) REVERT: g 17 ARG cc_start: 0.7888 (ptt-90) cc_final: 0.7469 (ptt90) REVERT: k 88 ASP cc_start: 0.7305 (m-30) cc_final: 0.7009 (m-30) REVERT: k 111 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7171 (tm-30) REVERT: k 114 ASP cc_start: 0.7689 (m-30) cc_final: 0.7123 (m-30) REVERT: l 11 LYS cc_start: 0.9088 (mtmm) cc_final: 0.8641 (mtmm) REVERT: l 71 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8123 (mtpp) REVERT: p 11 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9103 (mp) REVERT: p 26 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: p 37 GLN cc_start: 0.8320 (mt0) cc_final: 0.7895 (mt0) REVERT: u 27 MET cc_start: 0.8260 (mmm) cc_final: 0.8048 (mmp) REVERT: u 112 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7729 (mp10) REVERT: H 87 LYS cc_start: 0.8075 (pttt) cc_final: 0.7846 (ptpt) REVERT: 9 12 GLN cc_start: 0.8384 (mt0) cc_final: 0.8159 (mt0) outliers start: 97 outliers final: 36 residues processed: 909 average time/residue: 2.1174 time to fit residues: 2812.0441 Evaluate side-chains 844 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 801 time to evaluate : 6.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 24 ARG Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 66 VAL Chi-restraints excluded: chain j residue 69 ASP Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain O residue 160 ASP Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain V residue 121 LYS Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Z residue 20 SER Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 131 ILE Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 41 ASP Chi-restraints excluded: chain g residue 85 VAL Chi-restraints excluded: chain h residue 144 MET Chi-restraints excluded: chain l residue 40 VAL Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain m residue 64 SER Chi-restraints excluded: chain n residue 77 HIS Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain p residue 11 ILE Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain u residue 1 MET Chi-restraints excluded: chain u residue 112 GLN Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain o residue 54 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 548 optimal weight: 0.6980 chunk 306 optimal weight: 10.0000 chunk 820 optimal weight: 10.0000 chunk 671 optimal weight: 9.9990 chunk 272 optimal weight: 20.0000 chunk 987 optimal weight: 20.0000 chunk 1067 optimal weight: 9.9990 chunk 879 optimal weight: 5.9990 chunk 979 optimal weight: 9.9990 chunk 336 optimal weight: 10.0000 chunk 792 optimal weight: 20.0000 overall best weight: 7.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: y 3 HIS y 15 ASN ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 67 ASN K 164 GLN L 21 ASN L 99 GLN M 151 ASN M 208 ASN ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN Z 63 GLN 6 44 ASN ** 7 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 59 ASN ** G 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 GLN h 148 ASN k 57 ASN l 56 HIS m 73 GLN n 77 HIS q 107 ASN r 33 GLN u 24 ASN ** o 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 73 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 165970 Z= 0.438 Angle : 0.668 11.442 248334 Z= 0.343 Chirality : 0.040 0.327 31749 Planarity : 0.005 0.061 13529 Dihedral : 24.477 179.980 83224 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.14 % Favored : 93.81 % Rotamer: Outliers : 3.10 % Allowed : 14.58 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.95 (0.11), residues: 6188 helix: 0.66 (0.11), residues: 2034 sheet: -1.04 (0.15), residues: 1130 loop : -1.35 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP g 43 HIS 0.014 0.002 HIS n 77 PHE 0.020 0.002 PHE d 44 TYR 0.019 0.002 TYR Q 25 ARG 0.016 0.001 ARG 2 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 843 time to evaluate : 6.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 24 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.5302 (tpm170) REVERT: y 37 TYR cc_start: 0.5190 (OUTLIER) cc_final: 0.3041 (m-10) REVERT: d 36 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7686 (ptm-80) REVERT: j 5 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7953 (t) REVERT: j 73 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8225 (tm-30) REVERT: N 31 ASP cc_start: 0.8037 (m-30) cc_final: 0.7748 (m-30) REVERT: O 160 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7160 (m-30) REVERT: Q 4 ILE cc_start: 0.8880 (mt) cc_final: 0.8597 (mp) REVERT: R 83 LYS cc_start: 0.3510 (pttt) cc_final: 0.2889 (mptt) REVERT: T 135 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: U 73 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7827 (p0) REVERT: J 101 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: C 93 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.6886 (mtp85) REVERT: X 63 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7543 (tp30) REVERT: 6 20 ASP cc_start: 0.7535 (t0) cc_final: 0.6984 (t0) REVERT: 8 38 LYS cc_start: 0.8749 (mmtp) cc_final: 0.8533 (mmtp) REVERT: g 17 ARG cc_start: 0.7908 (ptt-90) cc_final: 0.7486 (ptt90) REVERT: h 9 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8520 (tmtm) REVERT: h 14 ASN cc_start: 0.8286 (t0) cc_final: 0.8081 (t0) REVERT: k 88 ASP cc_start: 0.7507 (m-30) cc_final: 0.7069 (m-30) REVERT: k 111 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7203 (tm-30) REVERT: l 45 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: m 73 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7750 (tp-100) REVERT: m 107 ARG cc_start: 0.7741 (ttm110) cc_final: 0.7349 (mtt-85) REVERT: u 112 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: I 768 MET cc_start: 0.1672 (tpt) cc_final: 0.0864 (mmt) REVERT: H 87 LYS cc_start: 0.8242 (pttt) cc_final: 0.8020 (ptmm) REVERT: 9 5 SER cc_start: 0.9191 (p) cc_final: 0.8986 (t) REVERT: 9 12 GLN cc_start: 0.8346 (mt0) cc_final: 0.8126 (mt0) outliers start: 159 outliers final: 76 residues processed: 913 average time/residue: 2.1540 time to fit residues: 2877.6976 Evaluate side-chains 880 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 790 time to evaluate : 6.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 24 ARG Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 37 TYR Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain j residue 69 ASP Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 151 ILE Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain O residue 160 ASP Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 88 MET Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain T residue 135 GLN Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 121 LYS Chi-restraints excluded: chain J residue 101 GLU Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 93 ARG Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 80 THR Chi-restraints excluded: chain Z residue 20 SER Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 6 residue 44 ASN Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain f residue 131 ILE Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 85 VAL Chi-restraints excluded: chain h residue 9 LYS Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 98 THR Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 40 VAL Chi-restraints excluded: chain l residue 45 GLU Chi-restraints excluded: chain l residue 60 ASP Chi-restraints excluded: chain l residue 95 SER Chi-restraints excluded: chain m residue 73 GLN Chi-restraints excluded: chain n residue 98 ILE Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain p residue 11 ILE Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain u residue 112 GLN Chi-restraints excluded: chain I residue 679 VAL Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain I residue 790 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain o residue 30 THR Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 81 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 976 optimal weight: 2.9990 chunk 742 optimal weight: 20.0000 chunk 512 optimal weight: 0.0040 chunk 109 optimal weight: 10.0000 chunk 471 optimal weight: 7.9990 chunk 663 optimal weight: 1.9990 chunk 991 optimal weight: 1.9990 chunk 1049 optimal weight: 40.0000 chunk 518 optimal weight: 1.9990 chunk 939 optimal weight: 9.9990 chunk 282 optimal weight: 7.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: y 3 HIS ** d 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 63 ASN ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 164 GLN M 121 ASN M 151 ASN M 208 ASN O 25 GLN O 62 ASN P 103 ASN ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 51 ASN J 17 GLN Z 58 ASN Z 63 GLN 2 14 ASN ** 7 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 GLN h 148 ASN m 73 GLN m 128 ASN n 77 HIS r 33 GLN u 203 ASN H 10 HIS ** o 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 165970 Z= 0.158 Angle : 0.547 11.091 248334 Z= 0.283 Chirality : 0.033 0.477 31749 Planarity : 0.004 0.062 13529 Dihedral : 24.458 179.412 83224 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.75 % Rotamer: Outliers : 2.77 % Allowed : 16.67 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.55 (0.11), residues: 6188 helix: 1.06 (0.12), residues: 2038 sheet: -0.86 (0.15), residues: 1165 loop : -1.14 (0.12), residues: 2985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP g 43 HIS 0.013 0.001 HIS H 10 PHE 0.018 0.001 PHE d 74 TYR 0.013 0.001 TYR i 49 ARG 0.012 0.000 ARG m 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 875 time to evaluate : 6.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: c 24 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.5098 (tpm170) REVERT: y 37 TYR cc_start: 0.4605 (OUTLIER) cc_final: 0.2895 (m-10) REVERT: d 36 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7497 (ptm-80) REVERT: j 5 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7753 (t) REVERT: N 31 ASP cc_start: 0.7900 (m-30) cc_final: 0.7692 (m-30) REVERT: L 170 MET cc_start: 0.7898 (ttp) cc_final: 0.7688 (ttp) REVERT: O 160 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7002 (m-30) REVERT: P 23 ASN cc_start: 0.7626 (t0) cc_final: 0.7323 (t0) REVERT: P 84 TYR cc_start: 0.8014 (m-80) cc_final: 0.7806 (m-80) REVERT: Q 4 ILE cc_start: 0.8949 (mt) cc_final: 0.8703 (mp) REVERT: Q 20 GLU cc_start: 0.7504 (tp30) cc_final: 0.7294 (tp30) REVERT: R 83 LYS cc_start: 0.3522 (pttt) cc_final: 0.2888 (mptt) REVERT: C 63 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7374 (tp30) REVERT: C 93 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.6449 (mtp85) REVERT: X 63 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7508 (tp30) REVERT: 2 45 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: 6 20 ASP cc_start: 0.7332 (t0) cc_final: 0.7109 (t0) REVERT: g 17 ARG cc_start: 0.7811 (ptt-90) cc_final: 0.7508 (ptt90) REVERT: g 92 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.8049 (mtm180) REVERT: k 88 ASP cc_start: 0.7374 (m-30) cc_final: 0.6968 (m-30) REVERT: k 111 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7245 (tm-30) REVERT: k 114 ASP cc_start: 0.7787 (m-30) cc_final: 0.6993 (m-30) REVERT: m 107 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7303 (mtt-85) REVERT: n 75 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7960 (mm-40) REVERT: p 4 THR cc_start: 0.8747 (p) cc_final: 0.8463 (t) REVERT: p 26 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7488 (mm-30) REVERT: u 112 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: u 212 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8596 (tp) REVERT: I 768 MET cc_start: 0.1528 (tpt) cc_final: 0.0876 (mmt) REVERT: H 87 LYS cc_start: 0.8267 (pttt) cc_final: 0.8040 (ptmm) REVERT: 9 12 GLN cc_start: 0.8246 (mt0) cc_final: 0.8040 (mt0) outliers start: 142 outliers final: 57 residues processed: 944 average time/residue: 2.1275 time to fit residues: 2958.8458 Evaluate side-chains 885 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 814 time to evaluate : 6.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 24 ARG Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 37 TYR Chi-restraints excluded: chain d residue 14 HIS Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain j residue 69 ASP Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain O residue 160 ASP Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 93 ARG Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 52 GLU Chi-restraints excluded: chain Z residue 20 SER Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 68 GLU Chi-restraints excluded: chain x residue 51 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 126 ARG Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain f residue 131 ILE Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 92 ARG Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain l residue 40 VAL Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain n residue 75 GLN Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain p residue 26 GLU Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain t residue 55 SER Chi-restraints excluded: chain u residue 112 GLN Chi-restraints excluded: chain u residue 212 LEU Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 34 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 874 optimal weight: 10.0000 chunk 595 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 781 optimal weight: 10.0000 chunk 433 optimal weight: 9.9990 chunk 895 optimal weight: 6.9990 chunk 725 optimal weight: 10.0000 chunk 1 optimal weight: 0.0270 chunk 536 optimal weight: 0.0970 chunk 942 optimal weight: 9.9990 chunk 264 optimal weight: 10.0000 overall best weight: 5.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 46 HIS y 3 HIS d 23 ASN ** d 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN M 151 ASN M 208 ASN O 25 GLN O 62 ASN ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN Q 118 GLN ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 GLN Z 58 ASN Z 63 GLN 2 14 ASN 6 44 ASN ** 7 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 GLN h 148 ASN m 125 GLN n 77 HIS r 33 GLN u 203 ASN H 10 HIS ** o 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 73 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 165970 Z= 0.328 Angle : 0.597 9.923 248334 Z= 0.308 Chirality : 0.037 0.307 31749 Planarity : 0.005 0.066 13529 Dihedral : 24.416 179.471 83224 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.08 % Favored : 93.89 % Rotamer: Outliers : 2.85 % Allowed : 18.25 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.46 (0.11), residues: 6188 helix: 1.10 (0.12), residues: 2030 sheet: -0.76 (0.15), residues: 1144 loop : -1.07 (0.12), residues: 3014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 34 HIS 0.012 0.001 HIS H 10 PHE 0.016 0.002 PHE d 44 TYR 0.015 0.001 TYR u 54 ARG 0.013 0.000 ARG m 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 834 time to evaluate : 6.417 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: c 24 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.5313 (tpm170) REVERT: y 37 TYR cc_start: 0.4967 (OUTLIER) cc_final: 0.2838 (m-10) REVERT: d 36 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7554 (ptm-80) REVERT: j 5 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7776 (t) REVERT: Q 4 ILE cc_start: 0.8940 (mt) cc_final: 0.8682 (mp) REVERT: Q 20 GLU cc_start: 0.7576 (tp30) cc_final: 0.7281 (tp30) REVERT: R 83 LYS cc_start: 0.3500 (pttt) cc_final: 0.2857 (mptt) REVERT: U 73 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7783 (p0) REVERT: J 101 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7581 (tt0) REVERT: C 93 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.6721 (mtp85) REVERT: X 63 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7508 (tp30) REVERT: 2 45 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8273 (mt0) REVERT: g 17 ARG cc_start: 0.7759 (ptt-90) cc_final: 0.7557 (ptt90) REVERT: k 88 ASP cc_start: 0.7479 (m-30) cc_final: 0.7037 (m-30) REVERT: k 111 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7256 (tm-30) REVERT: l 14 ASP cc_start: 0.7950 (t0) cc_final: 0.7703 (t0) REVERT: l 45 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.6477 (mp0) REVERT: p 4 THR cc_start: 0.8818 (p) cc_final: 0.8565 (t) REVERT: u 112 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7677 (mp10) REVERT: I 768 MET cc_start: 0.1751 (tpt) cc_final: 0.0888 (mmt) REVERT: H 87 LYS cc_start: 0.8418 (pttt) cc_final: 0.8210 (ptmm) REVERT: 9 12 GLN cc_start: 0.8289 (mt0) cc_final: 0.8076 (mt0) outliers start: 146 outliers final: 81 residues processed: 907 average time/residue: 2.1140 time to fit residues: 2804.4370 Evaluate side-chains 907 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 815 time to evaluate : 6.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 24 ARG Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 37 TYR Chi-restraints excluded: chain d residue 14 HIS Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain j residue 69 ASP Chi-restraints excluded: chain j residue 84 ILE Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 101 GLU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 93 ARG Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 80 THR Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 94 ASP Chi-restraints excluded: chain 1 residue 66 ILE Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 68 GLU Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain e residue 190 LEU Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 131 ILE Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 85 VAL Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain l residue 40 VAL Chi-restraints excluded: chain l residue 45 GLU Chi-restraints excluded: chain l residue 95 SER Chi-restraints excluded: chain n residue 98 ILE Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain p residue 11 ILE Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain u residue 112 GLN Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain I residue 790 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain o residue 30 THR Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain o residue 81 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 353 optimal weight: 8.9990 chunk 945 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 616 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 1050 optimal weight: 20.0000 chunk 872 optimal weight: 30.0000 chunk 486 optimal weight: 40.0000 chunk 87 optimal weight: 10.0000 chunk 347 optimal weight: 10.0000 chunk 551 optimal weight: 10.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: y 3 HIS ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN M 151 ASN M 208 ASN O 25 GLN O 62 ASN ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN Q 118 GLN U 51 ASN J 17 GLN Z 63 GLN 2 14 ASN 6 44 ASN ** 7 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN h 49 GLN h 148 ASN m 125 GLN m 128 ASN n 77 HIS r 33 GLN ** u 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 10 HIS ** o 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.099 165970 Z= 0.528 Angle : 0.704 10.245 248334 Z= 0.361 Chirality : 0.043 0.356 31749 Planarity : 0.005 0.070 13529 Dihedral : 24.509 179.565 83224 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.46 % Favored : 93.49 % Rotamer: Outliers : 3.42 % Allowed : 18.80 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.66 (0.11), residues: 6188 helix: 0.84 (0.11), residues: 2042 sheet: -0.82 (0.15), residues: 1139 loop : -1.14 (0.11), residues: 3007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 43 HIS 0.015 0.002 HIS H 10 PHE 0.019 0.002 PHE d 44 TYR 0.020 0.002 TYR G 23 ARG 0.014 0.001 ARG m 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 830 time to evaluate : 6.496 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: c 24 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.5614 (tpm170) REVERT: y 37 TYR cc_start: 0.5030 (OUTLIER) cc_final: 0.2653 (m-10) REVERT: d 36 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7742 (ptm-80) REVERT: j 5 VAL cc_start: 0.8110 (OUTLIER) cc_final: 0.7860 (t) REVERT: j 63 ASN cc_start: 0.8455 (m-40) cc_final: 0.8044 (m110) REVERT: Q 4 ILE cc_start: 0.8960 (mt) cc_final: 0.8713 (mp) REVERT: Q 20 GLU cc_start: 0.7737 (tp30) cc_final: 0.7399 (tp30) REVERT: R 83 LYS cc_start: 0.3303 (pttt) cc_final: 0.2715 (mptt) REVERT: T 135 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7584 (mp10) REVERT: U 73 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7830 (p0) REVERT: C 93 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8227 (mmp80) REVERT: X 63 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7507 (tp30) REVERT: Z 26 ASP cc_start: 0.7747 (t0) cc_final: 0.7467 (t0) REVERT: 2 45 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8322 (mt0) REVERT: 6 20 ASP cc_start: 0.7488 (t0) cc_final: 0.6939 (t0) REVERT: 6 65 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7789 (mt-10) REVERT: g 17 ARG cc_start: 0.7798 (ptt-90) cc_final: 0.7564 (ptt90) REVERT: h 66 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8856 (mm) REVERT: k 88 ASP cc_start: 0.7593 (m-30) cc_final: 0.7071 (m-30) REVERT: k 111 GLN cc_start: 0.7846 (tm-30) cc_final: 0.7232 (tm-30) REVERT: l 45 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: l 71 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8345 (mttm) REVERT: m 135 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7184 (ttp-110) REVERT: p 4 THR cc_start: 0.8925 (p) cc_final: 0.8673 (t) REVERT: u 112 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7742 (mp10) REVERT: u 213 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8699 (mm) REVERT: H 89 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6670 (mmt90) outliers start: 175 outliers final: 107 residues processed: 915 average time/residue: 2.1153 time to fit residues: 2847.4671 Evaluate side-chains 937 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 814 time to evaluate : 6.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 24 ARG Chi-restraints excluded: chain y residue 1 SER Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 37 TYR Chi-restraints excluded: chain d residue 14 HIS Chi-restraints excluded: chain d residue 15 LEU Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain j residue 69 ASP Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 173 ASP Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 88 MET Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 135 GLN Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 96 ASP Chi-restraints excluded: chain V residue 121 LYS Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 93 ARG Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 80 THR Chi-restraints excluded: chain Z residue 20 SER Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 53 LYS Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain 1 residue 66 ILE Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 151 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 68 GLU Chi-restraints excluded: chain 6 residue 40 GLN Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 59 VAL Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain e residue 133 SER Chi-restraints excluded: chain e residue 190 LEU Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 131 ILE Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 85 VAL Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain l residue 6 ILE Chi-restraints excluded: chain l residue 32 THR Chi-restraints excluded: chain l residue 40 VAL Chi-restraints excluded: chain l residue 45 GLU Chi-restraints excluded: chain l residue 71 LYS Chi-restraints excluded: chain l residue 95 SER Chi-restraints excluded: chain m residue 64 SER Chi-restraints excluded: chain m residue 135 ARG Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 98 ILE Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain p residue 11 ILE Chi-restraints excluded: chain p residue 74 ASP Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain u residue 112 GLN Chi-restraints excluded: chain u residue 213 LEU Chi-restraints excluded: chain I residue 679 VAL Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain I residue 790 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain o residue 30 THR Chi-restraints excluded: chain o residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 1013 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 598 optimal weight: 3.9990 chunk 767 optimal weight: 7.9990 chunk 594 optimal weight: 0.9990 chunk 884 optimal weight: 6.9990 chunk 586 optimal weight: 1.9990 chunk 1046 optimal weight: 30.0000 chunk 655 optimal weight: 20.0000 chunk 638 optimal weight: 8.9990 chunk 483 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 151 ASN M 208 ASN O 25 GLN O 62 ASN ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 51 ASN J 17 GLN Z 63 GLN ** 7 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 GLN h 148 ASN m 125 GLN m 128 ASN n 77 HIS r 33 GLN ** u 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 10 HIS ** o 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 12 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 165970 Z= 0.252 Angle : 0.578 10.425 248334 Z= 0.300 Chirality : 0.036 0.289 31749 Planarity : 0.005 0.070 13529 Dihedral : 24.480 179.994 83224 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 2.99 % Allowed : 19.95 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.38 (0.11), residues: 6188 helix: 1.11 (0.11), residues: 2034 sheet: -0.69 (0.15), residues: 1141 loop : -0.99 (0.12), residues: 3013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 34 HIS 0.014 0.001 HIS I 773 PHE 0.015 0.001 PHE d 74 TYR 0.020 0.001 TYR i 49 ARG 0.013 0.000 ARG m 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 848 time to evaluate : 6.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: c 24 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.5511 (tpm170) REVERT: y 37 TYR cc_start: 0.4794 (OUTLIER) cc_final: 0.2725 (m-10) REVERT: d 18 LYS cc_start: 0.8808 (mttm) cc_final: 0.8527 (mttt) REVERT: d 36 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7725 (ptm-80) REVERT: d 40 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8250 (mp) REVERT: j 5 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7763 (t) REVERT: j 63 ASN cc_start: 0.8377 (m-40) cc_final: 0.7954 (m110) REVERT: L 170 MET cc_start: 0.7933 (ttp) cc_final: 0.7720 (ttp) REVERT: O 140 ASN cc_start: 0.8491 (m-40) cc_final: 0.8162 (m-40) REVERT: Q 4 ILE cc_start: 0.8940 (mt) cc_final: 0.8698 (mp) REVERT: Q 20 GLU cc_start: 0.7609 (tp30) cc_final: 0.7347 (tp30) REVERT: R 83 LYS cc_start: 0.3393 (pttt) cc_final: 0.2775 (mptt) REVERT: J 101 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: C 93 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.7858 (mmp80) REVERT: X 63 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7457 (tp30) REVERT: Z 26 ASP cc_start: 0.7661 (t0) cc_final: 0.7452 (t0) REVERT: k 88 ASP cc_start: 0.7511 (m-30) cc_final: 0.7092 (m-30) REVERT: k 111 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7189 (tm-30) REVERT: k 114 ASP cc_start: 0.7786 (m-30) cc_final: 0.7182 (m-30) REVERT: l 45 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: l 71 LYS cc_start: 0.8707 (mttp) cc_final: 0.8340 (mttm) REVERT: p 4 THR cc_start: 0.8898 (p) cc_final: 0.8676 (t) REVERT: u 112 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7723 (mp10) outliers start: 153 outliers final: 86 residues processed: 928 average time/residue: 2.0866 time to fit residues: 2867.2097 Evaluate side-chains 913 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 817 time to evaluate : 6.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 24 ARG Chi-restraints excluded: chain y residue 1 SER Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 37 TYR Chi-restraints excluded: chain d residue 14 HIS Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 40 ILE Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 51 VAL Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain j residue 69 ASP Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 88 MET Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 101 GLU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 93 ARG Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 80 THR Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain Z residue 94 ASP Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 151 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 68 GLU Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 131 ILE Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 83 GLU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain l residue 6 ILE Chi-restraints excluded: chain l residue 40 VAL Chi-restraints excluded: chain l residue 45 GLU Chi-restraints excluded: chain l residue 95 SER Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain m residue 64 SER Chi-restraints excluded: chain n residue 77 HIS Chi-restraints excluded: chain n residue 98 ILE Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 95 VAL Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain u residue 112 GLN Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain I residue 790 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 57 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 647 optimal weight: 10.0000 chunk 418 optimal weight: 9.9990 chunk 625 optimal weight: 3.9990 chunk 315 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 665 optimal weight: 5.9990 chunk 713 optimal weight: 20.0000 chunk 517 optimal weight: 0.1980 chunk 97 optimal weight: 30.0000 chunk 822 optimal weight: 10.0000 overall best weight: 6.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN L 76 ASN M 208 ASN O 62 ASN ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN ** S 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 51 ASN D 48 HIS Z 63 GLN ** 7 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 HIS G 143 GLN f 173 GLN h 21 GLN h 49 GLN h 148 ASN m 125 GLN m 128 ASN n 77 HIS ** n 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 10 HIS ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 12 GLN ** 9 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 165970 Z= 0.363 Angle : 0.621 9.799 248334 Z= 0.321 Chirality : 0.038 0.316 31749 Planarity : 0.005 0.064 13529 Dihedral : 24.458 179.877 83224 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.27 % Favored : 93.70 % Rotamer: Outliers : 2.89 % Allowed : 20.87 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.03 % 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: -0.38 (0.11), residues: 6188 helix: 1.07 (0.11), residues: 2037 sheet: -0.71 (0.15), residues: 1135 loop : -0.96 (0.12), residues: 3016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP g 43 HIS 0.013 0.001 HIS n 77 PHE 0.033 0.002 PHE H 14 TYR 0.022 0.002 TYR G 23 ARG 0.016 0.000 ARG m 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 831 time to evaluate : 6.579 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: c 24 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.5558 (tpm170) REVERT: y 37 TYR cc_start: 0.4988 (OUTLIER) cc_final: 0.2668 (m-10) REVERT: d 18 LYS cc_start: 0.8819 (mttm) cc_final: 0.8479 (mttt) REVERT: d 36 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7750 (ptm-80) REVERT: d 40 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8337 (mp) REVERT: j 5 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7803 (t) REVERT: j 63 ASN cc_start: 0.8393 (m-40) cc_final: 0.7973 (m110) REVERT: O 140 ASN cc_start: 0.8543 (m-40) cc_final: 0.8216 (m-40) REVERT: Q 4 ILE cc_start: 0.8943 (mt) cc_final: 0.8682 (mp) REVERT: Q 20 GLU cc_start: 0.7652 (tp30) cc_final: 0.7337 (tp30) REVERT: R 83 LYS cc_start: 0.3415 (pttt) cc_final: 0.2796 (mptt) REVERT: S 137 MET cc_start: 0.1580 (tpt) cc_final: 0.1208 (tpp) REVERT: C 93 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7979 (mmp80) REVERT: X 63 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7477 (tp30) REVERT: Z 26 ASP cc_start: 0.7698 (t0) cc_final: 0.7384 (t0) REVERT: 2 45 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8336 (mt0) REVERT: f 211 GLU cc_start: 0.4337 (OUTLIER) cc_final: 0.3545 (pm20) REVERT: k 88 ASP cc_start: 0.7550 (m-30) cc_final: 0.7061 (m-30) REVERT: k 111 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7179 (tm-30) REVERT: l 45 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: l 71 LYS cc_start: 0.8772 (mttp) cc_final: 0.8309 (mttm) REVERT: p 4 THR cc_start: 0.8926 (p) cc_final: 0.8712 (t) REVERT: u 112 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7723 (mp10) outliers start: 148 outliers final: 97 residues processed: 911 average time/residue: 2.0418 time to fit residues: 2754.1903 Evaluate side-chains 925 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 817 time to evaluate : 6.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 24 ARG Chi-restraints excluded: chain y residue 1 SER Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 37 TYR Chi-restraints excluded: chain d residue 14 HIS Chi-restraints excluded: chain d residue 15 LEU Chi-restraints excluded: chain d residue 16 LEU Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 40 ILE Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 51 VAL Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain j residue 69 ASP Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 20 ASN Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 88 MET Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 93 ARG Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 80 THR Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain Z residue 56 SER Chi-restraints excluded: chain 1 residue 66 ILE Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 151 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 68 GLU Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 131 ILE Chi-restraints excluded: chain f residue 211 GLU Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 83 GLU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain l residue 6 ILE Chi-restraints excluded: chain l residue 32 THR Chi-restraints excluded: chain l residue 40 VAL Chi-restraints excluded: chain l residue 45 GLU Chi-restraints excluded: chain l residue 95 SER Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 98 ILE Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain u residue 112 GLN Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain I residue 790 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain o residue 30 THR Chi-restraints excluded: chain o residue 37 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 952 optimal weight: 5.9990 chunk 1002 optimal weight: 5.9990 chunk 914 optimal weight: 3.9990 chunk 975 optimal weight: 7.9990 chunk 587 optimal weight: 9.9990 chunk 424 optimal weight: 6.9990 chunk 765 optimal weight: 10.0000 chunk 299 optimal weight: 50.0000 chunk 881 optimal weight: 6.9990 chunk 922 optimal weight: 6.9990 chunk 972 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: y 3 HIS ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 52 HIS ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN L 76 ASN M 208 ASN O 25 GLN O 62 ASN ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN U 51 ASN Z 63 GLN ** 7 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 HIS h 21 GLN h 49 GLN h 148 ASN i 93 ASN m 125 GLN m 128 ASN n 77 HIS ** n 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 12 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 165970 Z= 0.351 Angle : 0.621 14.569 248334 Z= 0.320 Chirality : 0.038 0.312 31749 Planarity : 0.005 0.079 13529 Dihedral : 24.465 179.737 83224 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.29 % Favored : 93.68 % Rotamer: Outliers : 2.91 % Allowed : 21.12 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.03 % 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: -0.38 (0.11), residues: 6188 helix: 1.06 (0.11), residues: 2043 sheet: -0.70 (0.15), residues: 1128 loop : -0.96 (0.12), residues: 3017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP d 34 HIS 0.012 0.001 HIS I 773 PHE 0.040 0.002 PHE H 14 TYR 0.025 0.002 TYR i 49 ARG 0.016 0.000 ARG m 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 833 time to evaluate : 6.812 Fit side-chains TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: c 24 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.5559 (tpm170) REVERT: y 37 TYR cc_start: 0.4974 (OUTLIER) cc_final: 0.2674 (m-10) REVERT: d 18 LYS cc_start: 0.8836 (mttm) cc_final: 0.8553 (mttt) REVERT: d 36 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7707 (ptm-80) REVERT: d 40 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8308 (mp) REVERT: j 5 VAL cc_start: 0.8035 (OUTLIER) cc_final: 0.7774 (t) REVERT: j 63 ASN cc_start: 0.8398 (m-40) cc_final: 0.7983 (m110) REVERT: O 140 ASN cc_start: 0.8536 (m-40) cc_final: 0.8215 (m-40) REVERT: Q 4 ILE cc_start: 0.8927 (mt) cc_final: 0.8678 (mp) REVERT: Q 20 GLU cc_start: 0.7653 (tp30) cc_final: 0.7340 (tp30) REVERT: R 83 LYS cc_start: 0.3409 (pttt) cc_final: 0.2787 (mptt) REVERT: S 137 MET cc_start: 0.1575 (OUTLIER) cc_final: 0.1222 (tpp) REVERT: J 101 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: C 93 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.7971 (mmp80) REVERT: X 63 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7474 (tp30) REVERT: Z 26 ASP cc_start: 0.7666 (t0) cc_final: 0.7394 (t0) REVERT: 2 45 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8325 (mt0) REVERT: 7 38 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7277 (mm-30) REVERT: f 211 GLU cc_start: 0.4334 (OUTLIER) cc_final: 0.3451 (pm20) REVERT: h 66 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8765 (mm) REVERT: k 88 ASP cc_start: 0.7585 (m-30) cc_final: 0.7100 (m-30) REVERT: k 111 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7186 (tm-30) REVERT: l 45 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: l 71 LYS cc_start: 0.8772 (mttp) cc_final: 0.8314 (mttm) REVERT: p 4 THR cc_start: 0.8913 (p) cc_final: 0.8703 (t) REVERT: u 112 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7707 (mp10) REVERT: I 768 MET cc_start: 0.1157 (tpt) cc_final: 0.0324 (mpp) outliers start: 149 outliers final: 106 residues processed: 909 average time/residue: 2.0877 time to fit residues: 2799.5282 Evaluate side-chains 941 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 820 time to evaluate : 6.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 24 ARG Chi-restraints excluded: chain y residue 1 SER Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 37 TYR Chi-restraints excluded: chain d residue 14 HIS Chi-restraints excluded: chain d residue 15 LEU Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 40 ILE Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 51 VAL Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain j residue 69 ASP Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 173 ASP Chi-restraints excluded: chain M residue 151 ASN Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 20 ASN Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 88 MET Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 137 MET Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 101 GLU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 93 ARG Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 80 THR Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain 1 residue 66 ILE Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 151 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 68 GLU Chi-restraints excluded: chain 6 residue 14 THR Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 38 GLU Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 131 ILE Chi-restraints excluded: chain f residue 211 GLU Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 83 GLU Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain i residue 93 ASN Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain l residue 32 THR Chi-restraints excluded: chain l residue 40 VAL Chi-restraints excluded: chain l residue 45 GLU Chi-restraints excluded: chain l residue 95 SER Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain m residue 64 SER Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 77 HIS Chi-restraints excluded: chain n residue 98 ILE Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain u residue 112 GLN Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain I residue 790 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain o residue 30 THR Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 640 optimal weight: 6.9990 chunk 1031 optimal weight: 20.0000 chunk 629 optimal weight: 6.9990 chunk 489 optimal weight: 20.0000 chunk 717 optimal weight: 10.0000 chunk 1081 optimal weight: 5.9990 chunk 995 optimal weight: 0.7980 chunk 861 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 665 optimal weight: 7.9990 chunk 528 optimal weight: 4.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN L 76 ASN M 208 ASN O 62 ASN ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN U 51 ASN Z 63 GLN ** 7 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN h 49 GLN h 148 ASN ** k 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 125 GLN m 128 ASN ** n 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 12 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.140 165970 Z= 0.339 Angle : 0.647 59.198 248334 Z= 0.341 Chirality : 0.038 0.587 31749 Planarity : 0.005 0.218 13529 Dihedral : 24.467 179.732 83224 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.27 % Favored : 93.68 % Rotamer: Outliers : 2.65 % Allowed : 21.63 % Favored : 75.72 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.03 % 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: -0.38 (0.11), residues: 6188 helix: 1.07 (0.11), residues: 2043 sheet: -0.70 (0.15), residues: 1128 loop : -0.96 (0.12), residues: 3017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP d 34 HIS 0.354 0.003 HIS n 77 PHE 0.029 0.002 PHE H 14 TYR 0.022 0.002 TYR i 49 ARG 0.016 0.000 ARG m 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12376 Ramachandran restraints generated. 6188 Oldfield, 0 Emsley, 6188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 820 time to evaluate : 6.455 Fit side-chains TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: c 24 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.5556 (tpm170) REVERT: y 37 TYR cc_start: 0.4971 (OUTLIER) cc_final: 0.2672 (m-10) REVERT: d 18 LYS cc_start: 0.8829 (mttm) cc_final: 0.8545 (mttt) REVERT: d 36 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7704 (ptm-80) REVERT: d 40 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8307 (mp) REVERT: j 5 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7771 (t) REVERT: j 63 ASN cc_start: 0.8402 (m-40) cc_final: 0.7981 (m110) REVERT: O 140 ASN cc_start: 0.8538 (m-40) cc_final: 0.8216 (m-40) REVERT: Q 4 ILE cc_start: 0.8927 (mt) cc_final: 0.8678 (mp) REVERT: Q 20 GLU cc_start: 0.7654 (tp30) cc_final: 0.7340 (tp30) REVERT: R 83 LYS cc_start: 0.3410 (pttt) cc_final: 0.2786 (mptt) REVERT: S 137 MET cc_start: 0.1585 (OUTLIER) cc_final: 0.1233 (tpp) REVERT: U 73 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7797 (p0) REVERT: J 101 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: C 93 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.7944 (mmp80) REVERT: X 63 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: Z 26 ASP cc_start: 0.7668 (t0) cc_final: 0.7394 (t0) REVERT: 2 45 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8324 (mt0) REVERT: 6 17 GLU cc_start: 0.7886 (mp0) cc_final: 0.7681 (mp0) REVERT: 6 20 ASP cc_start: 0.7362 (t0) cc_final: 0.6809 (t0) REVERT: 6 24 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: 7 38 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: f 211 GLU cc_start: 0.4335 (OUTLIER) cc_final: 0.3451 (pm20) REVERT: h 66 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8768 (mm) REVERT: k 88 ASP cc_start: 0.7584 (m-30) cc_final: 0.7099 (m-30) REVERT: k 111 GLN cc_start: 0.7879 (tm-30) cc_final: 0.7189 (tm-30) REVERT: l 45 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: l 71 LYS cc_start: 0.8771 (mttp) cc_final: 0.8313 (mttm) REVERT: p 4 THR cc_start: 0.8911 (p) cc_final: 0.8702 (t) REVERT: u 112 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7706 (mp10) outliers start: 136 outliers final: 108 residues processed: 892 average time/residue: 2.0950 time to fit residues: 2767.8881 Evaluate side-chains 941 residues out of total 5151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 816 time to evaluate : 5.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 24 ARG Chi-restraints excluded: chain y residue 1 SER Chi-restraints excluded: chain y residue 17 VAL Chi-restraints excluded: chain y residue 37 TYR Chi-restraints excluded: chain d residue 14 HIS Chi-restraints excluded: chain d residue 15 LEU Chi-restraints excluded: chain d residue 27 THR Chi-restraints excluded: chain d residue 36 ARG Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 40 ILE Chi-restraints excluded: chain d residue 48 THR Chi-restraints excluded: chain d residue 51 VAL Chi-restraints excluded: chain j residue 5 VAL Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 51 ASP Chi-restraints excluded: chain j residue 64 LEU Chi-restraints excluded: chain j residue 69 ASP Chi-restraints excluded: chain j residue 116 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 88 ASP Chi-restraints excluded: chain L residue 173 ASP Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 20 ASN Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 88 MET Chi-restraints excluded: chain P residue 174 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 103 THR Chi-restraints excluded: chain S residue 137 MET Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 74 GLU Chi-restraints excluded: chain V residue 143 SER Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 101 GLU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 93 ARG Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 53 ASP Chi-restraints excluded: chain X residue 63 GLU Chi-restraints excluded: chain Y residue 11 THR Chi-restraints excluded: chain Y residue 20 SER Chi-restraints excluded: chain Y residue 80 THR Chi-restraints excluded: chain Z residue 30 THR Chi-restraints excluded: chain 1 residue 66 ILE Chi-restraints excluded: chain 2 residue 42 THR Chi-restraints excluded: chain 2 residue 45 GLN Chi-restraints excluded: chain 2 residue 125 THR Chi-restraints excluded: chain 2 residue 151 VAL Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 68 GLU Chi-restraints excluded: chain 6 residue 24 GLU Chi-restraints excluded: chain 7 residue 34 SER Chi-restraints excluded: chain 7 residue 38 GLU Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 66 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 192 THR Chi-restraints excluded: chain e residue 105 THR Chi-restraints excluded: chain f residue 37 ILE Chi-restraints excluded: chain f residue 42 SER Chi-restraints excluded: chain f residue 131 ILE Chi-restraints excluded: chain f residue 211 GLU Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 79 LEU Chi-restraints excluded: chain g residue 83 GLU Chi-restraints excluded: chain h residue 15 ASP Chi-restraints excluded: chain h residue 66 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 VAL Chi-restraints excluded: chain h residue 84 THR Chi-restraints excluded: chain h residue 134 SER Chi-restraints excluded: chain i residue 56 VAL Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain k residue 37 VAL Chi-restraints excluded: chain k residue 75 VAL Chi-restraints excluded: chain l residue 32 THR Chi-restraints excluded: chain l residue 40 VAL Chi-restraints excluded: chain l residue 45 GLU Chi-restraints excluded: chain l residue 95 SER Chi-restraints excluded: chain m residue 51 ILE Chi-restraints excluded: chain m residue 62 LYS Chi-restraints excluded: chain m residue 64 SER Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 98 ILE Chi-restraints excluded: chain n residue 104 THR Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain t residue 6 SER Chi-restraints excluded: chain u residue 112 GLN Chi-restraints excluded: chain I residue 774 LEU Chi-restraints excluded: chain I residue 790 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 9 TYR Chi-restraints excluded: chain H residue 14 PHE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 34 THR Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain o residue 30 THR Chi-restraints excluded: chain o residue 37 VAL Chi-restraints excluded: chain o residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1086 random chunks: chunk 684 optimal weight: 0.9980 chunk 917 optimal weight: 9.9990 chunk 263 optimal weight: 8.9990 chunk 794 optimal weight: 30.0000 chunk 127 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 862 optimal weight: 4.9990 chunk 361 optimal weight: 10.0000 chunk 886 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 21 ASN L 76 ASN M 208 ASN O 62 ASN ** O 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 51 ASN Z 63 GLN ** 7 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN h 49 GLN h 148 ASN ** i 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 125 GLN m 128 ASN ** n 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 12 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.068533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.046677 restraints weight = 470403.029| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.43 r_work: 0.2759 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.140 165970 Z= 0.339 Angle : 0.647 59.198 248334 Z= 0.341 Chirality : 0.038 0.587 31749 Planarity : 0.005 0.218 13529 Dihedral : 24.467 179.732 83224 Min Nonbonded Distance : 1.371 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.27 % Favored : 93.68 % Rotamer: Outliers : 2.52 % Allowed : 21.76 % Favored : 75.72 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.03 % 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: -0.38 (0.11), residues: 6188 helix: 1.07 (0.11), residues: 2043 sheet: -0.70 (0.15), residues: 1128 loop : -0.96 (0.12), residues: 3017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP d 34 HIS 0.354 0.003 HIS n 77 PHE 0.029 0.002 PHE H 14 TYR 0.022 0.002 TYR i 49 ARG 0.016 0.000 ARG m 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44962.00 seconds wall clock time: 784 minutes 32.86 seconds (47072.86 seconds total)