Starting phenix.real_space_refine on Thu Mar 21 08:45:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g38_29689/03_2024/8g38_29689_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g38_29689/03_2024/8g38_29689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g38_29689/03_2024/8g38_29689.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g38_29689/03_2024/8g38_29689.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g38_29689/03_2024/8g38_29689_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g38_29689/03_2024/8g38_29689_updated.pdb" } resolution = 3.2 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= 0.005 sd= 0.052 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 4559 5.49 5 S 146 5.16 5 C 72714 2.51 5 N 26901 2.21 5 O 39970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 103": "OD1" <-> "OD2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F ASP 55": "OD1" <-> "OD2" Residue "F PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 146": "OD1" <-> "OD2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G ASP 59": "OD1" <-> "OD2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "J ASP 14": "OD1" <-> "OD2" Residue "J TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 55": "OD1" <-> "OD2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O ASP 69": "OD1" <-> "OD2" Residue "O PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q ASP 101": "OD1" <-> "OD2" Residue "Q GLU 110": "OE1" <-> "OE2" Residue "S TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 42": "OE1" <-> "OE2" Residue "T ASP 79": "OD1" <-> "OD2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 8": "OD1" <-> "OD2" Residue "V GLU 55": "OE1" <-> "OE2" Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 28": "OE1" <-> "OE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 5": "OE1" <-> "OE2" Residue "Y GLU 12": "OE1" <-> "OE2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 81": "OD1" <-> "OD2" Residue "w GLU 174": "OE1" <-> "OE2" Residue "x PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 35": "OD1" <-> "OD2" Residue "x ASP 180": "OD1" <-> "OD2" Residue "x TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 165": "OE1" <-> "OE2" Residue "c ASP 173": "OD1" <-> "OD2" Residue "c GLU 196": "OE1" <-> "OE2" Residue "d GLU 9": "OE1" <-> "OE2" Residue "e TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 65": "OE1" <-> "OE2" Residue "e GLU 69": "OE1" <-> "OE2" Residue "f GLU 62": "OE1" <-> "OE2" Residue "f GLU 89": "OE1" <-> "OE2" Residue "f GLU 138": "OE1" <-> "OE2" Residue "g GLU 59": "OE1" <-> "OE2" Residue "g TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 89": "OD1" <-> "OD2" Residue "i TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 40": "OE1" <-> "OE2" Residue "m GLU 9": "OE1" <-> "OE2" Residue "m ASP 32": "OD1" <-> "OD2" Residue "n GLU 5": "OE1" <-> "OE2" Residue "n GLU 25": "OE1" <-> "OE2" Residue "o PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 48": "OE1" <-> "OE2" Residue "p PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 72": "OE1" <-> "OE2" Residue "s ASP 42": "OD1" <-> "OD2" Residue "u GLU 154": "OE1" <-> "OE2" Residue "6 GLU 9": "OE1" <-> "OE2" Residue "6 GLU 40": "OE1" <-> "OE2" Residue "6 GLU 97": "OE1" <-> "OE2" Residue "6 ASP 226": "OD1" <-> "OD2" Residue "6 PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 240": "OD1" <-> "OD2" Residue "6 ASP 243": "OD1" <-> "OD2" Residue "6 GLU 293": "OE1" <-> "OE2" Residue "6 ASP 306": "OD1" <-> "OD2" Residue "6 GLU 390": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 144290 Number of models: 1 Model: "" Number of chains: 53 Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2504 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 56, 'rna3p_pyr': 49} Link IDs: {'rna2p': 11, 'rna3p': 105} Chain: "B" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 267, 'rna2p_pyr': 156, 'rna3p_pur': 1407, 'rna3p_pyr': 1073} Link IDs: {'rna2p': 423, 'rna3p': 2479} Chain breaks: 1 Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1420 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 780 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 596 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "w" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "x" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "c" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1642 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "d" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1106 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "e" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "f" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "g" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "h" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "i" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "j" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "k" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "l" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "m" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "n" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "o" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "q" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "r" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "s" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "t" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 426 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "u" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 468 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "v" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 126, 'rna2p_pyr': 100, 'rna3p_pur': 748, 'rna3p_pyr': 565} Link IDs: {'rna2p': 225, 'rna3p': 1313} Chain: "6" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3403 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 52.44, per 1000 atoms: 0.36 Number of scatterers: 144290 At special positions: 0 Unit cell: (250.173, 265.553, 264.527, 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 146 16.00 P 4559 15.00 O 39970 8.00 N 26901 7.00 C 72714 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: 55.98 Conformation dependent library (CDL) restraints added in 6.6 seconds 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10882 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 177 helices and 63 sheets defined 38.0% alpha, 16.2% beta 1457 base pairs and 2505 stacking pairs defined. Time for finding SS restraints: 72.07 Creating SS restraints... Processing helix chain '0' and resid 8 through 20 removed outlier: 4.539A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP 0 19 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) Processing helix chain '1' and resid 25 through 30 Proline residue: 1 30 - end of helix Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.034A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '3' and resid 6 through 13 Processing helix chain '3' and resid 31 through 36 removed outlier: 5.195A pdb=" N LYS 3 35 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALA 3 36 " --> pdb=" O LEU 3 32 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 31 through 36' Processing helix chain '3' and resid 37 through 45 Proline residue: 3 45 - end of helix Processing helix chain '3' and resid 50 through 62 removed outlier: 6.353A pdb=" N LEU 3 54 " --> pdb=" O SER 3 50 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLY 3 55 " --> pdb=" O LYS 3 51 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU 3 56 " --> pdb=" O GLY 3 52 " (cutoff:3.500A) Proline residue: 3 62 - end of helix Processing helix chain 'C' and resid 9 through 15 removed outlier: 7.482A pdb=" N HIS C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N VAL C 15 " --> pdb=" O GLY C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 Proline residue: C 135 - end of helix Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.734A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 225 removed outlier: 4.901A pdb=" N ASN C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 267 removed outlier: 4.334A pdb=" N ASP C 263 " --> pdb=" O ASN C 259 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N PHE C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 6.571A pdb=" N VAL D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 61' Processing helix chain 'D' and resid 62 through 72 removed outlier: 5.050A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY D 72 " --> pdb=" O PHE D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 removed outlier: 3.978A pdb=" N PHE D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LYS D 105 " --> pdb=" O PHE D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 41 removed outlier: 5.553A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 165 removed outlier: 4.339A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N HIS E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 removed outlier: 5.568A pdb=" N ASP E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 1 through 18 removed outlier: 5.917A pdb=" N GLU F 10 " --> pdb=" O TYR F 6 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL F 11 " --> pdb=" O TYR F 7 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU F 15 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N MET F 16 " --> pdb=" O VAL F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 28 Proline residue: F 28 - end of helix Processing helix chain 'F' and resid 46 through 57 Processing helix chain 'F' and resid 92 through 107 Processing helix chain 'F' and resid 161 through 169 removed outlier: 4.003A pdb=" N GLY F 165 " --> pdb=" O SER F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 4.271A pdb=" N SER F 120 " --> pdb=" O SER F 117 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N PHE F 121 " --> pdb=" O ALA F 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 7 Proline residue: G 7 - end of helix Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 136 through 152 removed outlier: 4.059A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.695A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 removed outlier: 4.076A pdb=" N ARG J 96 " --> pdb=" O MET J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 109 removed outlier: 4.602A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 123 removed outlier: 3.754A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 119 removed outlier: 4.719A pdb=" N LYS K 113 " --> pdb=" O GLU K 109 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE K 114 " --> pdb=" O LYS K 110 " (cutoff:3.500A) Proline residue: K 119 - end of helix Processing helix chain 'L' and resid 37 through 42 removed outlier: 5.223A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 6.839A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 86 removed outlier: 3.744A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 138 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.704A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.957A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.619A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 81 Processing helix chain 'N' and resid 82 through 88 removed outlier: 4.094A pdb=" N ARG N 86 " --> pdb=" O GLU N 82 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 20 removed outlier: 4.627A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 1 through 12 removed outlier: 4.655A pdb=" N LYS P 5 " --> pdb=" O SER P 1 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN P 6 " --> pdb=" O ASN P 2 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLU P 8 " --> pdb=" O ILE P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 102 removed outlier: 3.801A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 21 Processing helix chain 'Q' and resid 25 through 30 removed outlier: 4.001A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 72 removed outlier: 4.236A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 86 removed outlier: 4.787A pdb=" N SER Q 86 " --> pdb=" O LEU Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 101 removed outlier: 4.548A pdb=" N ASP Q 96 " --> pdb=" O LYS Q 92 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE Q 97 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ALA Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 117 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.935A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 3.662A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.447A pdb=" N ASN S 61 " --> pdb=" O ASN S 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 9 removed outlier: 4.025A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 28 Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'U' and resid 65 through 70 removed outlier: 3.686A pdb=" N VAL U 69 " --> pdb=" O GLN U 65 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ALA U 70 " --> pdb=" O VAL U 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 65 through 70' Processing helix chain 'V' and resid 13 through 24 Processing helix chain 'V' and resid 43 through 54 removed outlier: 3.729A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ALA V 54 " --> pdb=" O MET V 50 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 44 removed outlier: 4.621A pdb=" N LYS W 43 " --> pdb=" O GLN W 39 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 Processing helix chain 'X' and resid 63 through 74 Processing helix chain 'Y' and resid 5 through 10 removed outlier: 3.503A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 5 through 10' Processing helix chain 'Y' and resid 12 through 35 removed outlier: 3.670A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU Y 24 " --> pdb=" O ASN Y 20 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 38 through 60 removed outlier: 3.925A pdb=" N LEU Y 42 " --> pdb=" O GLN Y 38 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 Processing helix chain 'w' and resid 23 through 31 removed outlier: 4.117A pdb=" N LYS w 27 " --> pdb=" O ASN w 23 " (cutoff:3.500A) Proline residue: w 28 - end of helix removed outlier: 5.536A pdb=" N PHE w 31 " --> pdb=" O LYS w 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 23 through 31' Processing helix chain 'w' and resid 41 through 59 Proline residue: w 47 - end of helix Processing helix chain 'w' and resid 75 through 82 removed outlier: 4.052A pdb=" N ASP w 81 " --> pdb=" O GLU w 77 " (cutoff:3.500A) Processing helix chain 'w' and resid 102 through 120 removed outlier: 3.703A pdb=" N GLN w 108 " --> pdb=" O LYS w 104 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLN w 119 " --> pdb=" O ASP w 115 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER w 120 " --> pdb=" O LEU w 116 " (cutoff:3.500A) Processing helix chain 'w' and resid 123 through 129 removed outlier: 5.294A pdb=" N LEU w 128 " --> pdb=" O THR w 124 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR w 129 " --> pdb=" O PHE w 125 " (cutoff:3.500A) Processing helix chain 'w' and resid 132 through 148 Processing helix chain 'w' and resid 149 through 154 Processing helix chain 'w' and resid 164 through 169 Processing helix chain 'w' and resid 170 through 179 Processing helix chain 'w' and resid 205 through 219 removed outlier: 5.236A pdb=" N THR w 219 " --> pdb=" O ALA w 215 " (cutoff:3.500A) Processing helix chain 'w' and resid 10 through 15 removed outlier: 4.860A pdb=" N VAL w 13 " --> pdb=" O LYS w 10 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N HIS w 14 " --> pdb=" O ALA w 11 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N PHE w 15 " --> pdb=" O GLY w 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 10 through 15' Processing helix chain 'x' and resid 5 through 11 Processing helix chain 'x' and resid 27 through 47 Processing helix chain 'x' and resid 71 through 77 removed outlier: 4.086A pdb=" N VAL x 75 " --> pdb=" O ARG x 71 " (cutoff:3.500A) Processing helix chain 'x' and resid 80 through 95 Processing helix chain 'x' and resid 107 through 112 removed outlier: 3.715A pdb=" N ASP x 111 " --> pdb=" O LYS x 107 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ALA x 112 " --> pdb=" O PRO x 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 107 through 112' Processing helix chain 'x' and resid 113 through 126 Processing helix chain 'x' and resid 128 through 144 Processing helix chain 'c' and resid 6 through 15 removed outlier: 4.575A pdb=" N LEU c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER c 11 " --> pdb=" O LYS c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 48 through 65 Processing helix chain 'c' and resid 67 through 82 removed outlier: 5.250A pdb=" N LYS c 82 " --> pdb=" O ALA c 78 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 97 removed outlier: 5.992A pdb=" N LEU c 97 " --> pdb=" O LEU c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 98 through 105 Processing helix chain 'c' and resid 109 through 120 removed outlier: 3.893A pdb=" N LYS c 120 " --> pdb=" O LEU c 116 " (cutoff:3.500A) Processing helix chain 'c' and resid 151 through 165 removed outlier: 5.066A pdb=" N GLU c 165 " --> pdb=" O ALA c 161 " (cutoff:3.500A) Processing helix chain 'c' and resid 186 through 191 Processing helix chain 'c' and resid 195 through 205 removed outlier: 4.050A pdb=" N ILE c 199 " --> pdb=" O ASN c 195 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 70 removed outlier: 4.641A pdb=" N ASN d 69 " --> pdb=" O LYS d 65 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N MET d 70 " --> pdb=" O ALA d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 118 removed outlier: 6.953A pdb=" N ALA d 112 " --> pdb=" O GLY d 108 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N VAL d 113 " --> pdb=" O ALA d 109 " (cutoff:3.500A) Processing helix chain 'd' and resid 131 through 147 removed outlier: 4.601A pdb=" N ARG d 137 " --> pdb=" O ILE d 133 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA d 138 " --> pdb=" O ASN d 134 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE d 140 " --> pdb=" O VAL d 136 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASN d 147 " --> pdb=" O LEU d 143 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 157 Processing helix chain 'e' and resid 14 through 33 removed outlier: 4.239A pdb=" N VAL e 18 " --> pdb=" O GLN e 14 " (cutoff:3.500A) Proline residue: e 19 - end of helix Processing helix chain 'e' and resid 67 through 81 removed outlier: 3.657A pdb=" N ILE e 71 " --> pdb=" O PRO e 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 19 through 30 Processing helix chain 'f' and resid 34 through 54 Processing helix chain 'f' and resid 56 through 69 Processing helix chain 'f' and resid 91 through 111 removed outlier: 5.241A pdb=" N GLY f 111 " --> pdb=" O ALA f 107 " (cutoff:3.500A) Processing helix chain 'f' and resid 114 through 129 Processing helix chain 'f' and resid 131 through 148 Processing helix chain 'g' and resid 4 through 20 Processing helix chain 'g' and resid 29 through 43 Processing helix chain 'g' and resid 111 through 119 Processing helix chain 'h' and resid 33 through 38 Processing helix chain 'h' and resid 41 through 53 removed outlier: 4.058A pdb=" N MET h 45 " --> pdb=" O GLU h 41 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL h 46 " --> pdb=" O THR h 42 " (cutoff:3.500A) Proline residue: h 50 - end of helix Processing helix chain 'h' and resid 56 through 61 removed outlier: 5.428A pdb=" N LEU h 60 " --> pdb=" O MET h 56 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP h 61 " --> pdb=" O VAL h 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 56 through 61' Processing helix chain 'h' and resid 70 through 90 Processing helix chain 'h' and resid 93 through 101 Processing helix chain 'i' and resid 14 through 33 Processing helix chain 'i' and resid 80 through 87 Processing helix chain 'j' and resid 45 through 50 Processing helix chain 'j' and resid 53 through 59 Proline residue: j 59 - end of helix Processing helix chain 'j' and resid 60 through 75 removed outlier: 4.742A pdb=" N GLU j 75 " --> pdb=" O ASP j 71 " (cutoff:3.500A) Processing helix chain 'j' and resid 91 through 103 Processing helix chain 'k' and resid 2 through 10 Proline residue: k 10 - end of helix Processing helix chain 'k' and resid 112 through 117 removed outlier: 4.992A pdb=" N TYR k 116 " --> pdb=" O ALA k 112 " (cutoff:3.500A) Processing helix chain 'l' and resid 13 through 22 removed outlier: 4.077A pdb=" N ALA l 17 " --> pdb=" O HIS l 13 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR l 22 " --> pdb=" O LEU l 18 " (cutoff:3.500A) Processing helix chain 'l' and resid 25 through 37 removed outlier: 4.155A pdb=" N SER l 29 " --> pdb=" O GLY l 25 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 63 removed outlier: 4.269A pdb=" N VAL l 63 " --> pdb=" O VAL l 59 " (cutoff:3.500A) Processing helix chain 'l' and resid 66 through 83 removed outlier: 4.283A pdb=" N ARG l 70 " --> pdb=" O GLY l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 84 through 93 removed outlier: 4.038A pdb=" N LEU l 88 " --> pdb=" O CYS l 84 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS l 90 " --> pdb=" O ARG l 86 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY l 93 " --> pdb=" O ARG l 89 " (cutoff:3.500A) Processing helix chain 'l' and resid 105 through 110 Processing helix chain 'm' and resid 2 through 17 Processing helix chain 'm' and resid 20 through 33 removed outlier: 6.212A pdb=" N ALA m 24 " --> pdb=" O PHE m 20 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU m 25 " --> pdb=" O ALA m 21 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N VAL m 33 " --> pdb=" O ILE m 29 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 52 Proline residue: m 52 - end of helix Processing helix chain 'm' and resid 80 through 91 Processing helix chain 'n' and resid 3 through 15 Processing helix chain 'n' and resid 23 through 43 removed outlier: 3.788A pdb=" N GLY n 40 " --> pdb=" O ASN n 36 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 73 removed outlier: 3.721A pdb=" N GLY n 54 " --> pdb=" O HIS n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 74 through 85 Processing helix chain 'o' and resid 53 through 64 Processing helix chain 'o' and resid 68 through 79 removed outlier: 4.022A pdb=" N ASN o 79 " --> pdb=" O ILE o 75 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 33 removed outlier: 3.991A pdb=" N ASN q 30 " --> pdb=" O ALA q 26 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR q 31 " --> pdb=" O THR q 27 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N THR q 33 " --> pdb=" O LYS q 29 " (cutoff:3.500A) Processing helix chain 'q' and resid 40 through 45 Processing helix chain 'q' and resid 47 through 65 Processing helix chain 'r' and resid 11 through 25 Processing helix chain 'r' and resid 69 through 75 removed outlier: 4.565A pdb=" N PHE r 73 " --> pdb=" O LYS r 69 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA r 74 " --> pdb=" O LEU r 70 " (cutoff:3.500A) Proline residue: r 75 - end of helix No H-bonds generated for 'chain 'r' and resid 69 through 75' Processing helix chain 's' and resid 7 through 40 Processing helix chain 's' and resid 43 through 64 Proline residue: s 55 - end of helix Processing helix chain 's' and resid 67 through 86 removed outlier: 6.145A pdb=" N ALA s 71 " --> pdb=" O HIS s 67 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA s 86 " --> pdb=" O ILE s 82 " (cutoff:3.500A) Processing helix chain 't' and resid 23 through 34 removed outlier: 4.625A pdb=" N ARG t 33 " --> pdb=" O ALA t 29 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ARG t 34 " --> pdb=" O GLU t 30 " (cutoff:3.500A) Processing helix chain 't' and resid 37 through 53 removed outlier: 6.031A pdb=" N THR t 41 " --> pdb=" O TYR t 37 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR t 42 " --> pdb=" O GLU t 38 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LYS t 53 " --> pdb=" O ALA t 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 174 through 179 removed outlier: 4.685A pdb=" N GLU u 179 " --> pdb=" O PHE u 175 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 38 Processing helix chain '6' and resid 59 through 74 Processing helix chain '6' and resid 85 through 97 removed outlier: 5.036A pdb=" N GLU 6 97 " --> pdb=" O GLU 6 93 " (cutoff:3.500A) Processing helix chain '6' and resid 102 through 115 Processing helix chain '6' and resid 117 through 136 removed outlier: 3.635A pdb=" N THR 6 134 " --> pdb=" O ARG 6 130 " (cutoff:3.500A) Processing helix chain '6' and resid 137 through 148 removed outlier: 3.755A pdb=" N THR 6 141 " --> pdb=" O VAL 6 137 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS 6 142 " --> pdb=" O ARG 6 138 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN 6 146 " --> pdb=" O HIS 6 142 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS 6 147 " --> pdb=" O LEU 6 143 " (cutoff:3.500A) Processing helix chain '6' and resid 158 through 190 removed outlier: 4.352A pdb=" N THR 6 162 " --> pdb=" O THR 6 158 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP 6 163 " --> pdb=" O GLN 6 159 " (cutoff:3.500A) Processing helix chain '6' and resid 210 through 218 removed outlier: 4.436A pdb=" N PHE 6 214 " --> pdb=" O LYS 6 210 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN 6 215 " --> pdb=" O SER 6 211 " (cutoff:3.500A) Processing helix chain '6' and resid 260 through 272 Processing helix chain '6' and resid 290 through 306 removed outlier: 3.840A pdb=" N ASN 6 294 " --> pdb=" O ARG 6 290 " (cutoff:3.500A) Processing helix chain '6' and resid 318 through 323 Processing helix chain '6' and resid 349 through 362 removed outlier: 4.395A pdb=" N LEU 6 353 " --> pdb=" O GLY 6 349 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N SER 6 362 " --> pdb=" O THR 6 358 " (cutoff:3.500A) Processing helix chain '6' and resid 375 through 387 Processing helix chain '6' and resid 406 through 414 Processing sheet with id= 1, first strand: chain '1' and resid 19 through 23 removed outlier: 6.052A pdb=" N LYS 1 9 " --> pdb=" O ALA 1 51 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA 1 51 " --> pdb=" O LYS 1 9 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL 1 11 " --> pdb=" O LYS 1 49 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '3' and resid 21 through 24 removed outlier: 5.499A pdb=" N PHE 3 21 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '4' and resid 13 through 18 removed outlier: 8.283A pdb=" N ASN 4 13 " --> pdb=" O SER 4 28 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER 4 28 " --> pdb=" O ASN 4 13 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 1 through 4 Processing sheet with id= 5, first strand: chain 'C' and resid 32 through 35 No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'C' and resid 99 through 104 removed outlier: 4.340A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASP C 113 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 137 through 141 removed outlier: 4.359A pdb=" N SER C 138 " --> pdb=" O ILE C 163 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 170 through 175 removed outlier: 4.230A pdb=" N GLU C 179 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 3 through 7 removed outlier: 7.022A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 10 through 15 removed outlier: 3.526A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 32 through 35 removed outlier: 6.615A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 47 through 51 Processing sheet with id= 13, first strand: chain 'E' and resid 2 through 5 removed outlier: 3.665A pdb=" N LEU E 3 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 117 through 120 Processing sheet with id= 15, first strand: chain 'F' and resid 64 through 67 removed outlier: 3.622A pdb=" N LEU F 65 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE F 84 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE F 33 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N THR F 156 " --> pdb=" O LYS F 32 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY F 38 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLY F 150 " --> pdb=" O GLY F 38 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU F 151 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL F 131 " --> pdb=" O LEU F 151 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 15 through 18 Processing sheet with id= 17, first strand: chain 'G' and resid 40 through 44 Processing sheet with id= 18, first strand: chain 'G' and resid 81 through 85 removed outlier: 4.321A pdb=" N GLY G 81 " --> pdb=" O GLY G 134 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLY G 134 " --> pdb=" O GLY G 81 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR G 83 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU G 132 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE G 130 " --> pdb=" O LYS G 85 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 93 through 97 Processing sheet with id= 20, first strand: chain 'J' and resid 52 through 57 removed outlier: 5.288A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.347A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'K' and resid 17 through 20 removed outlier: 4.227A pdb=" N THR K 5 " --> pdb=" O CYS K 20 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ASN K 81 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU K 85 " --> pdb=" O ALA K 10 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.878A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.488A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N TYR N 94 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.542A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'P' and resid 37 through 45 removed outlier: 3.675A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'P' and resid 56 through 63 removed outlier: 7.420A pdb=" N SER P 56 " --> pdb=" O THR P 75 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.931A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.283A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.687A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'S' and resid 73 through 79 removed outlier: 4.904A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'T' and resid 29 through 34 removed outlier: 3.526A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLY T 71 " --> pdb=" O GLN T 72 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE T 74 " --> pdb=" O ARG T 69 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ARG T 69 " --> pdb=" O ILE T 74 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG T 76 " --> pdb=" O VAL T 67 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL T 67 " --> pdb=" O ARG T 76 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N SER T 78 " --> pdb=" O GLY T 65 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLY T 65 " --> pdb=" O SER T 78 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'U' and resid 39 through 45 removed outlier: 4.777A pdb=" N ASN U 39 " --> pdb=" O ALA U 62 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'U' and resid 82 through 86 removed outlier: 5.895A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.981A pdb=" N THR V 62 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ILE V 29 " --> pdb=" O ILE V 89 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'W' and resid 64 through 70 Processing sheet with id= 37, first strand: chain 'X' and resid 11 through 17 removed outlier: 3.937A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'Z' and resid 34 through 38 removed outlier: 6.941A pdb=" N MET Z 53 " --> pdb=" O THR Z 9 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'w' and resid 158 through 161 Processing sheet with id= 40, first strand: chain 'x' and resid 52 through 58 removed outlier: 3.595A pdb=" N ARG x 53 " --> pdb=" O HIS x 68 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'x' and resid 163 through 168 removed outlier: 5.603A pdb=" N ARG x 163 " --> pdb=" O GLY x 154 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'c' and resid 140 through 144 removed outlier: 6.906A pdb=" N MET c 177 " --> pdb=" O ILE c 144 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'd' and resid 11 through 15 removed outlier: 6.789A pdb=" N LEU d 35 " --> pdb=" O ILE d 15 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'd' and resid 83 through 87 removed outlier: 4.032A pdb=" N ALA d 98 " --> pdb=" O ASN d 121 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ASN d 121 " --> pdb=" O ALA d 98 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'd' and resid 32 through 39 Processing sheet with id= 46, first strand: chain 'e' and resid 38 through 42 removed outlier: 3.632A pdb=" N ARG e 38 " --> pdb=" O ASN e 63 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN e 63 " --> pdb=" O ARG e 38 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N TYR e 59 " --> pdb=" O TRP e 42 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILE e 6 " --> pdb=" O MET e 62 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU e 5 " --> pdb=" O MET e 90 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG e 86 " --> pdb=" O MET e 9 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'e' and resid 43 through 47 removed outlier: 7.133A pdb=" N HIS e 55 " --> pdb=" O LEU e 47 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'f' and resid 72 through 76 Processing sheet with id= 49, first strand: chain 'g' and resid 22 through 28 removed outlier: 6.201A pdb=" N ALA g 22 " --> pdb=" O LEU g 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP g 47 " --> pdb=" O THR g 61 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'g' and resid 73 through 76 removed outlier: 6.635A pdb=" N VAL g 102 " --> pdb=" O ILE g 125 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'h' and resid 6 through 10 No H-bonds generated for sheet with id= 51 Processing sheet with id= 52, first strand: chain 'i' and resid 39 through 42 removed outlier: 4.142A pdb=" N LEU i 71 " --> pdb=" O LEU i 42 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL i 74 " --> pdb=" O ILE i 8 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE i 8 " --> pdb=" O VAL i 74 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'j' and resid 41 through 44 Processing sheet with id= 54, first strand: chain 'k' and resid 29 through 33 removed outlier: 5.015A pdb=" N SER k 77 " --> pdb=" O CYS k 33 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU k 80 " --> pdb=" O VAL k 97 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N HIS k 95 " --> pdb=" O ARG k 82 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'k' and resid 50 through 55 removed outlier: 4.932A pdb=" N LYS k 50 " --> pdb=" O ILE k 66 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'o' and resid 4 through 10 removed outlier: 5.838A pdb=" N PHE o 16 " --> pdb=" O HIS o 9 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N GLY o 49 " --> pdb=" O ASN o 40 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'p' and resid 6 through 10 removed outlier: 3.897A pdb=" N GLU p 59 " --> pdb=" O VAL p 75 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL p 75 " --> pdb=" O GLU p 59 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG p 61 " --> pdb=" O THR p 73 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'p' and resid 18 through 29 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'r' and resid 29 through 32 removed outlier: 3.959A pdb=" N VAL r 57 " --> pdb=" O VAL r 50 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'u' and resid 158 through 164 removed outlier: 3.543A pdb=" N VAL u 160 " --> pdb=" O VAL u 171 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain '6' and resid 43 through 47 removed outlier: 5.202A pdb=" N GLN 6 43 " --> pdb=" O ALA 6 11 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY 6 47 " --> pdb=" O HIS 6 15 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain '6' and resid 234 through 241 removed outlier: 4.173A pdb=" N THR 6 235 " --> pdb=" O ASP 6 251 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG 6 237 " --> pdb=" O LEU 6 249 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU 6 249 " --> pdb=" O ARG 6 237 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL 6 248 " --> pdb=" O PRO 6 198 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLY 6 204 " --> pdb=" O THR 6 252 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU 6 313 " --> pdb=" O LEU 6 280 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N HIS 6 282 " --> pdb=" O LEU 6 313 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain '6' and resid 391 through 396 removed outlier: 7.312A pdb=" N LYS 6 391 " --> pdb=" O GLN 6 403 " (cutoff:3.500A) 1848 hydrogen bonds defined for protein. 5466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3686 hydrogen bonds 5824 hydrogen bond angles 0 basepair planarities 1457 basepair parallelities 2505 stacking parallelities Total time for adding SS restraints: 248.06 Time building geometry restraints manager: 61.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.39 - 0.79: 1 0.79 - 1.18: 8 1.18 - 1.58: 147398 1.58 - 1.98: 9263 1.98 - 2.37: 1 Warning: very small bond lengths. Bond restraints: 156671 Sorted by residual: bond pdb=" CG PRO l 9 " pdb=" CD PRO l 9 " ideal model delta sigma weight residual 1.503 0.389 1.114 3.40e-02 8.65e+02 1.07e+03 bond pdb=" CB PRO l 9 " pdb=" CG PRO l 9 " ideal model delta sigma weight residual 1.492 2.375 -0.883 5.00e-02 4.00e+02 3.12e+02 bond pdb=" CG1 ILE w 199 " pdb=" CD1 ILE w 199 " ideal model delta sigma weight residual 1.513 1.237 0.276 3.90e-02 6.57e+02 5.00e+01 bond pdb=" O5' G B1753 " pdb=" C5' G B1753 " ideal model delta sigma weight residual 1.420 1.318 0.102 1.50e-02 4.44e+03 4.65e+01 bond pdb=" CG1 ILE F 84 " pdb=" CD1 ILE F 84 " ideal model delta sigma weight residual 1.513 1.256 0.257 3.90e-02 6.57e+02 4.34e+01 ... (remaining 156666 not shown) Histogram of bond angle deviations from ideal: 0.24 - 28.48: 1 28.48 - 56.71: 0 56.71 - 84.95: 3 84.95 - 113.18: 115883 113.18 - 141.41: 118259 Bond angle restraints: 234146 Sorted by residual: angle pdb=" CB PRO l 9 " pdb=" CG PRO l 9 " pdb=" CD PRO l 9 " ideal model delta sigma weight residual 106.10 0.24 105.86 3.20e+00 9.77e-02 1.09e+03 angle pdb=" CA PRO l 9 " pdb=" CB PRO l 9 " pdb=" CG PRO l 9 " ideal model delta sigma weight residual 104.50 74.52 29.98 1.90e+00 2.77e-01 2.49e+02 angle pdb=" O ILE l 8 " pdb=" C ILE l 8 " pdb=" N PRO l 9 " ideal model delta sigma weight residual 121.69 113.48 8.21 6.30e-01 2.52e+00 1.70e+02 angle pdb=" CA PRO l 9 " pdb=" N PRO l 9 " pdb=" CD PRO l 9 " ideal model delta sigma weight residual 112.00 95.59 16.41 1.40e+00 5.10e-01 1.37e+02 angle pdb=" N PRO F 28 " pdb=" CD PRO F 28 " pdb=" CG PRO F 28 " ideal model delta sigma weight residual 103.20 87.95 15.25 1.50e+00 4.44e-01 1.03e+02 ... (remaining 234141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 86131 35.97 - 71.94: 12854 71.94 - 107.92: 1267 107.92 - 143.89: 17 143.89 - 179.86: 46 Dihedral angle restraints: 100315 sinusoidal: 83452 harmonic: 16863 Sorted by residual: dihedral pdb=" O4' C B2858 " pdb=" C1' C B2858 " pdb=" N1 C B2858 " pdb=" C2 C B2858 " ideal model delta sinusoidal sigma weight residual 200.00 20.33 179.67 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U B2477 " pdb=" C1' U B2477 " pdb=" N1 U B2477 " pdb=" C2 U B2477 " ideal model delta sinusoidal sigma weight residual -160.00 17.16 -177.16 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 26 " pdb=" C1' C A 26 " pdb=" N1 C A 26 " pdb=" C2 C A 26 " ideal model delta sinusoidal sigma weight residual -160.00 9.41 -169.41 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 100312 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.997: 29867 0.997 - 1.994: 0 1.994 - 2.991: 0 2.991 - 3.988: 0 3.988 - 4.985: 1 Chirality restraints: 29868 Sorted by residual: chirality pdb=" C4' GTP 6 501 " pdb=" C3' GTP 6 501 " pdb=" C5' GTP 6 501 " pdb=" O4' GTP 6 501 " both_signs ideal model delta sigma weight residual False -2.47 2.51 -4.99 2.00e-01 2.50e+01 6.21e+02 chirality pdb=" CB THR N 70 " pdb=" CA THR N 70 " pdb=" OG1 THR N 70 " pdb=" CG2 THR N 70 " both_signs ideal model delta sigma weight residual False 2.55 1.72 0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" CB ILE l 8 " pdb=" CA ILE l 8 " pdb=" CG1 ILE l 8 " pdb=" CG2 ILE l 8 " both_signs ideal model delta sigma weight residual False 2.64 1.94 0.70 2.00e-01 2.50e+01 1.24e+01 ... (remaining 29865 not shown) Planarity restraints: 12746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 225 " -0.122 5.00e-02 4.00e+02 1.78e-01 5.06e+01 pdb=" N PRO C 226 " 0.307 5.00e-02 4.00e+02 pdb=" CA PRO C 226 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO C 226 " -0.090 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG W 38 " 0.572 9.50e-02 1.11e+02 2.57e-01 4.09e+01 pdb=" NE ARG W 38 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG W 38 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG W 38 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG W 38 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 6 " 0.099 5.00e-02 4.00e+02 1.46e-01 3.43e+01 pdb=" N PRO G 7 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO G 7 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO G 7 " 0.076 5.00e-02 4.00e+02 ... (remaining 12743 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.65: 5 1.65 - 2.47: 305 2.47 - 3.28: 137301 3.28 - 4.09: 493032 4.09 - 4.90: 721585 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1352228 Sorted by model distance: nonbonded pdb=" OP2 G B1907 " pdb=" N4 C B1920 " model vdw 0.842 2.520 nonbonded pdb=" N4 C B1908 " pdb=" C6 C B1920 " model vdw 1.124 3.420 nonbonded pdb=" N4 C B1908 " pdb=" C5 C B1920 " model vdw 1.244 3.420 nonbonded pdb=" CD LYS 6 210 " pdb=" ND2 ASN 6 317 " model vdw 1.516 3.520 nonbonded pdb=" OP2 G B1907 " pdb=" C4 C B1920 " model vdw 1.648 3.260 ... (remaining 1352223 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: 1.710 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: 13.440 Check model and map are aligned: 1.530 Set scattering table: 0.960 Process input model: 531.770 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 555.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 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 : 0.009 1.114 156671 Z= 0.492 Angle : 1.098 105.856 234146 Z= 0.568 Chirality : 0.070 4.985 29868 Planarity : 0.009 0.257 12746 Dihedral : 25.058 179.860 89433 Min Nonbonded Distance : 0.842 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.42 % Favored : 96.51 % Rotamer: Outliers : 4.67 % Allowed : 31.65 % Favored : 63.68 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.04 (0.10), residues: 5816 helix: -0.30 (0.10), residues: 1932 sheet: 0.44 (0.17), residues: 930 loop : -1.32 (0.10), residues: 2954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP F 96 HIS 0.051 0.003 HIS R 82 PHE 0.070 0.004 PHE C 239 TYR 0.063 0.003 TYR F 21 ARG 0.037 0.001 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 452 time to evaluate : 5.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 39 ARG cc_start: 0.7846 (ttm170) cc_final: 0.7601 (tpp-160) REVERT: 6 104 THR cc_start: 0.6218 (OUTLIER) cc_final: 0.5274 (t) REVERT: 6 126 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6719 (tp) REVERT: 6 129 LEU cc_start: 0.4715 (OUTLIER) cc_final: 0.4413 (tp) REVERT: 6 271 LEU cc_start: 0.5030 (OUTLIER) cc_final: 0.4646 (mm) REVERT: 6 353 LEU cc_start: 0.5042 (OUTLIER) cc_final: 0.4758 (mp) REVERT: 6 355 GLN cc_start: 0.5688 (OUTLIER) cc_final: 0.5437 (tt0) REVERT: 6 367 GLN cc_start: -0.0518 (OUTLIER) cc_final: -0.0980 (tm-30) REVERT: 6 387 GLN cc_start: 0.3485 (OUTLIER) cc_final: 0.3027 (tm130) REVERT: 6 408 ILE cc_start: -0.0730 (OUTLIER) cc_final: -0.0955 (tp) REVERT: 6 413 ARG cc_start: 0.1031 (OUTLIER) cc_final: 0.0780 (mtm-85) outliers start: 227 outliers final: 121 residues processed: 638 average time/residue: 1.4028 time to fit residues: 1522.0814 Evaluate side-chains 578 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 447 time to evaluate : 5.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 7 TYR Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain T residue 25 GLU Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain U residue 42 LYS Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 43 ASP Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain f residue 143 MET Chi-restraints excluded: chain g residue 124 ILE Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain r residue 61 VAL Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 3 ASP Chi-restraints excluded: chain 6 residue 4 ARG Chi-restraints excluded: chain 6 residue 6 ASP Chi-restraints excluded: chain 6 residue 10 GLN Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 17 TYR Chi-restraints excluded: chain 6 residue 26 ASP Chi-restraints excluded: chain 6 residue 36 SER Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 50 LYS Chi-restraints excluded: chain 6 residue 53 HIS Chi-restraints excluded: chain 6 residue 55 LYS Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 62 LYS Chi-restraints excluded: chain 6 residue 68 GLU Chi-restraints excluded: chain 6 residue 77 VAL Chi-restraints excluded: chain 6 residue 88 GLN Chi-restraints excluded: chain 6 residue 89 GLU Chi-restraints excluded: chain 6 residue 90 ARG Chi-restraints excluded: chain 6 residue 95 LEU Chi-restraints excluded: chain 6 residue 97 GLU Chi-restraints excluded: chain 6 residue 98 CYS Chi-restraints excluded: chain 6 residue 104 THR Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 6 residue 107 ILE Chi-restraints excluded: chain 6 residue 108 LEU Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 116 ARG Chi-restraints excluded: chain 6 residue 117 THR Chi-restraints excluded: chain 6 residue 119 GLU Chi-restraints excluded: chain 6 residue 121 LYS Chi-restraints excluded: chain 6 residue 123 GLN Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 129 LEU Chi-restraints excluded: chain 6 residue 134 THR Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 150 ILE Chi-restraints excluded: chain 6 residue 163 ASP Chi-restraints excluded: chain 6 residue 167 LEU Chi-restraints excluded: chain 6 residue 168 ARG Chi-restraints excluded: chain 6 residue 174 ILE Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 182 GLU Chi-restraints excluded: chain 6 residue 183 LYS Chi-restraints excluded: chain 6 residue 191 SER Chi-restraints excluded: chain 6 residue 194 LYS Chi-restraints excluded: chain 6 residue 202 LEU Chi-restraints excluded: chain 6 residue 206 THR Chi-restraints excluded: chain 6 residue 210 LYS Chi-restraints excluded: chain 6 residue 212 THR Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 217 ILE Chi-restraints excluded: chain 6 residue 222 VAL Chi-restraints excluded: chain 6 residue 228 LEU Chi-restraints excluded: chain 6 residue 235 THR Chi-restraints excluded: chain 6 residue 238 ARG Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 243 ASP Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 263 LEU Chi-restraints excluded: chain 6 residue 268 LYS Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 6 residue 275 ARG Chi-restraints excluded: chain 6 residue 283 VAL Chi-restraints excluded: chain 6 residue 290 ARG Chi-restraints excluded: chain 6 residue 291 VAL Chi-restraints excluded: chain 6 residue 304 GLU Chi-restraints excluded: chain 6 residue 310 ILE Chi-restraints excluded: chain 6 residue 315 VAL Chi-restraints excluded: chain 6 residue 317 ASN Chi-restraints excluded: chain 6 residue 318 LYS Chi-restraints excluded: chain 6 residue 321 MET Chi-restraints excluded: chain 6 residue 324 ASP Chi-restraints excluded: chain 6 residue 329 ILE Chi-restraints excluded: chain 6 residue 332 ASP Chi-restraints excluded: chain 6 residue 333 GLU Chi-restraints excluded: chain 6 residue 336 LYS Chi-restraints excluded: chain 6 residue 340 VAL Chi-restraints excluded: chain 6 residue 342 LEU Chi-restraints excluded: chain 6 residue 350 ILE Chi-restraints excluded: chain 6 residue 353 LEU Chi-restraints excluded: chain 6 residue 355 GLN Chi-restraints excluded: chain 6 residue 361 LEU Chi-restraints excluded: chain 6 residue 367 GLN Chi-restraints excluded: chain 6 residue 369 THR Chi-restraints excluded: chain 6 residue 372 LEU Chi-restraints excluded: chain 6 residue 376 GLU Chi-restraints excluded: chain 6 residue 378 ARG Chi-restraints excluded: chain 6 residue 380 ARG Chi-restraints excluded: chain 6 residue 382 ARG Chi-restraints excluded: chain 6 residue 387 GLN Chi-restraints excluded: chain 6 residue 390 GLU Chi-restraints excluded: chain 6 residue 394 MET Chi-restraints excluded: chain 6 residue 402 LEU Chi-restraints excluded: chain 6 residue 403 GLN Chi-restraints excluded: chain 6 residue 405 ARG Chi-restraints excluded: chain 6 residue 406 MET Chi-restraints excluded: chain 6 residue 408 ILE Chi-restraints excluded: chain 6 residue 413 ARG Chi-restraints excluded: chain 6 residue 416 LYS Chi-restraints excluded: chain 6 residue 421 LEU Chi-restraints excluded: chain 6 residue 422 ILE Chi-restraints excluded: chain 6 residue 426 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 863 optimal weight: 5.9990 chunk 775 optimal weight: 9.9990 chunk 430 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 523 optimal weight: 0.9980 chunk 414 optimal weight: 5.9990 chunk 801 optimal weight: 3.9990 chunk 310 optimal weight: 6.9990 chunk 487 optimal weight: 0.7980 chunk 596 optimal weight: 2.9990 chunk 928 optimal weight: 20.0000 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 18 HIS 0 37 HIS 1 18 HIS ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN J 132 HIS M 13 HIS ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 7 ASN c 119 HIS ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 69 ASN ** e 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 99 GLN l 104 ASN ** s 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 10 GLN 6 123 GLN 6 173 GLN 6 175 GLN ** 6 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 156671 Z= 0.289 Angle : 0.643 14.479 234146 Z= 0.333 Chirality : 0.041 0.357 29868 Planarity : 0.006 0.103 12746 Dihedral : 24.581 179.360 78048 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.06 % Rotamer: Outliers : 5.64 % Allowed : 31.20 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.58 (0.10), residues: 5816 helix: 0.52 (0.11), residues: 1931 sheet: 0.30 (0.16), residues: 934 loop : -1.23 (0.10), residues: 2951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP r 33 HIS 0.010 0.002 HIS D 134 PHE 0.027 0.002 PHE r 9 TYR 0.019 0.002 TYR J 75 ARG 0.008 0.001 ARG Q 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 470 time to evaluate : 5.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 7 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7813 (ttpt) REVERT: D 133 THR cc_start: 0.7003 (p) cc_final: 0.6638 (p) REVERT: G 82 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.5187 (m-80) REVERT: J 118 MET cc_start: 0.7543 (mtt) cc_final: 0.7038 (mtt) REVERT: R 31 GLU cc_start: 0.7095 (mp0) cc_final: 0.6524 (mp0) REVERT: U 85 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.5993 (ptt90) REVERT: x 172 VAL cc_start: 0.7283 (p) cc_final: 0.6936 (t) REVERT: c 123 MET cc_start: 0.5914 (tpp) cc_final: 0.5568 (tpp) REVERT: e 9 MET cc_start: 0.7158 (mtm) cc_final: 0.6869 (mtm) REVERT: f 104 VAL cc_start: 0.8025 (t) cc_final: 0.7703 (t) REVERT: h 21 LYS cc_start: 0.3525 (OUTLIER) cc_final: 0.3027 (tptt) REVERT: h 58 GLU cc_start: 0.0557 (OUTLIER) cc_final: 0.0339 (pm20) REVERT: l 80 MET cc_start: 0.1503 (mmm) cc_final: 0.0170 (mmm) REVERT: 6 9 GLU cc_start: 0.4193 (mt-10) cc_final: 0.3869 (mt-10) REVERT: 6 132 LEU cc_start: 0.6683 (mm) cc_final: 0.6459 (mm) REVERT: 6 167 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6437 (tp) REVERT: 6 182 GLU cc_start: 0.4618 (OUTLIER) cc_final: 0.4396 (mm-30) REVERT: 6 194 LYS cc_start: 0.6329 (OUTLIER) cc_final: 0.5562 (tptp) REVERT: 6 205 TYR cc_start: 0.6445 (OUTLIER) cc_final: 0.5100 (t80) REVERT: 6 342 LEU cc_start: 0.4917 (OUTLIER) cc_final: 0.4696 (pp) REVERT: 6 367 GLN cc_start: -0.0645 (OUTLIER) cc_final: -0.1059 (tm-30) REVERT: 6 387 GLN cc_start: 0.3788 (OUTLIER) cc_final: 0.3426 (tm130) REVERT: 6 394 MET cc_start: 0.1739 (mmt) cc_final: 0.1134 (mmp) outliers start: 274 outliers final: 142 residues processed: 701 average time/residue: 1.3441 time to fit residues: 1627.7341 Evaluate side-chains 613 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 460 time to evaluate : 5.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 25 ASN Chi-restraints excluded: chain 2 residue 3 ARG Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 82 PHE Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 85 ARG Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 85 LYS Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain w residue 46 VAL Chi-restraints excluded: chain w residue 48 MET Chi-restraints excluded: chain w residue 183 PHE Chi-restraints excluded: chain w residue 199 ILE Chi-restraints excluded: chain w residue 216 VAL Chi-restraints excluded: chain x residue 7 ASN Chi-restraints excluded: chain x residue 27 GLU Chi-restraints excluded: chain x residue 194 VAL Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain d residue 11 GLN Chi-restraints excluded: chain d residue 40 ASP Chi-restraints excluded: chain d residue 87 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 119 VAL Chi-restraints excluded: chain e residue 88 MET Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 3 ARG Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain g residue 72 GLU Chi-restraints excluded: chain g residue 75 GLN Chi-restraints excluded: chain g residue 125 ILE Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 58 GLU Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 18 ILE Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 100 ASN Chi-restraints excluded: chain l residue 27 THR Chi-restraints excluded: chain l residue 38 ILE Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain m residue 67 THR Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain p residue 11 VAL Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 61 VAL Chi-restraints excluded: chain 6 residue 6 ASP Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 17 TYR Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 48 SER Chi-restraints excluded: chain 6 residue 50 LYS Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 77 VAL Chi-restraints excluded: chain 6 residue 97 GLU Chi-restraints excluded: chain 6 residue 104 THR Chi-restraints excluded: chain 6 residue 108 LEU Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 116 ARG Chi-restraints excluded: chain 6 residue 121 LYS Chi-restraints excluded: chain 6 residue 122 LEU Chi-restraints excluded: chain 6 residue 134 THR Chi-restraints excluded: chain 6 residue 136 LEU Chi-restraints excluded: chain 6 residue 163 ASP Chi-restraints excluded: chain 6 residue 167 LEU Chi-restraints excluded: chain 6 residue 168 ARG Chi-restraints excluded: chain 6 residue 182 GLU Chi-restraints excluded: chain 6 residue 191 SER Chi-restraints excluded: chain 6 residue 194 LYS Chi-restraints excluded: chain 6 residue 202 LEU Chi-restraints excluded: chain 6 residue 205 TYR Chi-restraints excluded: chain 6 residue 210 LYS Chi-restraints excluded: chain 6 residue 222 VAL Chi-restraints excluded: chain 6 residue 228 LEU Chi-restraints excluded: chain 6 residue 235 THR Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 263 LEU Chi-restraints excluded: chain 6 residue 264 VAL Chi-restraints excluded: chain 6 residue 268 LYS Chi-restraints excluded: chain 6 residue 283 VAL Chi-restraints excluded: chain 6 residue 290 ARG Chi-restraints excluded: chain 6 residue 304 GLU Chi-restraints excluded: chain 6 residue 310 ILE Chi-restraints excluded: chain 6 residue 315 VAL Chi-restraints excluded: chain 6 residue 321 MET Chi-restraints excluded: chain 6 residue 340 VAL Chi-restraints excluded: chain 6 residue 342 LEU Chi-restraints excluded: chain 6 residue 350 ILE Chi-restraints excluded: chain 6 residue 353 LEU Chi-restraints excluded: chain 6 residue 367 GLN Chi-restraints excluded: chain 6 residue 380 ARG Chi-restraints excluded: chain 6 residue 382 ARG Chi-restraints excluded: chain 6 residue 387 GLN Chi-restraints excluded: chain 6 residue 402 LEU Chi-restraints excluded: chain 6 residue 406 MET Chi-restraints excluded: chain 6 residue 424 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 516 optimal weight: 0.9980 chunk 288 optimal weight: 6.9990 chunk 773 optimal weight: 0.7980 chunk 632 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 chunk 930 optimal weight: 40.0000 chunk 1005 optimal weight: 6.9990 chunk 828 optimal weight: 7.9990 chunk 922 optimal weight: 5.9990 chunk 317 optimal weight: 6.9990 chunk 746 optimal weight: 0.0980 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 6 GLN 3 30 HIS ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS K 92 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 16 HIS ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 HIS X 16 ASN x 7 ASN x 101 ASN ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 3 HIS ** e 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 GLN ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS ** s 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 53 HIS 6 128 GLN ** 6 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 156671 Z= 0.293 Angle : 0.622 12.543 234146 Z= 0.321 Chirality : 0.040 0.363 29868 Planarity : 0.005 0.076 12746 Dihedral : 24.250 179.787 77860 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.69 % Favored : 95.29 % Rotamer: Outliers : 5.82 % Allowed : 31.43 % Favored : 62.75 % Cbeta Deviations : 0.00 % 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: -0.54 (0.10), residues: 5816 helix: 0.69 (0.11), residues: 1943 sheet: 0.08 (0.16), residues: 956 loop : -1.25 (0.10), residues: 2917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP r 33 HIS 0.010 0.002 HIS D 134 PHE 0.029 0.002 PHE r 9 TYR 0.019 0.002 TYR c 64 ARG 0.009 0.001 ARG P 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 456 time to evaluate : 5.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ASN cc_start: 0.7171 (m110) cc_final: 0.6820 (m110) REVERT: D 104 VAL cc_start: 0.7912 (p) cc_final: 0.7647 (m) REVERT: D 133 THR cc_start: 0.7260 (p) cc_final: 0.6871 (p) REVERT: J 98 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6230 (pp20) REVERT: J 118 MET cc_start: 0.7524 (mtt) cc_final: 0.7042 (mtt) REVERT: M 38 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7775 (ttm-80) REVERT: N 73 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8008 (m-40) REVERT: R 85 LYS cc_start: 0.6933 (tttt) cc_final: 0.6717 (tttt) REVERT: S 57 ASN cc_start: 0.7145 (m-40) cc_final: 0.6918 (m-40) REVERT: T 5 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6500 (mm-30) REVERT: U 85 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6245 (ptt90) REVERT: c 123 MET cc_start: 0.6070 (tpp) cc_final: 0.5843 (ttp) REVERT: d 88 HIS cc_start: 0.6748 (OUTLIER) cc_final: 0.6314 (t70) REVERT: d 137 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.5924 (mtm-85) REVERT: d 158 LYS cc_start: 0.4378 (OUTLIER) cc_final: 0.2120 (tmtt) REVERT: e 9 MET cc_start: 0.7270 (mtm) cc_final: 0.7064 (mtm) REVERT: f 104 VAL cc_start: 0.7982 (t) cc_final: 0.7662 (t) REVERT: i 72 ARG cc_start: 0.8210 (mmt-90) cc_final: 0.7836 (mpt180) REVERT: k 93 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6403 (mtt180) REVERT: l 43 LYS cc_start: 0.4601 (OUTLIER) cc_final: 0.3696 (pttm) REVERT: l 80 MET cc_start: 0.1525 (mmm) cc_final: 0.0501 (mmm) REVERT: 6 6 ASP cc_start: 0.3219 (OUTLIER) cc_final: 0.2494 (m-30) REVERT: 6 40 GLU cc_start: 0.5037 (mm-30) cc_final: 0.4700 (mm-30) REVERT: 6 321 MET cc_start: 0.6282 (mtt) cc_final: 0.5957 (mtt) REVERT: 6 360 ARG cc_start: 0.7275 (tpp-160) cc_final: 0.6976 (tpp-160) REVERT: 6 394 MET cc_start: 0.1336 (mmt) cc_final: 0.0794 (mmp) outliers start: 283 outliers final: 167 residues processed: 700 average time/residue: 1.3392 time to fit residues: 1603.9089 Evaluate side-chains 630 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 453 time to evaluate : 5.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 1 residue 25 ASN Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 3 ARG Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 93 LYS Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 5 GLU Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 85 ARG Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain w residue 40 ILE Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 183 PHE Chi-restraints excluded: chain w residue 216 VAL Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 27 GLU Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 101 ASN Chi-restraints excluded: chain x residue 120 THR Chi-restraints excluded: chain x residue 180 ASP Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain d residue 11 GLN Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 40 ASP Chi-restraints excluded: chain d residue 88 HIS Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 119 VAL Chi-restraints excluded: chain d residue 137 ARG Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 158 LYS Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 141 HIS Chi-restraints excluded: chain g residue 75 GLN Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain g residue 125 ILE Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 42 THR Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 18 ILE Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 71 LEU Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 100 ASN Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 93 ARG Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 27 THR Chi-restraints excluded: chain l residue 38 ILE Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain m residue 67 THR Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain p residue 11 VAL Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain r residue 22 VAL Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 56 HIS Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain 6 residue 6 ASP Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 17 TYR Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 50 LYS Chi-restraints excluded: chain 6 residue 53 HIS Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 97 GLU Chi-restraints excluded: chain 6 residue 104 THR Chi-restraints excluded: chain 6 residue 108 LEU Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 116 ARG Chi-restraints excluded: chain 6 residue 117 THR Chi-restraints excluded: chain 6 residue 121 LYS Chi-restraints excluded: chain 6 residue 134 THR Chi-restraints excluded: chain 6 residue 163 ASP Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 194 LYS Chi-restraints excluded: chain 6 residue 202 LEU Chi-restraints excluded: chain 6 residue 210 LYS Chi-restraints excluded: chain 6 residue 235 THR Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 263 LEU Chi-restraints excluded: chain 6 residue 268 LYS Chi-restraints excluded: chain 6 residue 290 ARG Chi-restraints excluded: chain 6 residue 304 GLU Chi-restraints excluded: chain 6 residue 315 VAL Chi-restraints excluded: chain 6 residue 329 ILE Chi-restraints excluded: chain 6 residue 340 VAL Chi-restraints excluded: chain 6 residue 350 ILE Chi-restraints excluded: chain 6 residue 353 LEU Chi-restraints excluded: chain 6 residue 365 VAL Chi-restraints excluded: chain 6 residue 380 ARG Chi-restraints excluded: chain 6 residue 424 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 919 optimal weight: 5.9990 chunk 699 optimal weight: 3.9990 chunk 483 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 444 optimal weight: 0.5980 chunk 624 optimal weight: 0.7980 chunk 934 optimal weight: 6.9990 chunk 988 optimal weight: 1.9990 chunk 487 optimal weight: 0.8980 chunk 885 optimal weight: 4.9990 chunk 266 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 HIS X 16 ASN ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 76 ASN ** e 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 109 GLN h 125 GLN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 13 HIS s 74 HIS ** 6 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 292 GLN ** 6 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 156671 Z= 0.167 Angle : 0.528 9.750 234146 Z= 0.277 Chirality : 0.034 0.316 29868 Planarity : 0.004 0.063 12746 Dihedral : 24.058 179.883 77817 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.32 % Favored : 95.67 % Rotamer: Outliers : 5.25 % Allowed : 32.17 % Favored : 62.58 % Cbeta Deviations : 0.00 % 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: -0.26 (0.10), residues: 5816 helix: 1.09 (0.12), residues: 1942 sheet: 0.14 (0.17), residues: 948 loop : -1.17 (0.10), residues: 2926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 38 HIS 0.018 0.001 HIS 6 53 PHE 0.021 0.001 PHE e 8 TYR 0.015 0.001 TYR f 43 ARG 0.011 0.000 ARG P 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 458 time to evaluate : 5.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 ASN cc_start: 0.7153 (t0) cc_final: 0.6863 (t0) REVERT: C 89 ASN cc_start: 0.6631 (m-40) cc_final: 0.6397 (m110) REVERT: D 7 LYS cc_start: 0.8049 (ttpt) cc_final: 0.7820 (ttpt) REVERT: D 38 LYS cc_start: 0.6087 (OUTLIER) cc_final: 0.5660 (mttm) REVERT: D 104 VAL cc_start: 0.7914 (p) cc_final: 0.7635 (m) REVERT: D 133 THR cc_start: 0.7182 (p) cc_final: 0.6772 (p) REVERT: J 118 MET cc_start: 0.7462 (mtt) cc_final: 0.6886 (mtt) REVERT: M 75 GLU cc_start: 0.6187 (mp0) cc_final: 0.5973 (mp0) REVERT: N 64 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.6656 (mtt180) REVERT: N 73 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8092 (m-40) REVERT: R 6 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.6097 (tp-100) REVERT: S 57 ASN cc_start: 0.7152 (m-40) cc_final: 0.6888 (m-40) REVERT: T 49 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7666 (ttpp) REVERT: U 85 ARG cc_start: 0.6589 (OUTLIER) cc_final: 0.6131 (ptt90) REVERT: W 19 ARG cc_start: 0.4763 (OUTLIER) cc_final: 0.3967 (ptt90) REVERT: W 38 ARG cc_start: 0.7123 (mtt90) cc_final: 0.6562 (mtt90) REVERT: x 133 MET cc_start: 0.7362 (mtm) cc_final: 0.7124 (mtp) REVERT: x 178 ARG cc_start: 0.7265 (ttp-170) cc_final: 0.7010 (ttp-170) REVERT: c 123 MET cc_start: 0.6055 (tpp) cc_final: 0.5822 (tpp) REVERT: d 137 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.5805 (mtm-85) REVERT: f 3 ARG cc_start: 0.5167 (OUTLIER) cc_final: 0.4885 (mmm160) REVERT: f 104 VAL cc_start: 0.7966 (t) cc_final: 0.7617 (t) REVERT: i 62 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6429 (mtm110) REVERT: i 72 ARG cc_start: 0.8170 (mmt-90) cc_final: 0.7769 (mpt180) REVERT: 6 22 LYS cc_start: 0.5124 (OUTLIER) cc_final: 0.4902 (tttm) REVERT: 6 263 LEU cc_start: 0.4713 (OUTLIER) cc_final: 0.4479 (tp) REVERT: 6 321 MET cc_start: 0.6183 (mtt) cc_final: 0.5859 (mtt) REVERT: 6 360 ARG cc_start: 0.7173 (tpp-160) cc_final: 0.6958 (tpp-160) REVERT: 6 394 MET cc_start: 0.1252 (mmt) cc_final: 0.0886 (mmt) outliers start: 255 outliers final: 177 residues processed: 668 average time/residue: 1.3102 time to fit residues: 1489.7029 Evaluate side-chains 646 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 457 time to evaluate : 5.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 25 ASN Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 93 LYS Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 49 LYS Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 85 ARG Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 19 ARG Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 69 GLU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain w residue 14 HIS Chi-restraints excluded: chain w residue 40 ILE Chi-restraints excluded: chain w residue 183 PHE Chi-restraints excluded: chain w residue 185 ILE Chi-restraints excluded: chain w residue 199 ILE Chi-restraints excluded: chain w residue 216 VAL Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 27 GLU Chi-restraints excluded: chain x residue 42 LEU Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain d residue 11 GLN Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 40 ASP Chi-restraints excluded: chain d residue 87 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 119 VAL Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 137 ARG Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain f residue 3 ARG Chi-restraints excluded: chain f residue 9 ARG Chi-restraints excluded: chain f residue 141 HIS Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 75 GLN Chi-restraints excluded: chain g residue 110 MET Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 6 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 18 ILE Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 62 ARG Chi-restraints excluded: chain i residue 71 LEU Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 100 ASN Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain m residue 67 THR Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 61 VAL Chi-restraints excluded: chain p residue 11 VAL Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain q residue 64 LEU Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 56 HIS Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 17 TYR Chi-restraints excluded: chain 6 residue 22 LYS Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 53 HIS Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 90 ARG Chi-restraints excluded: chain 6 residue 97 GLU Chi-restraints excluded: chain 6 residue 104 THR Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 116 ARG Chi-restraints excluded: chain 6 residue 117 THR Chi-restraints excluded: chain 6 residue 121 LYS Chi-restraints excluded: chain 6 residue 134 THR Chi-restraints excluded: chain 6 residue 163 ASP Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 194 LYS Chi-restraints excluded: chain 6 residue 203 VAL Chi-restraints excluded: chain 6 residue 210 LYS Chi-restraints excluded: chain 6 residue 222 VAL Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 263 LEU Chi-restraints excluded: chain 6 residue 268 LYS Chi-restraints excluded: chain 6 residue 282 HIS Chi-restraints excluded: chain 6 residue 283 VAL Chi-restraints excluded: chain 6 residue 290 ARG Chi-restraints excluded: chain 6 residue 304 GLU Chi-restraints excluded: chain 6 residue 329 ILE Chi-restraints excluded: chain 6 residue 340 VAL Chi-restraints excluded: chain 6 residue 350 ILE Chi-restraints excluded: chain 6 residue 353 LEU Chi-restraints excluded: chain 6 residue 369 THR Chi-restraints excluded: chain 6 residue 380 ARG Chi-restraints excluded: chain 6 residue 406 MET Chi-restraints excluded: chain 6 residue 424 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 823 optimal weight: 50.0000 chunk 561 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 736 optimal weight: 9.9990 chunk 407 optimal weight: 30.0000 chunk 843 optimal weight: 10.0000 chunk 683 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 504 optimal weight: 0.5980 chunk 887 optimal weight: 6.9990 chunk 249 optimal weight: 320.0000 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 250 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS W 56 HIS X 16 ASN w 14 HIS ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 30 HIS q 53 GLN s 74 HIS 6 53 HIS ** 6 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 156671 Z= 0.549 Angle : 0.800 14.825 234146 Z= 0.400 Chirality : 0.051 0.544 29868 Planarity : 0.006 0.088 12746 Dihedral : 24.164 179.432 77803 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.81 % Favored : 94.14 % Rotamer: Outliers : 6.94 % Allowed : 30.69 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.82 (0.10), residues: 5816 helix: 0.40 (0.11), residues: 1945 sheet: 0.04 (0.16), residues: 929 loop : -1.39 (0.11), residues: 2942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP r 33 HIS 0.016 0.002 HIS e 94 PHE 0.041 0.003 PHE r 9 TYR 0.041 0.003 TYR c 134 ARG 0.013 0.001 ARG P 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 467 time to evaluate : 6.180 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR c 3 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 ASN cc_start: 0.7137 (m110) cc_final: 0.6863 (m110) REVERT: D 38 LYS cc_start: 0.6021 (OUTLIER) cc_final: 0.4457 (mttt) REVERT: D 133 THR cc_start: 0.7014 (p) cc_final: 0.6632 (p) REVERT: G 82 PHE cc_start: 0.5796 (OUTLIER) cc_final: 0.5260 (m-80) REVERT: J 118 MET cc_start: 0.7537 (mtt) cc_final: 0.7204 (mtt) REVERT: N 64 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.6878 (mtt180) REVERT: N 73 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8129 (m-40) REVERT: P 12 MET cc_start: 0.7198 (mmm) cc_final: 0.6972 (mtt) REVERT: P 20 ARG cc_start: 0.7855 (ttm110) cc_final: 0.7499 (ttm110) REVERT: P 52 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.5854 (mtm110) REVERT: P 81 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.7189 (t0) REVERT: R 6 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.6151 (tp-100) REVERT: S 57 ASN cc_start: 0.7204 (m-40) cc_final: 0.6926 (m-40) REVERT: T 49 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7533 (ttpp) REVERT: U 85 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.6297 (ptt90) REVERT: W 19 ARG cc_start: 0.5190 (OUTLIER) cc_final: 0.4151 (ptt90) REVERT: W 38 ARG cc_start: 0.7351 (mtt90) cc_final: 0.6585 (mtt90) REVERT: c 123 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5877 (tpp) REVERT: c 146 GLU cc_start: 0.6825 (tm-30) cc_final: 0.6553 (tm-30) REVERT: d 158 LYS cc_start: 0.4716 (OUTLIER) cc_final: 0.2598 (tmtt) REVERT: e 90 MET cc_start: 0.6802 (mmm) cc_final: 0.6504 (mmm) REVERT: h 56 MET cc_start: 0.3514 (OUTLIER) cc_final: 0.3255 (mmp) REVERT: l 80 MET cc_start: 0.0751 (mmm) cc_final: -0.0286 (mmt) REVERT: n 62 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7151 (ttp-110) REVERT: o 14 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7094 (mtp180) REVERT: 6 22 LYS cc_start: 0.5353 (OUTLIER) cc_final: 0.5119 (tttt) REVERT: 6 24 MET cc_start: 0.3558 (mmt) cc_final: 0.3063 (mmt) REVERT: 6 40 GLU cc_start: 0.5188 (mm-30) cc_final: 0.4899 (mm-30) REVERT: 6 122 LEU cc_start: 0.7727 (mt) cc_final: 0.7508 (tt) REVERT: 6 192 ARG cc_start: 0.6658 (mtp-110) cc_final: 0.6398 (mtp-110) REVERT: 6 255 PHE cc_start: 0.6075 (OUTLIER) cc_final: 0.5301 (m-80) REVERT: 6 321 MET cc_start: 0.6291 (mtt) cc_final: 0.6037 (mtt) REVERT: 6 360 ARG cc_start: 0.7308 (tpp-160) cc_final: 0.7011 (mmm160) REVERT: 6 394 MET cc_start: 0.1285 (mmt) cc_final: 0.0904 (mmt) outliers start: 337 outliers final: 233 residues processed: 744 average time/residue: 1.4252 time to fit residues: 1819.3484 Evaluate side-chains 716 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 466 time to evaluate : 5.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 3 ARG Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 82 PHE Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 119 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain P residue 93 LYS Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 49 LYS Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 85 ARG Chi-restraints excluded: chain V residue 31 TYR Chi-restraints excluded: chain V residue 48 MET Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 19 ARG Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 69 GLU Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 3 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain w residue 14 HIS Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 183 PHE Chi-restraints excluded: chain w residue 185 ILE Chi-restraints excluded: chain w residue 199 ILE Chi-restraints excluded: chain w residue 216 VAL Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 27 GLU Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 120 THR Chi-restraints excluded: chain x residue 180 ASP Chi-restraints excluded: chain x residue 194 VAL Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain c residue 135 GLN Chi-restraints excluded: chain c residue 173 ASP Chi-restraints excluded: chain d residue 11 GLN Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 40 ASP Chi-restraints excluded: chain d residue 87 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 119 VAL Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 158 LYS Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 9 ARG Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 141 HIS Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 98 LEU Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 5 TYR Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 18 ILE Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 62 ARG Chi-restraints excluded: chain i residue 71 LEU Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain j residue 22 ILE Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 100 ASN Chi-restraints excluded: chain k residue 3 VAL Chi-restraints excluded: chain k residue 71 HIS Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain m residue 67 THR Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 84 VAL Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 62 ARG Chi-restraints excluded: chain o residue 14 ARG Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 61 VAL Chi-restraints excluded: chain p residue 11 VAL Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 6 LYS Chi-restraints excluded: chain r residue 22 VAL Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 56 HIS Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain s residue 65 LEU Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 17 TYR Chi-restraints excluded: chain 6 residue 22 LYS Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 53 HIS Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 90 ARG Chi-restraints excluded: chain 6 residue 97 GLU Chi-restraints excluded: chain 6 residue 104 THR Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 116 ARG Chi-restraints excluded: chain 6 residue 117 THR Chi-restraints excluded: chain 6 residue 121 LYS Chi-restraints excluded: chain 6 residue 134 THR Chi-restraints excluded: chain 6 residue 163 ASP Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 194 LYS Chi-restraints excluded: chain 6 residue 203 VAL Chi-restraints excluded: chain 6 residue 210 LYS Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 222 VAL Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 268 LYS Chi-restraints excluded: chain 6 residue 282 HIS Chi-restraints excluded: chain 6 residue 290 ARG Chi-restraints excluded: chain 6 residue 304 GLU Chi-restraints excluded: chain 6 residue 313 LEU Chi-restraints excluded: chain 6 residue 329 ILE Chi-restraints excluded: chain 6 residue 340 VAL Chi-restraints excluded: chain 6 residue 350 ILE Chi-restraints excluded: chain 6 residue 353 LEU Chi-restraints excluded: chain 6 residue 357 LEU Chi-restraints excluded: chain 6 residue 365 VAL Chi-restraints excluded: chain 6 residue 369 THR Chi-restraints excluded: chain 6 residue 380 ARG Chi-restraints excluded: chain 6 residue 406 MET Chi-restraints excluded: chain 6 residue 424 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 332 optimal weight: 1.9990 chunk 890 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 580 optimal weight: 0.9980 chunk 244 optimal weight: 100.0000 chunk 989 optimal weight: 0.9980 chunk 821 optimal weight: 4.9990 chunk 458 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 327 optimal weight: 2.9990 chunk 519 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 GLN W 56 HIS X 16 ASN w 14 HIS w 177 ASN e 63 ASN g 75 GLN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS s 74 HIS ** 6 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 156671 Z= 0.195 Angle : 0.559 11.161 234146 Z= 0.290 Chirality : 0.036 0.323 29868 Planarity : 0.005 0.072 12746 Dihedral : 23.977 179.851 77800 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.69 % Favored : 95.29 % Rotamer: Outliers : 5.74 % Allowed : 31.84 % Favored : 62.42 % Cbeta Deviations : 0.00 % 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: -0.46 (0.11), residues: 5816 helix: 0.94 (0.12), residues: 1941 sheet: 0.10 (0.17), residues: 916 loop : -1.30 (0.11), residues: 2959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP j 43 HIS 0.027 0.001 HIS w 14 PHE 0.026 0.001 PHE e 8 TYR 0.019 0.001 TYR f 43 ARG 0.017 0.000 ARG W 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 471 time to evaluate : 5.950 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR c 3 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: D 7 LYS cc_start: 0.7982 (ttpt) cc_final: 0.7732 (ttpt) REVERT: D 38 LYS cc_start: 0.6028 (OUTLIER) cc_final: 0.4363 (mttt) REVERT: D 133 THR cc_start: 0.7185 (p) cc_final: 0.6726 (p) REVERT: G 82 PHE cc_start: 0.5698 (OUTLIER) cc_final: 0.5223 (m-80) REVERT: J 118 MET cc_start: 0.7504 (mtt) cc_final: 0.7106 (mtt) REVERT: K 19 MET cc_start: 0.7699 (OUTLIER) cc_final: 0.7440 (ttt) REVERT: N 64 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.6758 (mtt180) REVERT: N 73 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8021 (m-40) REVERT: O 30 ARG cc_start: 0.6397 (ttp80) cc_final: 0.5911 (ttp80) REVERT: P 20 ARG cc_start: 0.7601 (ttm110) cc_final: 0.7233 (ttm110) REVERT: R 6 GLN cc_start: 0.6475 (OUTLIER) cc_final: 0.6103 (tp-100) REVERT: R 71 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7872 (tttt) REVERT: S 57 ASN cc_start: 0.7169 (m-40) cc_final: 0.6919 (m-40) REVERT: T 49 LYS cc_start: 0.7841 (OUTLIER) cc_final: 0.7622 (ttpp) REVERT: U 85 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.6201 (ptt90) REVERT: V 77 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7707 (p) REVERT: W 19 ARG cc_start: 0.4969 (OUTLIER) cc_final: 0.4117 (ptt90) REVERT: W 38 ARG cc_start: 0.7279 (mtt90) cc_final: 0.6377 (mtt90) REVERT: c 123 MET cc_start: 0.6097 (OUTLIER) cc_final: 0.5821 (tpp) REVERT: e 90 MET cc_start: 0.6650 (mmm) cc_final: 0.6354 (mmm) REVERT: f 104 VAL cc_start: 0.7963 (t) cc_final: 0.7670 (t) REVERT: h 56 MET cc_start: 0.2877 (OUTLIER) cc_final: 0.2648 (mmp) REVERT: i 72 ARG cc_start: 0.8180 (mmt-90) cc_final: 0.7811 (mpt180) REVERT: l 43 LYS cc_start: 0.4614 (OUTLIER) cc_final: 0.3866 (pttm) REVERT: l 80 MET cc_start: 0.1296 (mmm) cc_final: -0.1285 (mmt) REVERT: n 62 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6628 (ttp-110) REVERT: 6 22 LYS cc_start: 0.5381 (OUTLIER) cc_final: 0.5127 (tttm) REVERT: 6 58 VAL cc_start: 0.1381 (OUTLIER) cc_final: 0.1143 (t) REVERT: 6 205 TYR cc_start: 0.6397 (OUTLIER) cc_final: 0.4896 (t80) REVERT: 6 321 MET cc_start: 0.6149 (mtt) cc_final: 0.5888 (mtt) REVERT: 6 360 ARG cc_start: 0.7182 (tpp-160) cc_final: 0.6929 (tpp-160) outliers start: 279 outliers final: 194 residues processed: 703 average time/residue: 1.3485 time to fit residues: 1610.0287 Evaluate side-chains 676 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 464 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 82 PHE Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 71 LYS Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 49 LYS Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 85 ARG Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain V residue 48 MET Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 19 ARG Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain w residue 14 HIS Chi-restraints excluded: chain w residue 40 ILE Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 183 PHE Chi-restraints excluded: chain w residue 185 ILE Chi-restraints excluded: chain w residue 199 ILE Chi-restraints excluded: chain w residue 216 VAL Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 27 GLU Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 120 THR Chi-restraints excluded: chain x residue 180 ASP Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain c residue 154 VAL Chi-restraints excluded: chain d residue 11 GLN Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 40 ASP Chi-restraints excluded: chain d residue 76 ASN Chi-restraints excluded: chain d residue 87 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 119 VAL Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain e residue 46 GLN Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 9 ARG Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 141 HIS Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 98 LEU Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 5 TYR Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 18 ILE Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 71 LEU Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 85 VAL Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 100 ASN Chi-restraints excluded: chain k residue 71 HIS Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 64 VAL Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain m residue 67 THR Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 62 ARG Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 61 VAL Chi-restraints excluded: chain p residue 11 VAL Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 56 HIS Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 17 TYR Chi-restraints excluded: chain 6 residue 22 LYS Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 90 ARG Chi-restraints excluded: chain 6 residue 108 LEU Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 116 ARG Chi-restraints excluded: chain 6 residue 117 THR Chi-restraints excluded: chain 6 residue 121 LYS Chi-restraints excluded: chain 6 residue 134 THR Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 194 LYS Chi-restraints excluded: chain 6 residue 205 TYR Chi-restraints excluded: chain 6 residue 210 LYS Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 222 VAL Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 268 LYS Chi-restraints excluded: chain 6 residue 282 HIS Chi-restraints excluded: chain 6 residue 283 VAL Chi-restraints excluded: chain 6 residue 290 ARG Chi-restraints excluded: chain 6 residue 329 ILE Chi-restraints excluded: chain 6 residue 340 VAL Chi-restraints excluded: chain 6 residue 350 ILE Chi-restraints excluded: chain 6 residue 353 LEU Chi-restraints excluded: chain 6 residue 357 LEU Chi-restraints excluded: chain 6 residue 365 VAL Chi-restraints excluded: chain 6 residue 369 THR Chi-restraints excluded: chain 6 residue 406 MET Chi-restraints excluded: chain 6 residue 424 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 954 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 563 optimal weight: 5.9990 chunk 722 optimal weight: 4.9990 chunk 560 optimal weight: 7.9990 chunk 833 optimal weight: 6.9990 chunk 552 optimal weight: 5.9990 chunk 986 optimal weight: 0.9990 chunk 617 optimal weight: 6.9990 chunk 601 optimal weight: 1.9990 chunk 455 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN C 250 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN w 14 HIS ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 58 ASN m 60 GLN s 74 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 156671 Z= 0.381 Angle : 0.664 13.898 234146 Z= 0.337 Chirality : 0.042 0.412 29868 Planarity : 0.005 0.077 12746 Dihedral : 23.978 179.803 77786 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.90 % Favored : 94.09 % Rotamer: Outliers : 6.07 % Allowed : 31.82 % Favored : 62.11 % Cbeta Deviations : 0.00 % 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: -0.64 (0.10), residues: 5816 helix: 0.68 (0.11), residues: 1943 sheet: 0.01 (0.17), residues: 920 loop : -1.33 (0.11), residues: 2953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP r 33 HIS 0.012 0.002 HIS D 134 PHE 0.034 0.002 PHE r 9 TYR 0.029 0.002 TYR c 134 ARG 0.010 0.000 ARG 6 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 467 time to evaluate : 5.809 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR c 3 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 259 ASN cc_start: 0.6891 (t0) cc_final: 0.6620 (t0) REVERT: D 38 LYS cc_start: 0.5890 (OUTLIER) cc_final: 0.4272 (mttt) REVERT: D 133 THR cc_start: 0.7170 (p) cc_final: 0.6762 (p) REVERT: E 176 ASP cc_start: 0.5788 (OUTLIER) cc_final: 0.5577 (m-30) REVERT: G 82 PHE cc_start: 0.5840 (OUTLIER) cc_final: 0.5324 (m-80) REVERT: J 118 MET cc_start: 0.7492 (mtt) cc_final: 0.7156 (mtt) REVERT: K 19 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7529 (ttt) REVERT: L 63 LYS cc_start: 0.6103 (OUTLIER) cc_final: 0.5738 (mttt) REVERT: N 64 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.6806 (mtt180) REVERT: N 73 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.8081 (m-40) REVERT: P 12 MET cc_start: 0.7201 (mmm) cc_final: 0.6945 (mtt) REVERT: R 6 GLN cc_start: 0.6535 (OUTLIER) cc_final: 0.6140 (tp-100) REVERT: R 82 HIS cc_start: 0.6652 (OUTLIER) cc_final: 0.6217 (t70) REVERT: S 57 ASN cc_start: 0.7197 (m-40) cc_final: 0.6914 (m-40) REVERT: T 49 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7578 (ttpp) REVERT: U 85 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6271 (ptt90) REVERT: V 77 VAL cc_start: 0.7941 (OUTLIER) cc_final: 0.7735 (p) REVERT: W 19 ARG cc_start: 0.5622 (OUTLIER) cc_final: 0.4442 (ptt90) REVERT: W 38 ARG cc_start: 0.7356 (mtt90) cc_final: 0.6540 (mtt90) REVERT: c 123 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5833 (tpp) REVERT: c 146 GLU cc_start: 0.6814 (tm-30) cc_final: 0.6488 (tm-30) REVERT: c 173 ASP cc_start: 0.5959 (OUTLIER) cc_final: 0.5428 (p0) REVERT: d 158 LYS cc_start: 0.4572 (OUTLIER) cc_final: 0.2663 (tmtt) REVERT: e 6 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7102 (mm) REVERT: e 90 MET cc_start: 0.6785 (mmm) cc_final: 0.6474 (mmm) REVERT: i 72 ARG cc_start: 0.8208 (mmt-90) cc_final: 0.7830 (mpt180) REVERT: k 115 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6903 (mtpt) REVERT: l 43 LYS cc_start: 0.4693 (OUTLIER) cc_final: 0.3899 (pttm) REVERT: l 80 MET cc_start: 0.0869 (mmm) cc_final: -0.1704 (mmt) REVERT: n 62 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7129 (ttp-110) REVERT: o 14 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7105 (mtp180) REVERT: 6 58 VAL cc_start: 0.1363 (OUTLIER) cc_final: 0.1153 (t) REVERT: 6 360 ARG cc_start: 0.7219 (tpp-160) cc_final: 0.6869 (tpp-160) outliers start: 295 outliers final: 227 residues processed: 709 average time/residue: 1.3457 time to fit residues: 1622.7521 Evaluate side-chains 714 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 465 time to evaluate : 5.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 82 PHE Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 63 LYS Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 5 LYS Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 93 LYS Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 49 LYS Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 85 ARG Chi-restraints excluded: chain V residue 31 TYR Chi-restraints excluded: chain V residue 48 MET Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 19 ARG Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 79 ILE Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain w residue 14 HIS Chi-restraints excluded: chain w residue 40 ILE Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 183 PHE Chi-restraints excluded: chain w residue 185 ILE Chi-restraints excluded: chain w residue 199 ILE Chi-restraints excluded: chain w residue 216 VAL Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 27 GLU Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 120 THR Chi-restraints excluded: chain x residue 180 ASP Chi-restraints excluded: chain x residue 194 VAL Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain c residue 135 GLN Chi-restraints excluded: chain c residue 173 ASP Chi-restraints excluded: chain d residue 11 GLN Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 40 ASP Chi-restraints excluded: chain d residue 87 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 119 VAL Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 158 LYS Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 46 GLN Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 88 MET Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 9 ARG Chi-restraints excluded: chain f residue 29 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 141 HIS Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 98 LEU Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 5 TYR Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 18 ILE Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 71 LEU Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain j residue 22 ILE Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 85 VAL Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 100 ASN Chi-restraints excluded: chain k residue 71 HIS Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 115 LYS Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 64 VAL Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain m residue 67 THR Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 62 ARG Chi-restraints excluded: chain o residue 14 ARG Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 33 ILE Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 61 VAL Chi-restraints excluded: chain p residue 11 VAL Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain s residue 65 LEU Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 17 TYR Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 90 ARG Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 116 ARG Chi-restraints excluded: chain 6 residue 117 THR Chi-restraints excluded: chain 6 residue 121 LYS Chi-restraints excluded: chain 6 residue 134 THR Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 194 LYS Chi-restraints excluded: chain 6 residue 203 VAL Chi-restraints excluded: chain 6 residue 210 LYS Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 222 VAL Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 268 LYS Chi-restraints excluded: chain 6 residue 282 HIS Chi-restraints excluded: chain 6 residue 290 ARG Chi-restraints excluded: chain 6 residue 329 ILE Chi-restraints excluded: chain 6 residue 340 VAL Chi-restraints excluded: chain 6 residue 350 ILE Chi-restraints excluded: chain 6 residue 353 LEU Chi-restraints excluded: chain 6 residue 357 LEU Chi-restraints excluded: chain 6 residue 365 VAL Chi-restraints excluded: chain 6 residue 424 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 610 optimal weight: 20.0000 chunk 393 optimal weight: 6.9990 chunk 588 optimal weight: 1.9990 chunk 297 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 626 optimal weight: 3.9990 chunk 671 optimal weight: 0.9990 chunk 487 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 775 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 14 HIS ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 74 HIS ** 6 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 156671 Z= 0.358 Angle : 0.651 13.499 234146 Z= 0.332 Chirality : 0.042 0.438 29868 Planarity : 0.005 0.083 12746 Dihedral : 23.967 179.993 77786 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.79 % Favored : 94.19 % Rotamer: Outliers : 6.03 % Allowed : 32.11 % Favored : 61.86 % Cbeta Deviations : 0.00 % 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: -0.73 (0.10), residues: 5816 helix: 0.63 (0.11), residues: 1940 sheet: -0.04 (0.17), residues: 922 loop : -1.41 (0.11), residues: 2954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP r 33 HIS 0.036 0.002 HIS w 14 PHE 0.036 0.002 PHE w 15 TYR 0.026 0.002 TYR c 134 ARG 0.014 0.000 ARG P 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 465 time to evaluate : 5.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR c 3 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 102 TYR cc_start: 0.7220 (m-10) cc_final: 0.6952 (m-80) REVERT: C 259 ASN cc_start: 0.6892 (t0) cc_final: 0.6629 (t0) REVERT: D 38 LYS cc_start: 0.5898 (OUTLIER) cc_final: 0.4366 (mttt) REVERT: D 133 THR cc_start: 0.7204 (p) cc_final: 0.6792 (p) REVERT: E 176 ASP cc_start: 0.5762 (OUTLIER) cc_final: 0.5546 (m-30) REVERT: G 82 PHE cc_start: 0.5701 (OUTLIER) cc_final: 0.5186 (m-80) REVERT: J 118 MET cc_start: 0.7490 (mtt) cc_final: 0.7140 (mtt) REVERT: K 19 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7505 (ttt) REVERT: K 50 LYS cc_start: 0.6450 (OUTLIER) cc_final: 0.6192 (mtmt) REVERT: L 63 LYS cc_start: 0.6107 (OUTLIER) cc_final: 0.5771 (mttt) REVERT: M 136 MET cc_start: 0.4281 (pmm) cc_final: 0.3985 (pmm) REVERT: N 64 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6842 (mtt180) REVERT: N 73 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8084 (m-40) REVERT: P 12 MET cc_start: 0.7228 (mmm) cc_final: 0.6974 (mtt) REVERT: R 6 GLN cc_start: 0.6464 (OUTLIER) cc_final: 0.6070 (tp-100) REVERT: R 82 HIS cc_start: 0.6622 (OUTLIER) cc_final: 0.6160 (t70) REVERT: S 57 ASN cc_start: 0.7200 (m-40) cc_final: 0.6926 (m-40) REVERT: T 49 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7579 (ttpp) REVERT: W 19 ARG cc_start: 0.5598 (OUTLIER) cc_final: 0.4645 (ptt90) REVERT: W 38 ARG cc_start: 0.7364 (mtt90) cc_final: 0.6655 (mtt90) REVERT: c 123 MET cc_start: 0.6153 (OUTLIER) cc_final: 0.5847 (tpp) REVERT: c 146 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6445 (tm-30) REVERT: c 173 ASP cc_start: 0.5908 (OUTLIER) cc_final: 0.5373 (p0) REVERT: d 158 LYS cc_start: 0.4518 (OUTLIER) cc_final: 0.2603 (tmtt) REVERT: e 6 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7125 (mm) REVERT: e 9 MET cc_start: 0.7039 (mtm) cc_final: 0.6792 (ptp) REVERT: e 90 MET cc_start: 0.6764 (mmm) cc_final: 0.6483 (mmm) REVERT: i 72 ARG cc_start: 0.8205 (mmt-90) cc_final: 0.7832 (mpt180) REVERT: k 115 LYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6947 (mtpt) REVERT: l 80 MET cc_start: 0.1241 (mmm) cc_final: -0.1636 (mmt) REVERT: n 44 GLU cc_start: 0.4557 (OUTLIER) cc_final: 0.4147 (pp20) REVERT: n 62 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7130 (ttp-110) REVERT: o 14 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7112 (mtp180) REVERT: r 6 LYS cc_start: 0.3683 (OUTLIER) cc_final: 0.2422 (pttt) REVERT: 6 58 VAL cc_start: 0.1461 (OUTLIER) cc_final: 0.1238 (t) REVERT: 6 192 ARG cc_start: 0.6580 (mtp85) cc_final: 0.5946 (mtp-110) outliers start: 293 outliers final: 228 residues processed: 706 average time/residue: 1.4319 time to fit residues: 1732.9834 Evaluate side-chains 715 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 465 time to evaluate : 5.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 47 ASN Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 82 PHE Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 50 LYS Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 63 LYS Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 5 LYS Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 93 LYS Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 49 LYS Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 31 TYR Chi-restraints excluded: chain V residue 48 MET Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 19 ARG Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain W residue 69 GLU Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain w residue 40 ILE Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 183 PHE Chi-restraints excluded: chain w residue 199 ILE Chi-restraints excluded: chain w residue 216 VAL Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 27 GLU Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 120 THR Chi-restraints excluded: chain x residue 180 ASP Chi-restraints excluded: chain x residue 194 VAL Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain c residue 135 GLN Chi-restraints excluded: chain c residue 173 ASP Chi-restraints excluded: chain d residue 11 GLN Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 40 ASP Chi-restraints excluded: chain d residue 76 ASN Chi-restraints excluded: chain d residue 87 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 119 VAL Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 158 LYS Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 46 GLN Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 88 MET Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 9 ARG Chi-restraints excluded: chain f residue 29 LEU Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 141 HIS Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 98 LEU Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 5 TYR Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 6 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 18 ILE Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 67 ILE Chi-restraints excluded: chain i residue 71 LEU Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain j residue 22 ILE Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 85 VAL Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 100 ASN Chi-restraints excluded: chain k residue 71 HIS Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 115 LYS Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 64 VAL Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain m residue 67 THR Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 84 VAL Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 62 ARG Chi-restraints excluded: chain o residue 14 ARG Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 33 ILE Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 61 VAL Chi-restraints excluded: chain p residue 11 VAL Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 6 LYS Chi-restraints excluded: chain r residue 10 ILE Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 12 VAL Chi-restraints excluded: chain 6 residue 17 TYR Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 116 ARG Chi-restraints excluded: chain 6 residue 117 THR Chi-restraints excluded: chain 6 residue 121 LYS Chi-restraints excluded: chain 6 residue 134 THR Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 194 LYS Chi-restraints excluded: chain 6 residue 203 VAL Chi-restraints excluded: chain 6 residue 210 LYS Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 222 VAL Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 268 LYS Chi-restraints excluded: chain 6 residue 282 HIS Chi-restraints excluded: chain 6 residue 290 ARG Chi-restraints excluded: chain 6 residue 329 ILE Chi-restraints excluded: chain 6 residue 340 VAL Chi-restraints excluded: chain 6 residue 350 ILE Chi-restraints excluded: chain 6 residue 353 LEU Chi-restraints excluded: chain 6 residue 357 LEU Chi-restraints excluded: chain 6 residue 365 VAL Chi-restraints excluded: chain 6 residue 369 THR Chi-restraints excluded: chain 6 residue 406 MET Chi-restraints excluded: chain 6 residue 424 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 896 optimal weight: 10.0000 chunk 944 optimal weight: 10.0000 chunk 861 optimal weight: 5.9990 chunk 918 optimal weight: 5.9990 chunk 553 optimal weight: 7.9990 chunk 400 optimal weight: 8.9990 chunk 721 optimal weight: 0.3980 chunk 281 optimal weight: 8.9990 chunk 830 optimal weight: 4.9990 chunk 869 optimal weight: 10.0000 chunk 915 optimal weight: 4.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 37 ASN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 74 HIS ** 6 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 156671 Z= 0.423 Angle : 0.708 14.266 234146 Z= 0.359 Chirality : 0.045 0.530 29868 Planarity : 0.006 0.086 12746 Dihedral : 24.004 179.792 77783 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.38 % Favored : 93.57 % Rotamer: Outliers : 5.78 % Allowed : 32.25 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.89 (0.10), residues: 5816 helix: 0.43 (0.11), residues: 1940 sheet: -0.05 (0.17), residues: 900 loop : -1.48 (0.10), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP r 33 HIS 0.013 0.002 HIS e 94 PHE 0.036 0.002 PHE r 9 TYR 0.030 0.002 TYR c 134 ARG 0.019 0.001 ARG 6 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 471 time to evaluate : 5.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR c 3 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 2 3 ARG cc_start: 0.6859 (OUTLIER) cc_final: 0.6410 (mmp-170) REVERT: C 259 ASN cc_start: 0.7021 (t0) cc_final: 0.6725 (t0) REVERT: D 38 LYS cc_start: 0.5876 (OUTLIER) cc_final: 0.4367 (mttt) REVERT: D 133 THR cc_start: 0.7039 (p) cc_final: 0.6651 (p) REVERT: E 176 ASP cc_start: 0.5863 (OUTLIER) cc_final: 0.5654 (m-30) REVERT: G 82 PHE cc_start: 0.5789 (OUTLIER) cc_final: 0.5227 (m-80) REVERT: J 118 MET cc_start: 0.7498 (mtt) cc_final: 0.7166 (mtt) REVERT: K 19 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7548 (ttt) REVERT: M 136 MET cc_start: 0.4364 (pmm) cc_final: 0.4054 (pmm) REVERT: N 64 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.6847 (mtt180) REVERT: N 73 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8090 (m-40) REVERT: R 6 GLN cc_start: 0.6493 (OUTLIER) cc_final: 0.6116 (tp-100) REVERT: R 82 HIS cc_start: 0.6696 (OUTLIER) cc_final: 0.6296 (t70) REVERT: S 57 ASN cc_start: 0.7252 (m-40) cc_final: 0.6961 (m-40) REVERT: U 85 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6346 (ptt90) REVERT: W 38 ARG cc_start: 0.7366 (mtt90) cc_final: 0.6705 (mtt90) REVERT: Y 30 MET cc_start: 0.3503 (mtt) cc_final: 0.3275 (mtt) REVERT: c 123 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.5838 (tpp) REVERT: d 158 LYS cc_start: 0.4706 (OUTLIER) cc_final: 0.2788 (tmtt) REVERT: e 6 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.7076 (mm) REVERT: e 9 MET cc_start: 0.7199 (mtm) cc_final: 0.6929 (ptp) REVERT: e 90 MET cc_start: 0.6807 (mmm) cc_final: 0.6554 (mmm) REVERT: i 72 ARG cc_start: 0.8213 (mmt-90) cc_final: 0.7835 (mpt180) REVERT: j 127 ARG cc_start: 0.5868 (OUTLIER) cc_final: 0.3974 (ptt90) REVERT: k 115 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.6954 (mtpt) REVERT: l 43 LYS cc_start: 0.4705 (OUTLIER) cc_final: 0.4101 (pttm) REVERT: l 80 MET cc_start: 0.1164 (mmm) cc_final: -0.1599 (mmt) REVERT: n 62 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7127 (ttp-110) REVERT: o 14 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7101 (mtp180) REVERT: 6 50 LYS cc_start: 0.6179 (mmtm) cc_final: 0.5718 (mttm) REVERT: 6 58 VAL cc_start: 0.1295 (OUTLIER) cc_final: 0.1051 (t) REVERT: 6 205 TYR cc_start: 0.6482 (OUTLIER) cc_final: 0.5025 (t80) REVERT: 6 255 PHE cc_start: 0.6195 (OUTLIER) cc_final: 0.5428 (m-80) outliers start: 281 outliers final: 234 residues processed: 699 average time/residue: 1.3265 time to fit residues: 1575.9758 Evaluate side-chains 725 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 470 time to evaluate : 5.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 2 residue 3 ARG Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 82 PHE Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 5 LYS Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 93 LYS Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 85 ARG Chi-restraints excluded: chain V residue 31 TYR Chi-restraints excluded: chain V residue 48 MET Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 19 ARG Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain w residue 40 ILE Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 183 PHE Chi-restraints excluded: chain w residue 185 ILE Chi-restraints excluded: chain w residue 199 ILE Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 27 GLU Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 120 THR Chi-restraints excluded: chain x residue 180 ASP Chi-restraints excluded: chain x residue 194 VAL Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain c residue 135 GLN Chi-restraints excluded: chain c residue 166 LYS Chi-restraints excluded: chain c residue 173 ASP Chi-restraints excluded: chain d residue 11 GLN Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 40 ASP Chi-restraints excluded: chain d residue 87 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 119 VAL Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 158 LYS Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 46 GLN Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 88 MET Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 9 ARG Chi-restraints excluded: chain f residue 29 LEU Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 141 HIS Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 98 LEU Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 5 TYR Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 18 ILE Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 71 LEU Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain j residue 22 ILE Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 85 VAL Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 100 ASN Chi-restraints excluded: chain j residue 127 ARG Chi-restraints excluded: chain k residue 71 HIS Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 115 LYS Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 64 VAL Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain m residue 67 THR Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain m residue 84 VAL Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 62 ARG Chi-restraints excluded: chain o residue 14 ARG Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 33 ILE Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 61 VAL Chi-restraints excluded: chain p residue 11 VAL Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 49 ASN Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 6 LYS Chi-restraints excluded: chain r residue 10 ILE Chi-restraints excluded: chain r residue 18 VAL Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain s residue 65 LEU Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 90 ARG Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 114 ARG Chi-restraints excluded: chain 6 residue 116 ARG Chi-restraints excluded: chain 6 residue 117 THR Chi-restraints excluded: chain 6 residue 121 LYS Chi-restraints excluded: chain 6 residue 134 THR Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 194 LYS Chi-restraints excluded: chain 6 residue 203 VAL Chi-restraints excluded: chain 6 residue 205 TYR Chi-restraints excluded: chain 6 residue 210 LYS Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 222 VAL Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 268 LYS Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 6 residue 282 HIS Chi-restraints excluded: chain 6 residue 290 ARG Chi-restraints excluded: chain 6 residue 313 LEU Chi-restraints excluded: chain 6 residue 329 ILE Chi-restraints excluded: chain 6 residue 340 VAL Chi-restraints excluded: chain 6 residue 350 ILE Chi-restraints excluded: chain 6 residue 353 LEU Chi-restraints excluded: chain 6 residue 357 LEU Chi-restraints excluded: chain 6 residue 365 VAL Chi-restraints excluded: chain 6 residue 369 THR Chi-restraints excluded: chain 6 residue 406 MET Chi-restraints excluded: chain 6 residue 424 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 603 optimal weight: 8.9990 chunk 971 optimal weight: 6.9990 chunk 593 optimal weight: 0.9980 chunk 460 optimal weight: 0.2980 chunk 675 optimal weight: 5.9990 chunk 1019 optimal weight: 20.0000 chunk 938 optimal weight: 6.9990 chunk 811 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 626 optimal weight: 8.9990 chunk 497 optimal weight: 2.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 HIS ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 64 GLN ** j 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 42 ASN s 74 HIS ** 6 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 156671 Z= 0.230 Angle : 0.581 12.721 234146 Z= 0.300 Chirality : 0.036 0.327 29868 Planarity : 0.005 0.072 12746 Dihedral : 23.897 179.806 77781 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.58 % Rotamer: Outliers : 5.15 % Allowed : 32.95 % Favored : 61.91 % Cbeta Deviations : 0.00 % 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: -0.62 (0.11), residues: 5816 helix: 0.79 (0.12), residues: 1937 sheet: -0.01 (0.17), residues: 907 loop : -1.39 (0.11), residues: 2972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP X 38 HIS 0.007 0.001 HIS e 94 PHE 0.028 0.001 PHE r 9 TYR 0.016 0.001 TYR c 134 ARG 0.015 0.000 ARG P 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 463 time to evaluate : 5.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "TYR c 3 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: C 259 ASN cc_start: 0.6857 (t0) cc_final: 0.6629 (t0) REVERT: D 38 LYS cc_start: 0.5856 (OUTLIER) cc_final: 0.4318 (mttt) REVERT: D 133 THR cc_start: 0.7168 (p) cc_final: 0.6712 (p) REVERT: E 176 ASP cc_start: 0.5611 (OUTLIER) cc_final: 0.5388 (m-30) REVERT: G 82 PHE cc_start: 0.5631 (OUTLIER) cc_final: 0.5139 (m-80) REVERT: J 118 MET cc_start: 0.7500 (mtt) cc_final: 0.7110 (mtt) REVERT: K 19 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7448 (ttt) REVERT: M 136 MET cc_start: 0.4344 (pmm) cc_final: 0.4036 (pmm) REVERT: N 64 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6820 (mtt180) REVERT: N 73 ASN cc_start: 0.8392 (OUTLIER) cc_final: 0.8062 (m-40) REVERT: O 30 ARG cc_start: 0.6419 (ttp80) cc_final: 0.5976 (ttp80) REVERT: R 6 GLN cc_start: 0.6445 (OUTLIER) cc_final: 0.6071 (tp-100) REVERT: S 57 ASN cc_start: 0.7173 (m-40) cc_final: 0.6890 (m-40) REVERT: T 49 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7650 (ttpp) REVERT: U 85 ARG cc_start: 0.6485 (OUTLIER) cc_final: 0.5641 (ptt90) REVERT: W 38 ARG cc_start: 0.7357 (mtt90) cc_final: 0.6667 (mtt90) REVERT: c 123 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5812 (tpp) REVERT: c 146 GLU cc_start: 0.6751 (tm-30) cc_final: 0.6372 (tm-30) REVERT: d 158 LYS cc_start: 0.4467 (OUTLIER) cc_final: 0.2625 (tmtt) REVERT: e 6 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7096 (mm) REVERT: e 9 MET cc_start: 0.7056 (mtm) cc_final: 0.6803 (ptp) REVERT: e 90 MET cc_start: 0.6700 (mmm) cc_final: 0.6459 (mmm) REVERT: i 72 ARG cc_start: 0.8196 (mmt-90) cc_final: 0.7812 (mpt180) REVERT: j 127 ARG cc_start: 0.5761 (OUTLIER) cc_final: 0.3894 (ptt90) REVERT: k 115 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6942 (mtpt) REVERT: l 80 MET cc_start: 0.1227 (mmm) cc_final: -0.1236 (mmt) REVERT: n 62 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7110 (ttp-110) REVERT: 6 50 LYS cc_start: 0.6077 (mmtm) cc_final: 0.5737 (mmtm) REVERT: 6 58 VAL cc_start: 0.1170 (OUTLIER) cc_final: 0.0909 (t) REVERT: 6 205 TYR cc_start: 0.6320 (OUTLIER) cc_final: 0.4763 (t80) outliers start: 250 outliers final: 216 residues processed: 668 average time/residue: 1.3538 time to fit residues: 1536.9954 Evaluate side-chains 695 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 462 time to evaluate : 5.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 82 PHE Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 1 ILE Chi-restraints excluded: chain K residue 19 MET Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain L residue 142 ILE Chi-restraints excluded: chain M residue 31 PHE Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 131 VAL Chi-restraints excluded: chain N residue 64 ARG Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 25 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 93 LYS Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 8 LEU Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 49 LYS Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain U residue 23 LYS Chi-restraints excluded: chain U residue 40 LEU Chi-restraints excluded: chain U residue 76 THR Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 85 ARG Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain V residue 48 MET Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 19 ARG Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 57 THR Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 55 LYS Chi-restraints excluded: chain w residue 40 ILE Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 183 PHE Chi-restraints excluded: chain w residue 185 ILE Chi-restraints excluded: chain w residue 199 ILE Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 27 GLU Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 120 THR Chi-restraints excluded: chain x residue 180 ASP Chi-restraints excluded: chain x residue 194 VAL Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain c residue 135 GLN Chi-restraints excluded: chain c residue 173 ASP Chi-restraints excluded: chain d residue 11 GLN Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 40 ASP Chi-restraints excluded: chain d residue 87 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 119 VAL Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 140 ILE Chi-restraints excluded: chain d residue 158 LYS Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 46 GLN Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 9 ARG Chi-restraints excluded: chain f residue 29 LEU Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 141 HIS Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 98 LEU Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 5 TYR Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 18 ILE Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 71 LEU Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain j residue 22 ILE Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 85 VAL Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 100 ASN Chi-restraints excluded: chain j residue 127 ARG Chi-restraints excluded: chain k residue 71 HIS Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 115 LYS Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 33 LEU Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 64 VAL Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain m residue 67 THR Chi-restraints excluded: chain m residue 79 LEU Chi-restraints excluded: chain m residue 82 ILE Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain n residue 55 LEU Chi-restraints excluded: chain n residue 62 ARG Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 61 VAL Chi-restraints excluded: chain p residue 11 VAL Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 10 ILE Chi-restraints excluded: chain r residue 18 VAL Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain 6 residue 1 MET Chi-restraints excluded: chain 6 residue 39 VAL Chi-restraints excluded: chain 6 residue 58 VAL Chi-restraints excluded: chain 6 residue 110 ILE Chi-restraints excluded: chain 6 residue 116 ARG Chi-restraints excluded: chain 6 residue 117 THR Chi-restraints excluded: chain 6 residue 121 LYS Chi-restraints excluded: chain 6 residue 134 THR Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 194 LYS Chi-restraints excluded: chain 6 residue 203 VAL Chi-restraints excluded: chain 6 residue 205 TYR Chi-restraints excluded: chain 6 residue 210 LYS Chi-restraints excluded: chain 6 residue 213 LEU Chi-restraints excluded: chain 6 residue 222 VAL Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 268 LYS Chi-restraints excluded: chain 6 residue 271 LEU Chi-restraints excluded: chain 6 residue 282 HIS Chi-restraints excluded: chain 6 residue 290 ARG Chi-restraints excluded: chain 6 residue 329 ILE Chi-restraints excluded: chain 6 residue 350 ILE Chi-restraints excluded: chain 6 residue 353 LEU Chi-restraints excluded: chain 6 residue 357 LEU Chi-restraints excluded: chain 6 residue 365 VAL Chi-restraints excluded: chain 6 residue 369 THR Chi-restraints excluded: chain 6 residue 424 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 644 optimal weight: 1.9990 chunk 864 optimal weight: 5.9990 chunk 248 optimal weight: 220.0000 chunk 748 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 225 optimal weight: 50.0000 chunk 812 optimal weight: 3.9990 chunk 340 optimal weight: 0.0050 chunk 834 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN J 132 HIS ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 ASN s 74 HIS ** 6 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.163333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.133606 restraints weight = 196496.922| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.19 r_work: 0.3366 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 156671 Z= 0.344 Angle : 0.644 12.245 234146 Z= 0.328 Chirality : 0.041 0.427 29868 Planarity : 0.005 0.077 12746 Dihedral : 23.896 179.946 77780 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.19 % Favored : 93.76 % Rotamer: Outliers : 5.27 % Allowed : 32.68 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.71 (0.11), residues: 5816 helix: 0.68 (0.12), residues: 1928 sheet: 0.03 (0.17), residues: 883 loop : -1.42 (0.11), residues: 3005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP X 38 HIS 0.009 0.001 HIS e 94 PHE 0.033 0.002 PHE r 9 TYR 0.025 0.002 TYR c 134 ARG 0.016 0.000 ARG P 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27322.06 seconds wall clock time: 484 minutes 10.69 seconds (29050.69 seconds total)