Starting phenix.real_space_refine on Sun Mar 3 03:45:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9l_43076/03_2024/8v9l_43076_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9l_43076/03_2024/8v9l_43076.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9l_43076/03_2024/8v9l_43076_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9l_43076/03_2024/8v9l_43076_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9l_43076/03_2024/8v9l_43076_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9l_43076/03_2024/8v9l_43076.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9l_43076/03_2024/8v9l_43076.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9l_43076/03_2024/8v9l_43076_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9l_43076/03_2024/8v9l_43076_updated.pdb" } resolution = 3.0 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= 0.002 sd= 1.016 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4781 5.49 5 S 124 5.16 5 C 78782 2.51 5 N 29037 2.21 5 O 42921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 38": "OE1" <-> "OE2" Residue "e GLU 187": "OE1" <-> "OE2" Residue "f TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 77": "OE1" <-> "OE2" Residue "k ASP 121": "OD1" <-> "OD2" Residue "l TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 103": "OD1" <-> "OD2" Residue "r TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 44": "OE1" <-> "OE2" Residue "x PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 120": "OE1" <-> "OE2" Residue "x PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 269": "OD1" <-> "OD2" Residue "z ASP 32": "OD1" <-> "OD2" Residue "z ASP 143": "OD1" <-> "OD2" Residue "z TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C ASP 124": "OD1" <-> "OD2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D ASP 173": "OD1" <-> "OD2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "G PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 156": "OD1" <-> "OD2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 10": "OD1" <-> "OD2" Residue "L ASP 52": "OD1" <-> "OD2" Residue "L PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "M ASP 92": "OD1" <-> "OD2" Residue "N ASP 96": "OD1" <-> "OD2" Residue "O GLU 38": "OE1" <-> "OE2" Residue "O GLU 48": "OE1" <-> "OE2" Residue "O ASP 71": "OD1" <-> "OD2" Residue "P ASP 74": "OD1" <-> "OD2" Residue "P TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 101": "OE1" <-> "OE2" Residue "R ASP 84": "OD1" <-> "OD2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S GLU 97": "OE1" <-> "OE2" Residue "S ASP 111": "OD1" <-> "OD2" Residue "T TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 66": "OE1" <-> "OE2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 69": "OE1" <-> "OE2" Residue "V GLU 47": "OE1" <-> "OE2" Residue "V ASP 51": "OD1" <-> "OD2" Residue "V ASP 55": "OD1" <-> "OD2" Residue "W TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 30": "OD1" <-> "OD2" Residue "X ASP 53": "OD1" <-> "OD2" Residue "7 ASP 45": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 155647 Number of models: 1 Model: "" Number of chains: 62 Chain: "a" Number of atoms: 32439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1511, 32439 Classifications: {'RNA': 1511} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 85, 'rna3p_pur': 737, 'rna3p_pyr': 577} Link IDs: {'rna2p': 197, 'rna3p': 1313} Chain: "b" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1793 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "c" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1660 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 5, 'TRANS': 202} Chain: "d" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1641 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 11, 'TRANS': 188} Chain: "e" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1296 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 8, 'TRANS': 171} Chain: "f" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 771 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "g" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1232 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "h" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1010 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "i" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Chain: "j" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 788 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 7, 'TRANS': 91} Chain: "k" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 855 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "l" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 958 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "m" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 935 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "n" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 477 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 891 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 8, 'TRANS': 104} Chain: "q" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 748 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "r" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 513 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "s" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 662 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "t" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 660 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 280 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "v" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Classifications: {'RNA': 4} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 3} Link IDs: {'rna3p': 3} Chain: "x" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2997 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 365} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "y" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1581 Classifications: {'RNA': 74} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p': 5, 'rna3p_pur': 33, 'rna3p_pyr': 27} Link IDs: {'rna2p': 9, 'rna3p': 64} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "z" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2909 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 360} Chain: "A" Number of atoms: 65997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3073, 65997 Classifications: {'RNA': 3073} Modifications used: {'rna2p_pur': 295, 'rna2p_pyr': 151, 'rna3p_pur': 1464, 'rna3p_pyr': 1163} Link IDs: {'rna2p': 446, 'rna3p': 2626} Chain breaks: 1 Chain: "B" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2522 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 47} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "C" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2110 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 19, 'TRANS': 255} Chain: "D" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1587 Classifications: {'peptide': 214} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 205} Chain: "E" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1569 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1439 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 173} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1348 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "H" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1018 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 3, 'TRANS': 147} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 68 Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 918 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain: "J" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 990 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain: "L" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'TRANS': 135} Chain: "M" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "N" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1078 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "O" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Chain: "P" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 928 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "Q" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "R" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 907 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "S" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "T" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "U" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 873 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 8, 'TRANS': 105} Chain: "V" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 756 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "W" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 732 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain breaks: 1 Chain: "X" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1428 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain: "Y" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 586 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "Z" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 470 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 4, 'TRANS': 58} Chain: "1" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 531 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "2" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 474 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "3" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 413 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "4" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 423 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "5" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "6" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "7" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "8" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "9" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "x" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A13S5 SG CYS Z 5 186.735 124.250 191.115 1.00 23.20 S ATOM A13SR SG CYS Z 8 185.856 126.439 193.951 1.00 25.45 S ATOM A1429 SG CYS Z 52 186.090 127.920 190.395 1.00 25.18 S ATOM A142S SG CYS Z 55 189.198 127.028 192.320 1.00 28.65 S ATOM A15LT SG CYS 5 15 149.209 187.351 186.256 1.00 30.04 S ATOM A15MF SG CYS 5 18 150.957 185.323 189.005 1.00 30.58 S ATOM A15SE SG CYS 5 42 147.356 185.805 189.198 1.00 26.05 S ATOM A15SZ SG CYS 5 45 149.648 188.702 189.950 1.00 28.25 S Time building chain proxies: 53.21, per 1000 atoms: 0.34 Number of scatterers: 155647 At special positions: 0 Unit cell: (255.85, 243.1, 286.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 124 16.00 P 4781 15.00 O 42921 8.00 N 29037 7.00 C 78782 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: 59.63 Conformation dependent library (CDL) restraints added in 8.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 18 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 42 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 45 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 15 " pdb=" ZN Z 101 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 8 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 5 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 55 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 52 " Number of angles added : 12 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12494 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: 208 helices and 84 sheets defined 38.8% alpha, 19.7% beta 1608 base pairs and 2468 stacking pairs defined. Time for finding SS restraints: 80.54 Creating SS restraints... Processing helix chain 'b' and resid 5 through 13 Processing helix chain 'b' and resid 42 through 64 removed outlier: 3.840A pdb=" N THR b 46 " --> pdb=" O ASP b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 88 removed outlier: 5.261A pdb=" N GLU b 78 " --> pdb=" O LYS b 74 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N SER b 79 " --> pdb=" O GLN b 75 " (cutoff:3.500A) Processing helix chain 'b' and resid 99 through 104 removed outlier: 4.670A pdb=" N PHE b 104 " --> pdb=" O MET b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 124 Processing helix chain 'b' and resid 130 through 149 removed outlier: 3.878A pdb=" N ARG b 146 " --> pdb=" O ASN b 142 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N SER b 147 " --> pdb=" O LYS b 143 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 155 removed outlier: 3.693A pdb=" N MET b 154 " --> pdb=" O GLY b 150 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLN b 155 " --> pdb=" O ILE b 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 150 through 155' Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 192 through 197 removed outlier: 4.143A pdb=" N VAL b 196 " --> pdb=" O ASP b 192 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ASP b 197 " --> pdb=" O PRO b 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 192 through 197' Processing helix chain 'b' and resid 206 through 228 Processing helix chain 'c' and resid 6 through 13 removed outlier: 3.657A pdb=" N LEU c 12 " --> pdb=" O HIS c 8 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLY c 13 " --> pdb=" O GLY c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 47 removed outlier: 3.519A pdb=" N LEU c 46 " --> pdb=" O LEU c 42 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU c 47 " --> pdb=" O ALA c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 76 removed outlier: 4.242A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 94 removed outlier: 3.786A pdb=" N THR c 94 " --> pdb=" O LEU c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 4.111A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.554A pdb=" N ALA c 132 " --> pdb=" O ALA c 128 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN c 143 " --> pdb=" O SER c 139 " (cutoff:3.500A) Proline residue: c 144 - end of helix Processing helix chain 'd' and resid 7 through 16 removed outlier: 3.964A pdb=" N LYS d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 30 removed outlier: 4.979A pdb=" N GLU d 27 " --> pdb=" O ASP d 23 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS d 28 " --> pdb=" O GLN d 24 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG d 29 " --> pdb=" O SER d 25 " (cutoff:3.500A) Proline residue: d 30 - end of helix No H-bonds generated for 'chain 'd' and resid 23 through 30' Processing helix chain 'd' and resid 44 through 61 removed outlier: 4.262A pdb=" N TYR d 60 " --> pdb=" O ALA d 56 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY d 61 " --> pdb=" O ARG d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 63 through 78 removed outlier: 3.929A pdb=" N GLN d 77 " --> pdb=" O GLU d 73 " (cutoff:3.500A) Proline residue: d 78 - end of helix Processing helix chain 'd' and resid 80 through 92 removed outlier: 4.223A pdb=" N ARG d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 removed outlier: 3.633A pdb=" N GLY d 101 " --> pdb=" O VAL d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 116 removed outlier: 3.909A pdb=" N HIS d 115 " --> pdb=" O GLN d 111 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY d 116 " --> pdb=" O LEU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 141 through 146 removed outlier: 3.876A pdb=" N LEU d 145 " --> pdb=" O LYS d 141 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASN d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 141 through 146' Processing helix chain 'd' and resid 147 through 157 removed outlier: 3.579A pdb=" N THR d 156 " --> pdb=" O ILE d 152 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 187 removed outlier: 3.548A pdb=" N ASP d 187 " --> pdb=" O ARG d 183 " (cutoff:3.500A) Processing helix chain 'd' and resid 191 through 201 removed outlier: 5.045A pdb=" N ILE d 195 " --> pdb=" O THR d 191 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL d 196 " --> pdb=" O GLU d 192 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 80 through 96 removed outlier: 3.512A pdb=" N LYS e 94 " --> pdb=" O GLU e 90 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN e 95 " --> pdb=" O GLU e 91 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE e 96 " --> pdb=" O ALA e 92 " (cutoff:3.500A) Processing helix chain 'e' and resid 134 through 144 Processing helix chain 'e' and resid 157 through 172 removed outlier: 3.647A pdb=" N LEU e 172 " --> pdb=" O ALA e 168 " (cutoff:3.500A) Processing helix chain 'e' and resid 174 through 183 Processing helix chain 'e' and resid 185 through 190 removed outlier: 3.627A pdb=" N VAL e 189 " --> pdb=" O PRO e 185 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 214 removed outlier: 3.591A pdb=" N ALA e 214 " --> pdb=" O ARG e 210 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 32 removed outlier: 3.692A pdb=" N VAL f 19 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Proline residue: f 21 - end of helix removed outlier: 3.567A pdb=" N PHE f 26 " --> pdb=" O SER f 22 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL f 29 " --> pdb=" O THR f 25 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 82 removed outlier: 3.751A pdb=" N LEU f 81 " --> pdb=" O ARG f 77 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN f 82 " --> pdb=" O GLN f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 4.481A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.860A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 109 removed outlier: 4.261A pdb=" N ARG g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 149 removed outlier: 3.545A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 114 through 122 Processing helix chain 'i' and resid 54 through 59 removed outlier: 4.842A pdb=" N PHE i 59 " --> pdb=" O LEU i 55 " (cutoff:3.500A) Processing helix chain 'i' and resid 61 through 76 Proline residue: i 71 - end of helix Processing helix chain 'i' and resid 91 through 112 Proline residue: i 112 - end of helix Processing helix chain 'i' and resid 113 through 122 removed outlier: 5.452A pdb=" N ALA i 117 " --> pdb=" O GLU i 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU i 118 " --> pdb=" O ASP i 114 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS i 119 " --> pdb=" O ARG i 115 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS i 120 " --> pdb=" O PRO i 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 88 removed outlier: 4.614A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 60 removed outlier: 3.515A pdb=" N VAL k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY k 60 " --> pdb=" O SER k 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 55 through 60' Processing helix chain 'k' and resid 63 through 68 removed outlier: 4.459A pdb=" N SER k 67 " --> pdb=" O GLY k 63 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR k 68 " --> pdb=" O SER k 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 63 through 68' Processing helix chain 'k' and resid 69 through 87 removed outlier: 3.580A pdb=" N HIS k 86 " --> pdb=" O LYS k 82 " (cutoff:3.500A) Processing helix chain 'k' and resid 101 through 113 removed outlier: 3.971A pdb=" N GLY k 113 " --> pdb=" O LEU k 109 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 3.920A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.375A pdb=" N THR m 20 " --> pdb=" O GLU m 16 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 4.093A pdb=" N SER m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN m 31 " --> pdb=" O ARG m 27 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 5.745A pdb=" N THR m 49 " --> pdb=" O THR m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 50 through 64 removed outlier: 3.714A pdb=" N LEU m 64 " --> pdb=" O ILE m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 85 removed outlier: 4.080A pdb=" N ILE m 84 " --> pdb=" O ARG m 80 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLY m 85 " --> pdb=" O LYS m 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 95 removed outlier: 3.631A pdb=" N GLY m 95 " --> pdb=" O ARG m 91 " (cutoff:3.500A) Processing helix chain 'm' and resid 107 through 112 Processing helix chain 'n' and resid 3 through 13 removed outlier: 4.846A pdb=" N LYS n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 51 Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 47 removed outlier: 4.041A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS o 47 " --> pdb=" O LEU o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 52 through 63 Processing helix chain 'p' and resid 67 through 78 Processing helix chain 'p' and resid 79 through 85 Processing helix chain 'p' and resid 101 through 114 Processing helix chain 'r' and resid 20 through 25 removed outlier: 3.594A pdb=" N SER r 24 " --> pdb=" O CYS r 20 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS r 25 " --> pdb=" O VAL r 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 20 through 25' Processing helix chain 'r' and resid 34 through 43 removed outlier: 3.955A pdb=" N TYR r 41 " --> pdb=" O LEU r 37 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N SER r 43 " --> pdb=" O ARG r 39 " (cutoff:3.500A) Processing helix chain 'r' and resid 50 through 55 Processing helix chain 'r' and resid 57 through 75 Processing helix chain 's' and resid 12 through 26 removed outlier: 3.822A pdb=" N LEU s 16 " --> pdb=" O ASP s 12 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 46 removed outlier: 3.565A pdb=" N ILE s 45 " --> pdb=" O ILE s 41 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY s 46 " --> pdb=" O PRO s 42 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 41 through 46' Processing helix chain 's' and resid 70 through 76 removed outlier: 4.270A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 42 Processing helix chain 't' and resid 44 through 65 removed outlier: 3.782A pdb=" N ALA t 53 " --> pdb=" O GLU t 49 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 86 removed outlier: 3.798A pdb=" N LEU t 86 " --> pdb=" O ALA t 82 " (cutoff:3.500A) Processing helix chain 'u' and resid 3 through 25 removed outlier: 4.232A pdb=" N LYS u 7 " --> pdb=" O SER u 3 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG u 25 " --> pdb=" O LEU u 21 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 33 Processing helix chain 'x' and resid 24 through 41 Proline residue: x 41 - end of helix Processing helix chain 'x' and resid 48 through 55 removed outlier: 4.659A pdb=" N ALA x 55 " --> pdb=" O GLN x 51 " (cutoff:3.500A) Processing helix chain 'x' and resid 86 through 97 Processing helix chain 'x' and resid 115 through 129 Processing helix chain 'x' and resid 139 through 144 removed outlier: 4.960A pdb=" N ASP x 144 " --> pdb=" O SER x 140 " (cutoff:3.500A) Processing helix chain 'x' and resid 145 through 164 removed outlier: 3.721A pdb=" N ILE x 149 " --> pdb=" O ASP x 145 " (cutoff:3.500A) Processing helix chain 'x' and resid 175 through 182 Processing helix chain 'x' and resid 183 through 201 removed outlier: 3.959A pdb=" N LYS x 188 " --> pdb=" O PRO x 184 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N SER x 189 " --> pdb=" O LYS x 185 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE x 201 " --> pdb=" O VAL x 197 " (cutoff:3.500A) Processing helix chain 'x' and resid 206 through 211 Proline residue: x 211 - end of helix Processing helix chain 'x' and resid 285 through 290 removed outlier: 3.931A pdb=" N VAL x 289 " --> pdb=" O LYS x 285 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N GLU x 290 " --> pdb=" O ARG x 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 285 through 290' Processing helix chain 'z' and resid 8 through 18 removed outlier: 3.539A pdb=" N GLN z 17 " --> pdb=" O ARG z 13 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG z 18 " --> pdb=" O ASP z 14 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 59 removed outlier: 4.066A pdb=" N ASP z 58 " --> pdb=" O ARG z 54 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY z 59 " --> pdb=" O MET z 55 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 83 removed outlier: 3.780A pdb=" N ARG z 74 " --> pdb=" O LEU z 70 " (cutoff:3.500A) Proline residue: z 75 - end of helix removed outlier: 4.311A pdb=" N GLU z 78 " --> pdb=" O ARG z 74 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY z 83 " --> pdb=" O THR z 79 " (cutoff:3.500A) Processing helix chain 'z' and resid 122 through 133 removed outlier: 3.969A pdb=" N ARG z 133 " --> pdb=" O LEU z 129 " (cutoff:3.500A) Processing helix chain 'z' and resid 176 through 207 Processing helix chain 'z' and resid 219 through 227 removed outlier: 4.370A pdb=" N ALA z 223 " --> pdb=" O TRP z 219 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE z 227 " --> pdb=" O ALA z 223 " (cutoff:3.500A) Processing helix chain 'z' and resid 245 through 277 removed outlier: 5.657A pdb=" N GLY z 277 " --> pdb=" O CYS z 273 " (cutoff:3.500A) Processing helix chain 'z' and resid 284 through 295 Processing helix chain 'z' and resid 336 through 349 removed outlier: 4.009A pdb=" N ARG z 340 " --> pdb=" O ARG z 336 " (cutoff:3.500A) Processing helix chain 'z' and resid 357 through 362 removed outlier: 4.520A pdb=" N ALA z 361 " --> pdb=" O GLY z 357 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL z 362 " --> pdb=" O ALA z 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 357 through 362' Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.639A pdb=" N ILE C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Proline residue: C 137 - end of helix No H-bonds generated for 'chain 'C' and resid 132 through 137' Processing helix chain 'C' and resid 208 through 216 removed outlier: 3.999A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY C 216 " --> pdb=" O MET C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 4.158A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 227' Processing helix chain 'C' and resid 262 through 269 removed outlier: 4.568A pdb=" N LYS C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LEU C 267 " --> pdb=" O PRO C 263 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N VAL C 269 " --> pdb=" O ASP C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 262 through 269' Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.613A pdb=" N GLN D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 95 removed outlier: 3.774A pdb=" N VAL D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 95' Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 102 through 107 removed outlier: 5.269A pdb=" N SER D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 30 through 47 removed outlier: 3.764A pdb=" N GLN E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLN E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 122 removed outlier: 3.606A pdb=" N LEU E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 149 Processing helix chain 'E' and resid 162 through 171 removed outlier: 3.582A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASN E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 192 removed outlier: 3.540A pdb=" N ALA E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ASP E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 210 removed outlier: 3.594A pdb=" N ALA E 203 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA E 207 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN E 208 " --> pdb=" O TYR E 204 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS E 210 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 18 removed outlier: 3.815A pdb=" N GLU F 17 " --> pdb=" O GLN F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 28 removed outlier: 3.639A pdb=" N GLN F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN F 25 " --> pdb=" O GLU F 21 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU F 26 " --> pdb=" O ALA F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 removed outlier: 4.019A pdb=" N ASP F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 49 through 54' Processing helix chain 'F' and resid 55 through 69 removed outlier: 3.528A pdb=" N ALA F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA F 65 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 118 removed outlier: 3.538A pdb=" N TRP F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE F 106 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU F 115 " --> pdb=" O ILE F 111 " (cutoff:3.500A) Proline residue: F 116 - end of helix Processing helix chain 'F' and resid 149 through 154 removed outlier: 5.684A pdb=" N ASP F 154 " --> pdb=" O VAL F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 181 Processing helix chain 'G' and resid 2 through 7 removed outlier: 4.331A pdb=" N GLN G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.685A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 152 removed outlier: 3.614A pdb=" N ARG G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 41 through 60 removed outlier: 3.646A pdb=" N ILE H 50 " --> pdb=" O GLN H 46 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG H 60 " --> pdb=" O SER H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 74 removed outlier: 4.183A pdb=" N GLU H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 108 removed outlier: 4.032A pdb=" N VAL H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS H 106 " --> pdb=" O ASN H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 removed outlier: 4.550A pdb=" N VAL H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLN H 118 " --> pdb=" O LYS H 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 113 through 118' Processing helix chain 'I' and resid 2 through 20 removed outlier: 3.558A pdb=" N ALA I 11 " --> pdb=" O ALA I 7 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE I 17 " --> pdb=" O ILE I 13 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS I 18 " --> pdb=" O ALA I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 44 removed outlier: 3.512A pdb=" N GLU I 38 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU I 39 " --> pdb=" O ASN I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 65 removed outlier: 3.713A pdb=" N LYS I 58 " --> pdb=" O ASN I 54 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLY I 65 " --> pdb=" O ALA I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 101 removed outlier: 5.956A pdb=" N ALA I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA I 92 " --> pdb=" O ASP I 88 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP I 99 " --> pdb=" O LYS I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 126 removed outlier: 3.709A pdb=" N LYS I 122 " --> pdb=" O ALA I 118 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA I 124 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP I 125 " --> pdb=" O GLU I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 34 Proline residue: J 28 - end of helix removed outlier: 5.270A pdb=" N HIS J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY J 34 " --> pdb=" O LEU J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 49 removed outlier: 3.786A pdb=" N PHE J 40 " --> pdb=" O ASN J 36 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU J 49 " --> pdb=" O ASN J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 86 Processing helix chain 'J' and resid 103 through 115 Processing helix chain 'J' and resid 122 through 138 removed outlier: 3.541A pdb=" N LYS J 128 " --> pdb=" O ASP J 124 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER J 136 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET J 137 " --> pdb=" O THR J 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 38 removed outlier: 3.592A pdb=" N THR L 34 " --> pdb=" O SER L 30 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG L 37 " --> pdb=" O ALA L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 96 removed outlier: 3.698A pdb=" N GLU L 94 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 110 removed outlier: 4.033A pdb=" N VAL L 101 " --> pdb=" O PRO L 97 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU L 109 " --> pdb=" O ILE L 105 " (cutoff:3.500A) Proline residue: L 110 - end of helix Processing helix chain 'L' and resid 112 through 122 removed outlier: 3.770A pdb=" N GLN L 117 " --> pdb=" O LYS L 113 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN L 119 " --> pdb=" O GLY L 115 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYS L 120 " --> pdb=" O ARG L 116 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS L 121 " --> pdb=" O GLN L 117 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU L 122 " --> pdb=" O ILE L 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 110 removed outlier: 4.231A pdb=" N GLU M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 118 Processing helix chain 'N' and resid 39 through 44 removed outlier: 3.969A pdb=" N ARG N 43 " --> pdb=" O GLY N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 3.959A pdb=" N LEU N 61 " --> pdb=" O ILE N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 87 removed outlier: 3.572A pdb=" N ILE N 83 " --> pdb=" O ASN N 79 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN N 84 " --> pdb=" O VAL N 80 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS N 85 " --> pdb=" O GLY N 81 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA N 86 " --> pdb=" O ASP N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 102 Processing helix chain 'N' and resid 130 through 141 removed outlier: 3.764A pdb=" N ALA N 140 " --> pdb=" O ALA N 136 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLY N 141 " --> pdb=" O ILE N 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 59 removed outlier: 3.676A pdb=" N ILE O 54 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 126 removed outlier: 3.607A pdb=" N ALA O 114 " --> pdb=" O ASP O 110 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS O 124 " --> pdb=" O ARG O 120 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Proline residue: O 126 - end of helix Processing helix chain 'P' and resid 13 through 32 removed outlier: 3.778A pdb=" N SER P 18 " --> pdb=" O SER P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 57 removed outlier: 3.570A pdb=" N ARG P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) Proline residue: P 46 - end of helix removed outlier: 3.578A pdb=" N LYS P 50 " --> pdb=" O PRO P 46 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS P 54 " --> pdb=" O LYS P 50 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS P 57 " --> pdb=" O THR P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 70 removed outlier: 3.753A pdb=" N LYS P 68 " --> pdb=" O ARG P 64 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS P 69 " --> pdb=" O GLU P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 82 removed outlier: 3.521A pdb=" N THR P 78 " --> pdb=" O ASP P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 89 removed outlier: 3.747A pdb=" N TYR P 87 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA P 88 " --> pdb=" O GLY P 84 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASP P 89 " --> pdb=" O PRO P 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 83 through 89' Processing helix chain 'Q' and resid 9 through 29 removed outlier: 3.516A pdb=" N ARG Q 24 " --> pdb=" O ARG Q 20 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU Q 25 " --> pdb=" O ARG Q 21 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS Q 28 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL Q 29 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 73 removed outlier: 3.602A pdb=" N ALA Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE Q 73 " --> pdb=" O ASP Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 96 removed outlier: 3.540A pdb=" N ARG Q 83 " --> pdb=" O ALA Q 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA Q 95 " --> pdb=" O ARG Q 91 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY Q 96 " --> pdb=" O ALA Q 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 124 removed outlier: 3.505A pdb=" N ALA Q 123 " --> pdb=" O ALA Q 119 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY Q 124 " --> pdb=" O ALA Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 12 removed outlier: 5.177A pdb=" N ALA R 10 " --> pdb=" O PHE R 6 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER R 11 " --> pdb=" O VAL R 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 103 removed outlier: 4.856A pdb=" N ARG R 100 " --> pdb=" O LEU R 96 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLU R 101 " --> pdb=" O TYR R 97 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ARG R 103 " --> pdb=" O LEU R 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 96 through 103' Processing helix chain 'S' and resid 8 through 22 removed outlier: 4.070A pdb=" N LYS S 12 " --> pdb=" O LEU S 8 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS S 13 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG S 14 " --> pdb=" O ALA S 10 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS S 22 " --> pdb=" O LEU S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 31 removed outlier: 3.870A pdb=" N ARG S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 73 removed outlier: 3.515A pdb=" N LEU S 40 " --> pdb=" O LYS S 36 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA S 67 " --> pdb=" O SER S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 Processing helix chain 'S' and resid 91 through 101 removed outlier: 3.720A pdb=" N GLU S 97 " --> pdb=" O LYS S 93 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL S 100 " --> pdb=" O ALA S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 118 removed outlier: 3.715A pdb=" N ALA S 108 " --> pdb=" O ALA S 104 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL S 112 " --> pdb=" O ALA S 108 " (cutoff:3.500A) Proline residue: S 118 - end of helix Processing helix chain 'T' and resid 51 through 59 removed outlier: 3.582A pdb=" N ALA T 56 " --> pdb=" O ALA T 52 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS T 57 " --> pdb=" O ASP T 53 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL T 58 " --> pdb=" O ASP T 54 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ALA T 59 " --> pdb=" O LEU T 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 32 removed outlier: 3.515A pdb=" N ARG U 26 " --> pdb=" O THR U 22 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL U 27 " --> pdb=" O LYS U 23 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU U 30 " --> pdb=" O ARG U 26 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 46 removed outlier: 3.912A pdb=" N ASP U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG U 44 " --> pdb=" O LEU U 40 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TRP U 45 " --> pdb=" O ASP U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 50 through 68 removed outlier: 3.658A pdb=" N VAL U 54 " --> pdb=" O ALA U 50 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL U 57 " --> pdb=" O PRO U 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 6 through 12 removed outlier: 4.842A pdb=" N ILE V 10 " --> pdb=" O ASP V 6 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE V 11 " --> pdb=" O PRO V 7 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU V 12 " --> pdb=" O ARG V 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 6 through 12' Processing helix chain 'V' and resid 17 through 27 removed outlier: 3.577A pdb=" N GLU V 25 " --> pdb=" O TYR V 21 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP V 26 " --> pdb=" O GLY V 22 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN V 27 " --> pdb=" O LEU V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 51 Processing helix chain 'W' and resid 67 through 72 removed outlier: 4.489A pdb=" N VAL W 71 " --> pdb=" O HIS W 67 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N MET W 72 " --> pdb=" O VAL W 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 67 through 72' Processing helix chain 'X' and resid 20 through 31 Processing helix chain 'X' and resid 50 through 61 Processing helix chain 'X' and resid 186 through 194 removed outlier: 3.638A pdb=" N GLU X 191 " --> pdb=" O ALA X 187 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY X 194 " --> pdb=" O LEU X 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 59 Processing helix chain '1' and resid 6 through 13 removed outlier: 3.574A pdb=" N LEU 1 10 " --> pdb=" O THR 1 6 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG 1 11 " --> pdb=" O PRO 1 7 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU 1 12 " --> pdb=" O GLY 1 8 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU 1 13 " --> pdb=" O GLU 1 9 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 6 through 13' Processing helix chain '1' and resid 14 through 39 removed outlier: 3.517A pdb=" N GLU 1 24 " --> pdb=" O ASP 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 67 removed outlier: 4.540A pdb=" N LEU 1 47 " --> pdb=" O ASN 1 43 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG 1 48 " --> pdb=" O ASN 1 44 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE 1 54 " --> pdb=" O VAL 1 50 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA 1 55 " --> pdb=" O ARG 1 51 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 removed outlier: 3.513A pdb=" N SER 2 22 " --> pdb=" O LYS 2 18 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG 2 24 " --> pdb=" O ARG 2 20 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU 2 26 " --> pdb=" O SER 2 22 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 51 removed outlier: 3.540A pdb=" N VAL 2 50 " --> pdb=" O LEU 2 46 " (cutoff:3.500A) Processing helix chain '3' and resid 42 through 47 Processing helix chain '3' and resid 56 through 65 removed outlier: 3.828A pdb=" N TYR 3 65 " --> pdb=" O PHE 3 61 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 21 removed outlier: 4.152A pdb=" N ARG 4 16 " --> pdb=" O ASN 4 12 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA 4 18 " --> pdb=" O ARG 4 14 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLN 4 19 " --> pdb=" O SER 4 15 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TRP 4 20 " --> pdb=" O ARG 4 16 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LYS 4 21 " --> pdb=" O ARG 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 40 through 50 removed outlier: 3.503A pdb=" N LEU 4 44 " --> pdb=" O PRO 4 40 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N LYS 4 45 " --> pdb=" O ARG 4 41 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA 4 46 " --> pdb=" O ARG 4 42 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG 4 48 " --> pdb=" O LEU 4 44 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU 4 49 " --> pdb=" O LYS 4 45 " (cutoff:3.500A) Processing helix chain '5' and resid 28 through 33 Proline residue: 5 33 - end of helix Processing helix chain '6' and resid 11 through 19 Processing helix chain '6' and resid 20 through 27 removed outlier: 3.810A pdb=" N ARG 6 26 " --> pdb=" O ARG 6 22 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR 6 27 " --> pdb=" O LEU 6 23 " (cutoff:3.500A) Processing helix chain '6' and resid 28 through 41 removed outlier: 3.806A pdb=" N ALA 6 32 " --> pdb=" O ARG 6 28 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE 6 33 " --> pdb=" O ALA 6 29 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 14 removed outlier: 3.811A pdb=" N LYS 7 12 " --> pdb=" O SER 7 8 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE 7 14 " --> pdb=" O ALA 7 10 " (cutoff:3.500A) Processing helix chain '7' and resid 32 through 37 removed outlier: 4.728A pdb=" N LYS 7 36 " --> pdb=" O LEU 7 32 " (cutoff:3.500A) Proline residue: 7 37 - end of helix No H-bonds generated for 'chain '7' and resid 32 through 37' Processing helix chain '7' and resid 38 through 45 removed outlier: 3.949A pdb=" N ASP 7 45 " --> pdb=" O THR 7 41 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 64 removed outlier: 4.523A pdb=" N SER 7 56 " --> pdb=" O ALA 7 52 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG 7 57 " --> pdb=" O ALA 7 53 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS 7 60 " --> pdb=" O SER 7 56 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU 7 61 " --> pdb=" O ARG 7 57 " (cutoff:3.500A) Processing helix chain '9' and resid 2 through 12 removed outlier: 4.456A pdb=" N LYS 9 12 " --> pdb=" O LYS 9 8 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 67 through 71 removed outlier: 3.789A pdb=" N VAL b 164 " --> pdb=" O VAL b 70 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.902A pdb=" N ASP c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN c 99 " --> pdb=" O VAL c 63 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL c 65 " --> pdb=" O GLN c 99 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL c 105 " --> pdb=" O THR c 69 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 164 through 169 removed outlier: 5.031A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'd' and resid 136 through 139 Processing sheet with id= 5, first strand: chain 'e' and resid 37 through 41 removed outlier: 6.852A pdb=" N LEU e 61 " --> pdb=" O VAL e 41 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 109 through 113 removed outlier: 4.749A pdb=" N VAL e 118 " --> pdb=" O LEU e 153 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA e 124 " --> pdb=" O ASP e 147 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ASP e 147 " --> pdb=" O ALA e 124 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 58 through 65 Processing sheet with id= 8, first strand: chain 'f' and resid 37 through 44 removed outlier: 4.466A pdb=" N VAL f 37 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'g' and resid 73 through 79 Processing sheet with id= 10, first strand: chain 'h' and resid 23 through 28 removed outlier: 6.269A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.740A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'i' and resid 27 through 31 removed outlier: 4.192A pdb=" N GLN i 47 " --> pdb=" O PHE i 81 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE i 83 " --> pdb=" O GLN i 47 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'j' and resid 42 through 52 removed outlier: 4.383A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'k' and resid 39 through 44 removed outlier: 6.859A pdb=" N VAL k 93 " --> pdb=" O GLY k 117 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'k' and resid 92 through 96 Processing sheet with id= 16, first strand: chain 'l' and resid 29 through 33 removed outlier: 5.204A pdb=" N LEU l 81 " --> pdb=" O ILE l 98 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'l' and resid 35 through 41 removed outlier: 5.128A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'p' and resid 5 through 11 Processing sheet with id= 19, first strand: chain 'q' and resid 21 through 26 removed outlier: 5.041A pdb=" N LYS q 21 " --> pdb=" O GLU q 78 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N SER q 75 " --> pdb=" O VAL q 91 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'q' and resid 34 through 45 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 's' and resid 30 through 34 Processing sheet with id= 22, first strand: chain 'x' and resid 67 through 74 removed outlier: 3.782A pdb=" N THR x 74 " --> pdb=" O ARG x 77 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG x 77 " --> pdb=" O THR x 74 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N HIS x 78 " --> pdb=" O PRO x 11 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ALA x 84 " --> pdb=" O THR x 17 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N GLY x 19 " --> pdb=" O ALA x 84 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY x 103 " --> pdb=" O ASN x 14 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY x 16 " --> pdb=" O GLY x 103 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL x 108 " --> pdb=" O ALA x 136 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL x 135 " --> pdb=" O PRO x 170 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL x 172 " --> pdb=" O VAL x 135 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'x' and resid 218 through 222 removed outlier: 3.503A pdb=" N ASP x 218 " --> pdb=" O THR x 230 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE x 220 " --> pdb=" O VAL x 228 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE x 222 " --> pdb=" O GLY x 226 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY x 231 " --> pdb=" O VAL x 277 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL x 277 " --> pdb=" O GLY x 231 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'x' and resid 236 through 239 removed outlier: 7.325A pdb=" N GLY x 236 " --> pdb=" O ALA x 273 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'x' and resid 243 through 247 Processing sheet with id= 26, first strand: chain 'x' and resid 307 through 313 removed outlier: 3.735A pdb=" N ASP x 357 " --> pdb=" O ILE x 313 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR x 329 " --> pdb=" O VAL x 344 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU x 375 " --> pdb=" O VAL x 391 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'x' and resid 308 through 313 removed outlier: 6.617A pdb=" N GLU x 308 " --> pdb=" O THR x 392 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'z' and resid 100 through 107 removed outlier: 5.349A pdb=" N TRP z 100 " --> pdb=" O GLY z 95 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ARG z 88 " --> pdb=" O ALA z 31 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY z 23 " --> pdb=" O LEU z 96 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ASN z 30 " --> pdb=" O THR z 111 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR z 111 " --> pdb=" O ASN z 30 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'z' and resid 154 through 158 removed outlier: 6.751A pdb=" N LEU z 147 " --> pdb=" O ILE z 158 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP z 144 " --> pdb=" O SER z 141 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG z 210 " --> pdb=" O PRO z 134 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY z 215 " --> pdb=" O ASP z 238 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'z' and resid 280 through 283 removed outlier: 7.252A pdb=" N ASP z 280 " --> pdb=" O LEU z 373 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLY z 368 " --> pdb=" O ASP z 303 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS z 299 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG z 351 " --> pdb=" O ASP z 298 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR z 302 " --> pdb=" O SER z 353 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'z' and resid 317 through 320 removed outlier: 4.471A pdb=" N SER z 317 " --> pdb=" O GLY z 313 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'z' and resid 144 through 147 Processing sheet with id= 33, first strand: chain 'C' and resid 2 through 6 removed outlier: 5.220A pdb=" N ALA C 16 " --> pdb=" O TYR C 6 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 34 Processing sheet with id= 35, first strand: chain 'C' and resid 81 through 84 removed outlier: 3.692A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU C 94 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL C 75 " --> pdb=" O SER C 119 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N SER C 119 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C 117 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP C 115 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'C' and resid 163 through 166 removed outlier: 3.697A pdb=" N GLN C 164 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA C 174 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 91 through 97 removed outlier: 5.431A pdb=" N ASN C 91 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'D' and resid 4 through 8 removed outlier: 5.713A pdb=" N LYS D 4 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA D 110 " --> pdb=" O VAL D 182 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'D' and resid 12 through 18 removed outlier: 3.586A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS D 184 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'D' and resid 34 through 37 removed outlier: 6.776A pdb=" N GLN D 51 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SER D 48 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.822A pdb=" N GLY E 16 " --> pdb=" O VAL E 7 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'E' and resid 123 through 126 Processing sheet with id= 43, first strand: chain 'F' and resid 72 through 76 removed outlier: 8.109A pdb=" N ILE F 92 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN F 44 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N GLY F 46 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY F 158 " --> pdb=" O GLY F 46 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET F 159 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'F' and resid 79 through 82 removed outlier: 6.730A pdb=" N LYS F 79 " --> pdb=" O GLU F 88 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU F 88 " --> pdb=" O LYS F 79 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 46, first strand: chain 'G' and resid 41 through 46 removed outlier: 3.632A pdb=" N SER G 42 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR G 54 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'G' and resid 83 through 90 removed outlier: 3.630A pdb=" N ILE G 90 " --> pdb=" O THR G 130 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR G 130 " --> pdb=" O ILE G 90 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.539A pdb=" N ARG G 96 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'H' and resid 2 through 5 removed outlier: 6.023A pdb=" N LYS H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA H 39 " --> pdb=" O LYS H 2 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'H' and resid 77 through 83 removed outlier: 3.744A pdb=" N VAL H 78 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL H 148 " --> pdb=" O GLY H 128 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY H 128 " --> pdb=" O VAL H 148 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'I' and resid 47 through 51 removed outlier: 3.710A pdb=" N ALA I 22 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL I 25 " --> pdb=" O LYS I 106 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL I 104 " --> pdb=" O GLU I 27 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'I' and resid 22 through 25 removed outlier: 3.562A pdb=" N THR I 23 " --> pdb=" O TYR I 109 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY I 107 " --> pdb=" O VAL I 25 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'J' and resid 10 through 16 removed outlier: 4.246A pdb=" N SER J 67 " --> pdb=" O TYR J 63 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'L' and resid 52 through 57 removed outlier: 4.910A pdb=" N ASP L 19 " --> pdb=" O PHE L 140 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'L' and resid 74 through 78 removed outlier: 3.628A pdb=" N ARG L 87 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLY L 83 " --> pdb=" O SER L 78 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'M' and resid 18 through 21 removed outlier: 4.077A pdb=" N SER M 6 " --> pdb=" O CYS M 21 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN M 82 " --> pdb=" O ARG M 7 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU M 81 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL M 66 " --> pdb=" O GLU M 81 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'M' and resid 39 through 42 Processing sheet with id= 58, first strand: chain 'M' and resid 68 through 71 removed outlier: 3.978A pdb=" N SER M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'N' and resid 75 through 78 Processing sheet with id= 60, first strand: chain 'O' and resid 38 through 41 removed outlier: 6.718A pdb=" N GLU O 38 " --> pdb=" O PRO O 99 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'O' and resid 62 through 66 removed outlier: 4.057A pdb=" N PHE O 104 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N ASP O 31 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG O 134 " --> pdb=" O ASP O 31 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LYS O 128 " --> pdb=" O LEU O 37 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'P' and resid 33 through 37 Processing sheet with id= 63, first strand: chain 'Q' and resid 61 through 65 removed outlier: 3.966A pdb=" N ALA Q 61 " --> pdb=" O LEU Q 51 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE Q 47 " --> pdb=" O SER Q 65 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'R' and resid 37 through 44 removed outlier: 6.751A pdb=" N THR R 24 " --> pdb=" O LEU R 86 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N HIS R 82 " --> pdb=" O HIS R 28 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'R' and resid 48 through 51 removed outlier: 4.013A pdb=" N ARG R 48 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR R 57 " --> pdb=" O GLN R 50 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLU R 56 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'T' and resid 13 through 16 removed outlier: 3.960A pdb=" N LEU T 41 " --> pdb=" O ILE T 6 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN T 47 " --> pdb=" O ASP T 44 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'T' and resid 19 through 22 removed outlier: 4.229A pdb=" N ASP T 20 " --> pdb=" O VAL T 99 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL T 96 " --> pdb=" O LEU T 65 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR T 61 " --> pdb=" O THR T 100 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA T 33 " --> pdb=" O VAL T 64 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'T' and resid 66 through 71 removed outlier: 3.701A pdb=" N GLU T 66 " --> pdb=" O VAL T 96 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN T 92 " --> pdb=" O GLY T 70 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'U' and resid 8 through 15 removed outlier: 6.909A pdb=" N ILE U 113 " --> pdb=" O ALA U 79 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N THR U 75 " --> pdb=" O ARG U 117 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'U' and resid 80 through 86 removed outlier: 4.828A pdb=" N THR U 107 " --> pdb=" O GLY U 86 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'V' and resid 28 through 33 removed outlier: 4.407A pdb=" N LYS V 80 " --> pdb=" O VAL V 33 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS V 65 " --> pdb=" O ARG V 76 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N SER V 78 " --> pdb=" O GLN V 63 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN V 63 " --> pdb=" O SER V 78 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS V 80 " --> pdb=" O ASN V 61 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN V 61 " --> pdb=" O LYS V 80 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA V 82 " --> pdb=" O THR V 59 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR V 59 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL V 84 " --> pdb=" O VAL V 57 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL V 57 " --> pdb=" O VAL V 84 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'W' and resid 39 through 44 removed outlier: 5.334A pdb=" N ASN W 39 " --> pdb=" O ALA W 64 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN W 62 " --> pdb=" O ILE W 41 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'W' and resid 82 through 87 removed outlier: 6.858A pdb=" N ARG W 82 " --> pdb=" O LYS W 99 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'X' and resid 8 through 12 Processing sheet with id= 75, first strand: chain 'X' and resid 44 through 49 removed outlier: 3.626A pdb=" N HIS X 94 " --> pdb=" O ASP X 84 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA X 82 " --> pdb=" O ASP X 96 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP X 84 " --> pdb=" O GLN X 93 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS X 86 " --> pdb=" O ASN X 91 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN X 91 " --> pdb=" O HIS X 86 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'X' and resid 122 through 127 removed outlier: 3.608A pdb=" N THR X 125 " --> pdb=" O ASN X 180 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL X 178 " --> pdb=" O ASP X 127 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL X 179 " --> pdb=" O ILE X 157 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLU X 183 " --> pdb=" O ALA X 153 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ALA X 153 " --> pdb=" O GLU X 183 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'X' and resid 143 through 147 removed outlier: 6.885A pdb=" N GLU X 132 " --> pdb=" O ILE X 171 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN X 169 " --> pdb=" O GLU X 134 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Y' and resid 66 through 71 removed outlier: 3.527A pdb=" N THR Y 77 " --> pdb=" O GLY Y 70 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'Z' and resid 3 through 6 removed outlier: 9.405A pdb=" N ALA Z 3 " --> pdb=" O PRO Z 12 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS Z 10 " --> pdb=" O CYS Z 5 " (cutoff:3.500A) removed outlier: 12.600A pdb=" N GLY Z 9 " --> pdb=" O ILE Z 33 " (cutoff:3.500A) removed outlier: 11.248A pdb=" N ILE Z 33 " --> pdb=" O GLY Z 9 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N GLY Z 11 " --> pdb=" O PRO Z 31 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG Z 27 " --> pdb=" O GLY Z 15 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR Z 25 " --> pdb=" O SER Z 17 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain '2' and resid 32 through 38 removed outlier: 4.333A pdb=" N GLN 2 33 " --> pdb=" O GLN 2 8 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLU 2 3 " --> pdb=" O VAL 2 59 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU 2 53 " --> pdb=" O VAL 2 9 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain '3' and resid 20 through 24 removed outlier: 4.431A pdb=" N HIS 3 20 " --> pdb=" O CYS 3 16 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL 3 14 " --> pdb=" O PHE 3 22 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain '4' and resid 28 through 31 Processing sheet with id= 83, first strand: chain '5' and resid 23 through 26 removed outlier: 6.942A pdb=" N THR 5 12 " --> pdb=" O SER 5 54 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU 5 36 " --> pdb=" O GLU 5 53 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain '7' and resid 22 through 25 removed outlier: 6.529A pdb=" N ILE 7 22 " --> pdb=" O VAL 7 50 " (cutoff:3.500A) 2204 hydrogen bonds defined for protein. 6516 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4127 hydrogen bonds 6570 hydrogen bond angles 0 basepair planarities 1608 basepair parallelities 2468 stacking parallelities Total time for adding SS restraints: 281.02 Time building geometry restraints manager: 65.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 20408 1.33 - 1.45: 69873 1.45 - 1.57: 68652 1.57 - 1.69: 9554 1.69 - 1.81: 211 Bond restraints: 168698 Sorted by residual: bond pdb=" C4 5MU y 54 " pdb=" C5 5MU y 54 " ideal model delta sigma weight residual 1.802 1.459 0.343 2.00e-02 2.50e+03 2.94e+02 bond pdb=" N1 5MU y 54 " pdb=" C6 5MU y 54 " ideal model delta sigma weight residual 1.635 1.319 0.316 2.00e-02 2.50e+03 2.50e+02 bond pdb=" C5 5MU y 54 " pdb=" C6 5MU y 54 " ideal model delta sigma weight residual 1.155 1.368 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" N1 7MG y 46 " pdb=" C2 7MG y 46 " ideal model delta sigma weight residual 1.468 1.292 0.176 2.00e-02 2.50e+03 7.74e+01 bond pdb=" C2 4SU y 8 " pdb=" N3 4SU y 8 " ideal model delta sigma weight residual 1.499 1.336 0.163 2.00e-02 2.50e+03 6.65e+01 ... (remaining 168693 not shown) Histogram of bond angle deviations from ideal: 89.68 - 99.61: 22 99.61 - 109.54: 68258 109.54 - 119.47: 105699 119.47 - 129.40: 74194 129.40 - 139.33: 3544 Bond angle restraints: 251717 Sorted by residual: angle pdb=" O2* PSU y 55 " pdb=" C2* PSU y 55 " pdb=" C1* PSU y 55 " ideal model delta sigma weight residual 108.40 89.68 18.72 1.50e+00 4.44e-01 1.56e+02 angle pdb=" O2' C y 43 " pdb=" C2' C y 43 " pdb=" C1' C y 43 " ideal model delta sigma weight residual 108.40 91.45 16.95 1.50e+00 4.44e-01 1.28e+02 angle pdb=" O4* PSU y 55 " pdb=" C1* PSU y 55 " pdb=" C2* PSU y 55 " ideal model delta sigma weight residual 107.60 97.93 9.67 1.00e+00 1.00e+00 9.34e+01 angle pdb=" C4' 5MU y 54 " pdb=" C3' 5MU y 54 " pdb=" C2' 5MU y 54 " ideal model delta sigma weight residual 102.60 93.61 8.99 1.00e+00 1.00e+00 8.08e+01 angle pdb=" O2' 5MU y 54 " pdb=" C2' 5MU y 54 " pdb=" C1' 5MU y 54 " ideal model delta sigma weight residual 108.40 96.65 11.75 1.50e+00 4.44e-01 6.13e+01 ... (remaining 251712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 96424 35.99 - 71.98: 10648 71.98 - 107.97: 1275 107.97 - 143.96: 33 143.96 - 179.95: 42 Dihedral angle restraints: 108422 sinusoidal: 88988 harmonic: 19434 Sorted by residual: dihedral pdb=" O4' U a 328 " pdb=" C1' U a 328 " pdb=" N1 U a 328 " pdb=" C2 U a 328 " ideal model delta sinusoidal sigma weight residual 200.00 20.05 179.95 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A 139 " pdb=" C1' U A 139 " pdb=" N1 U A 139 " pdb=" C2 U A 139 " ideal model delta sinusoidal sigma weight residual 200.00 24.94 175.06 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C A2025 " pdb=" C1' C A2025 " pdb=" N1 C A2025 " pdb=" C2 C A2025 " ideal model delta sinusoidal sigma weight residual -160.00 11.34 -171.34 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 108419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 29081 0.063 - 0.126: 2671 0.126 - 0.189: 288 0.189 - 0.252: 29 0.252 - 0.315: 8 Chirality restraints: 32077 Sorted by residual: chirality pdb=" C3' U y 45 " pdb=" C4' U y 45 " pdb=" O3' U y 45 " pdb=" C2' U y 45 " both_signs ideal model delta sigma weight residual False -2.48 -2.79 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" C3' U a1482 " pdb=" C4' U a1482 " pdb=" O3' U a1482 " pdb=" C2' U a1482 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C1' A A1098 " pdb=" O4' A A1098 " pdb=" C2' A A1098 " pdb=" N9 A A1098 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 32074 not shown) Planarity restraints: 14232 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU y 54 " 0.113 2.00e-02 2.50e+03 5.65e-01 7.18e+03 pdb=" C4' 5MU y 54 " 0.385 2.00e-02 2.50e+03 pdb=" O4' 5MU y 54 " 0.284 2.00e-02 2.50e+03 pdb=" C3' 5MU y 54 " -0.635 2.00e-02 2.50e+03 pdb=" O3' 5MU y 54 " -0.552 2.00e-02 2.50e+03 pdb=" C2' 5MU y 54 " -0.152 2.00e-02 2.50e+03 pdb=" O2' 5MU y 54 " 1.119 2.00e-02 2.50e+03 pdb=" C1' 5MU y 54 " 0.213 2.00e-02 2.50e+03 pdb=" N1 5MU y 54 " -0.776 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG y 46 " 0.312 2.00e-02 2.50e+03 3.45e-01 2.68e+03 pdb=" C4' 7MG y 46 " -0.311 2.00e-02 2.50e+03 pdb=" O4' 7MG y 46 " -0.089 2.00e-02 2.50e+03 pdb=" C3' 7MG y 46 " 0.319 2.00e-02 2.50e+03 pdb=" O3' 7MG y 46 " -0.547 2.00e-02 2.50e+03 pdb=" C2' 7MG y 46 " 0.556 2.00e-02 2.50e+03 pdb=" O2' 7MG y 46 " 0.166 2.00e-02 2.50e+03 pdb=" C1' 7MG y 46 " -0.358 2.00e-02 2.50e+03 pdb=" N9 7MG y 46 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 11 " 0.069 5.00e-02 4.00e+02 9.95e-02 1.59e+01 pdb=" N PRO G 12 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO G 12 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO G 12 " 0.053 5.00e-02 4.00e+02 ... (remaining 14229 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 7457 2.67 - 3.23: 128295 3.23 - 3.78: 289525 3.78 - 4.34: 402839 4.34 - 4.90: 550683 Nonbonded interactions: 1378799 Sorted by model distance: nonbonded pdb=" O2 U A 337 " pdb=" O6 G A 344 " model vdw 2.110 2.432 nonbonded pdb=" OP1 G A1379 " pdb=" NH2 ARG 4 16 " model vdw 2.115 2.520 nonbonded pdb=" O2' A a 772 " pdb=" N7 A a 774 " model vdw 2.120 2.520 nonbonded pdb=" O2' A a 941 " pdb=" O2' C a 966 " model vdw 2.133 2.440 nonbonded pdb=" OP1 A A 978 " pdb=" OG SER O 22 " model vdw 2.137 2.440 ... (remaining 1378794 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: 7.290 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: 0.130 Extract box with map and model: 28.780 Check model and map are aligned: 1.510 Set scattering table: 0.990 Process input model: 606.910 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:9.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 659.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 : 0.005 0.343 168698 Z= 0.337 Angle : 0.624 18.723 251717 Z= 0.324 Chirality : 0.038 0.315 32077 Planarity : 0.008 0.565 14232 Dihedral : 22.850 179.951 95928 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % 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: -0.83 (0.10), residues: 6737 helix: -0.13 (0.11), residues: 2126 sheet: -0.41 (0.13), residues: 1421 loop : -0.80 (0.11), residues: 3190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 92 HIS 0.014 0.001 HIS P 16 PHE 0.021 0.002 PHE V 96 TYR 0.025 0.002 TYR H 25 ARG 0.013 0.001 ARG L 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 885 time to evaluate : 6.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 154 MET cc_start: 0.3314 (ppp) cc_final: 0.2639 (mtp) REVERT: b 178 LYS cc_start: 0.5880 (ttmm) cc_final: 0.3592 (pttt) REVERT: C 109 GLN cc_start: 0.7676 (tp-100) cc_final: 0.7454 (tp-100) REVERT: C 134 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7201 (ttm170) REVERT: D 4 LYS cc_start: 0.8069 (mttm) cc_final: 0.7859 (mttp) REVERT: F 88 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6964 (tm-30) REVERT: T 54 ASP cc_start: 0.8724 (m-30) cc_final: 0.8453 (m-30) REVERT: U 41 ASP cc_start: 0.8376 (m-30) cc_final: 0.8141 (m-30) REVERT: U 74 SER cc_start: 0.8852 (p) cc_final: 0.8574 (p) outliers start: 0 outliers final: 1 residues processed: 885 average time/residue: 2.3515 time to fit residues: 2951.1840 Evaluate side-chains 703 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 702 time to evaluate : 6.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain g residue 101 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1135 random chunks: chunk 958 optimal weight: 8.9990 chunk 860 optimal weight: 7.9990 chunk 477 optimal weight: 10.0000 chunk 293 optimal weight: 0.3980 chunk 580 optimal weight: 10.0000 chunk 459 optimal weight: 0.0970 chunk 889 optimal weight: 20.0000 chunk 344 optimal weight: 6.9990 chunk 540 optimal weight: 10.0000 chunk 662 optimal weight: 7.9990 chunk 1030 optimal weight: 4.9990 overall best weight: 4.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 15 HIS c 27 GLN c 122 GLN d 84 ASN e 111 GLN e 163 HIS f 28 ASN f 80 ASN g 129 ASN ** i 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 95 GLN j 64 HIS k 84 GLN k 125 GLN m 31 ASN m 52 GLN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 GLN s 47 HIS ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS t 71 GLN ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 327 ASN z 38 GLN z 112 ASN z 217 GLN C 87 ASN C 113 GLN C 198 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN F 34 GLN F 70 GLN ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 HIS G 98 GLN G 112 HIS O 17 GLN Q 16 ASN Q 41 ASN Q 48 HIS ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 34 HIS Z 45 ASN Z 47 GLN ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 29 GLN ** 3 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 36 GLN 5 22 ASN 9 17 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.0543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 168698 Z= 0.293 Angle : 0.610 12.891 251717 Z= 0.315 Chirality : 0.038 0.308 32077 Planarity : 0.005 0.121 14232 Dihedral : 23.364 179.865 82806 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.38 % Favored : 95.58 % Rotamer: Outliers : 1.89 % Allowed : 10.90 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % 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: -0.59 (0.10), residues: 6737 helix: 0.38 (0.11), residues: 2215 sheet: -0.40 (0.13), residues: 1437 loop : -0.86 (0.11), residues: 3085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP k 53 HIS 0.011 0.001 HIS C 53 PHE 0.018 0.002 PHE G 106 TYR 0.025 0.002 TYR p 40 ARG 0.009 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 752 time to evaluate : 6.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 74 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.5395 (mttp) REVERT: f 47 ARG cc_start: 0.8064 (ttp80) cc_final: 0.7785 (ttp-170) REVERT: g 59 VAL cc_start: 0.5977 (p) cc_final: 0.5585 (t) REVERT: m 43 MET cc_start: 0.4332 (OUTLIER) cc_final: 0.2745 (mpt) REVERT: o 38 ASP cc_start: 0.8550 (m-30) cc_final: 0.8329 (m-30) REVERT: t 60 LYS cc_start: 0.8013 (mtpt) cc_final: 0.7725 (mttm) REVERT: C 101 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: C 109 GLN cc_start: 0.7723 (tp-100) cc_final: 0.7469 (tp-100) REVERT: D 4 LYS cc_start: 0.8075 (mttm) cc_final: 0.7863 (mttp) REVERT: E 28 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6796 (tt0) REVERT: L 37 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7992 (ttt90) REVERT: L 135 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.7551 (mm-40) REVERT: N 97 GLU cc_start: 0.7558 (mp0) cc_final: 0.7352 (mp0) REVERT: P 117 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7368 (mmp80) REVERT: Q 83 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7414 (tpt170) REVERT: R 111 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: T 54 ASP cc_start: 0.8712 (m-30) cc_final: 0.8342 (m-30) REVERT: U 41 ASP cc_start: 0.8323 (m-30) cc_final: 0.8070 (m-30) REVERT: U 74 SER cc_start: 0.8882 (p) cc_final: 0.8600 (p) REVERT: X 66 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8641 (tp) REVERT: Z 33 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8174 (pp) REVERT: 1 40 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8170 (pm20) REVERT: 3 40 GLN cc_start: 0.8295 (mp10) cc_final: 0.7969 (mp10) REVERT: 9 10 ASP cc_start: 0.7390 (m-30) cc_final: 0.7185 (m-30) outliers start: 105 outliers final: 45 residues processed: 784 average time/residue: 2.2275 time to fit residues: 2522.2575 Evaluate side-chains 749 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 692 time to evaluate : 9.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain d residue 88 ILE Chi-restraints excluded: chain e residue 104 SER Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain f residue 52 ILE Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain m residue 43 MET Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain x residue 227 THR Chi-restraints excluded: chain x residue 360 ASP Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain P residue 117 ARG Chi-restraints excluded: chain Q residue 83 ARG Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain 1 residue 40 GLN Chi-restraints excluded: chain 3 residue 33 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1135 random chunks: chunk 572 optimal weight: 7.9990 chunk 319 optimal weight: 8.9990 chunk 857 optimal weight: 7.9990 chunk 701 optimal weight: 10.0000 chunk 284 optimal weight: 5.9990 chunk 1032 optimal weight: 7.9990 chunk 1115 optimal weight: 2.9990 chunk 919 optimal weight: 3.9990 chunk 1023 optimal weight: 0.9980 chunk 352 optimal weight: 9.9990 chunk 828 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 125 ASN i 57 ASN ** i 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 HIS k 125 GLN n 31 HIS ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 GLN ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 54 ASN ** x 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 121 HIS z 38 GLN C 203 ASN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 34 GLN ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 GLN G 98 GLN L 135 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 156 GLN Z 45 ASN ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 36 GLN 7 55 ASN 8 20 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.0716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.186 168698 Z= 0.310 Angle : 0.618 16.820 251717 Z= 0.318 Chirality : 0.039 0.315 32077 Planarity : 0.005 0.117 14232 Dihedral : 23.303 179.783 82804 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 3.17 % Allowed : 14.09 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % 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: -0.44 (0.10), residues: 6737 helix: 0.70 (0.11), residues: 2214 sheet: -0.43 (0.13), residues: 1462 loop : -0.89 (0.11), residues: 3061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP k 53 HIS 0.010 0.001 HIS C 53 PHE 0.027 0.002 PHE t 35 TYR 0.016 0.002 TYR d 71 ARG 0.016 0.000 ARG m 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 741 time to evaluate : 6.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 74 LYS cc_start: 0.6439 (OUTLIER) cc_final: 0.5327 (tptt) REVERT: b 154 MET cc_start: 0.4648 (ppp) cc_final: 0.2930 (mtm) REVERT: e 177 GLU cc_start: 0.8258 (pm20) cc_final: 0.7733 (pm20) REVERT: f 31 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7669 (mpp80) REVERT: f 47 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7824 (ttp-170) REVERT: g 59 VAL cc_start: 0.6035 (p) cc_final: 0.5648 (t) REVERT: i 77 ARG cc_start: 0.6456 (ttp-110) cc_final: 0.4812 (tmt-80) REVERT: m 43 MET cc_start: 0.4292 (OUTLIER) cc_final: 0.2471 (mpt) REVERT: o 41 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: C 101 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: C 109 GLN cc_start: 0.7726 (tp-100) cc_final: 0.7475 (tp-100) REVERT: C 265 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8024 (m-30) REVERT: D 4 LYS cc_start: 0.8105 (mttm) cc_final: 0.7858 (mttp) REVERT: E 23 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7679 (pp20) REVERT: F 105 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: I 3 LYS cc_start: 0.5255 (OUTLIER) cc_final: 0.3377 (mptt) REVERT: L 37 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7956 (ttt90) REVERT: L 135 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.7935 (mm110) REVERT: P 117 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7353 (mmp80) REVERT: Q 83 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7693 (tpt90) REVERT: Q 126 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7688 (ptmt) REVERT: R 111 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: T 54 ASP cc_start: 0.8735 (m-30) cc_final: 0.8358 (m-30) REVERT: U 41 ASP cc_start: 0.8316 (m-30) cc_final: 0.8036 (m-30) REVERT: U 74 SER cc_start: 0.8913 (p) cc_final: 0.8644 (p) REVERT: W 40 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7786 (mtp85) REVERT: X 66 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8549 (tp) REVERT: Z 33 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8259 (pp) REVERT: 1 40 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: 3 24 THR cc_start: 0.8784 (t) cc_final: 0.8350 (p) REVERT: 3 40 GLN cc_start: 0.8354 (mp10) cc_final: 0.8036 (mp10) REVERT: 4 6 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.6218 (mmt180) REVERT: 9 10 ASP cc_start: 0.7396 (m-30) cc_final: 0.7170 (m-30) outliers start: 176 outliers final: 85 residues processed: 826 average time/residue: 2.2027 time to fit residues: 2635.2709 Evaluate side-chains 805 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 700 time to evaluate : 6.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain d residue 88 ILE Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 104 SER Chi-restraints excluded: chain f residue 31 ARG Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 52 ILE Chi-restraints excluded: chain g residue 117 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain m residue 43 MET Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 72 GLN Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 77 THR Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain x residue 13 VAL Chi-restraints excluded: chain x residue 54 ASN Chi-restraints excluded: chain x residue 227 THR Chi-restraints excluded: chain x residue 229 VAL Chi-restraints excluded: chain x residue 360 ASP Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain z residue 123 HIS Chi-restraints excluded: chain z residue 298 ASP Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 23 GLU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain P residue 117 ARG Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 83 ARG Chi-restraints excluded: chain Q residue 126 LYS Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 40 ARG Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 96 ASP Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain 1 residue 9 GLU Chi-restraints excluded: chain 1 residue 40 GLN Chi-restraints excluded: chain 4 residue 6 ARG Chi-restraints excluded: chain 6 residue 23 LEU Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 8 residue 24 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1135 random chunks: chunk 1020 optimal weight: 4.9990 chunk 776 optimal weight: 10.0000 chunk 535 optimal weight: 7.9990 chunk 114 optimal weight: 30.0000 chunk 492 optimal weight: 40.0000 chunk 693 optimal weight: 40.0000 chunk 1036 optimal weight: 1.9990 chunk 1097 optimal weight: 0.8980 chunk 541 optimal weight: 7.9990 chunk 982 optimal weight: 0.9990 chunk 295 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 27 GLN ** d 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 121 ASN ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 HIS ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 GLN ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS t 71 GLN ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 54 ASN ** x 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 38 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 34 GLN ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS O 67 ASN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 27 ASN ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 36 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 168698 Z= 0.245 Angle : 0.579 12.981 251717 Z= 0.300 Chirality : 0.036 0.295 32077 Planarity : 0.005 0.115 14232 Dihedral : 23.274 179.855 82804 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.05 % Favored : 95.90 % Rotamer: Outliers : 3.19 % Allowed : 16.48 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % 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: -0.28 (0.10), residues: 6737 helix: 0.92 (0.11), residues: 2208 sheet: -0.29 (0.13), residues: 1439 loop : -0.88 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP c 22 HIS 0.007 0.001 HIS P 16 PHE 0.021 0.001 PHE J 70 TYR 0.023 0.001 TYR d 70 ARG 0.006 0.000 ARG 5 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 743 time to evaluate : 6.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 74 LYS cc_start: 0.6431 (OUTLIER) cc_final: 0.5217 (mttp) REVERT: b 154 MET cc_start: 0.4745 (ppp) cc_final: 0.3103 (OUTLIER) REVERT: f 31 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7634 (mpp80) REVERT: g 59 VAL cc_start: 0.5965 (p) cc_final: 0.5614 (t) REVERT: i 77 ARG cc_start: 0.6439 (ttp-110) cc_final: 0.4905 (tmt-80) REVERT: k 85 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7398 (tp30) REVERT: m 43 MET cc_start: 0.4273 (OUTLIER) cc_final: 0.2369 (mpt) REVERT: o 41 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7281 (mp0) REVERT: o 44 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8427 (mttp) REVERT: o 47 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7857 (mttp) REVERT: t 56 ARG cc_start: 0.8275 (ttt90) cc_final: 0.8072 (ttt-90) REVERT: z 50 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8555 (mp) REVERT: z 202 LEU cc_start: 0.8593 (mt) cc_final: 0.8385 (mt) REVERT: C 101 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: C 265 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: D 4 LYS cc_start: 0.8091 (mttm) cc_final: 0.7877 (mttp) REVERT: F 105 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7443 (mt-10) REVERT: L 37 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7932 (ttt90) REVERT: P 117 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7250 (mmp80) REVERT: Q 83 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7644 (tpt90) REVERT: Q 126 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7564 (ptmt) REVERT: R 111 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: T 54 ASP cc_start: 0.8721 (m-30) cc_final: 0.8325 (m-30) REVERT: U 41 ASP cc_start: 0.8303 (m-30) cc_final: 0.7985 (m-30) REVERT: U 74 SER cc_start: 0.8901 (p) cc_final: 0.8629 (p) REVERT: W 40 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7794 (mtp85) REVERT: X 66 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8519 (tp) REVERT: Z 33 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8196 (pp) REVERT: 1 40 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: 3 24 THR cc_start: 0.8794 (t) cc_final: 0.8428 (p) REVERT: 3 40 GLN cc_start: 0.8405 (mp10) cc_final: 0.7880 (mp10) outliers start: 177 outliers final: 100 residues processed: 830 average time/residue: 2.2376 time to fit residues: 2705.9110 Evaluate side-chains 837 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 718 time to evaluate : 6.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain d residue 48 GLN Chi-restraints excluded: chain d residue 88 ILE Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 104 SER Chi-restraints excluded: chain e residue 200 GLU Chi-restraints excluded: chain f residue 31 ARG Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain f residue 52 ILE Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 117 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 45 ASP Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 85 GLU Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain m residue 8 ASP Chi-restraints excluded: chain m residue 43 MET Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 72 GLN Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 77 THR Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain p residue 110 LEU Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 70 ILE Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain x residue 54 ASN Chi-restraints excluded: chain x residue 65 ILE Chi-restraints excluded: chain x residue 227 THR Chi-restraints excluded: chain x residue 229 VAL Chi-restraints excluded: chain x residue 360 ASP Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain z residue 50 LEU Chi-restraints excluded: chain z residue 123 HIS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain P residue 117 ARG Chi-restraints excluded: chain Q residue 83 ARG Chi-restraints excluded: chain Q residue 126 LYS Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 40 ARG Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain 1 residue 40 GLN Chi-restraints excluded: chain 6 residue 39 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1135 random chunks: chunk 913 optimal weight: 3.9990 chunk 622 optimal weight: 40.0000 chunk 15 optimal weight: 20.0000 chunk 816 optimal weight: 3.9990 chunk 452 optimal weight: 0.9980 chunk 936 optimal weight: 4.9990 chunk 758 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 560 optimal weight: 10.0000 chunk 984 optimal weight: 7.9990 chunk 276 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 HIS ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 65 GLN ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS t 71 GLN ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 54 ASN ** x 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 38 GLN C 109 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 34 GLN ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 GLN O 67 ASN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 36 GLN 7 55 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 168698 Z= 0.284 Angle : 0.599 13.146 251717 Z= 0.309 Chirality : 0.037 0.307 32077 Planarity : 0.005 0.116 14232 Dihedral : 23.260 179.788 82804 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 3.69 % Allowed : 17.16 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % 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: -0.28 (0.10), residues: 6737 helix: 0.95 (0.11), residues: 2210 sheet: -0.34 (0.13), residues: 1461 loop : -0.88 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 22 HIS 0.007 0.001 HIS P 16 PHE 0.023 0.002 PHE x 220 TYR 0.019 0.001 TYR x 90 ARG 0.010 0.000 ARG N 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 742 time to evaluate : 6.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 74 LYS cc_start: 0.6426 (OUTLIER) cc_final: 0.5199 (mttp) REVERT: b 136 MET cc_start: 0.3512 (pmm) cc_final: 0.3170 (pmm) REVERT: b 154 MET cc_start: 0.4683 (ppp) cc_final: 0.3068 (mtp) REVERT: e 177 GLU cc_start: 0.8199 (pm20) cc_final: 0.7895 (pm20) REVERT: f 31 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7659 (mpp80) REVERT: g 59 VAL cc_start: 0.5979 (p) cc_final: 0.5601 (t) REVERT: i 77 ARG cc_start: 0.6402 (ttp-110) cc_final: 0.4882 (tmt-80) REVERT: m 43 MET cc_start: 0.4384 (OUTLIER) cc_final: 0.2401 (mpt) REVERT: o 41 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: o 44 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8454 (mttp) REVERT: o 47 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7871 (mttp) REVERT: p 41 HIS cc_start: 0.7987 (m-70) cc_final: 0.7757 (m170) REVERT: x 282 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5711 (ptm160) REVERT: z 50 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8558 (mp) REVERT: z 202 LEU cc_start: 0.8594 (mt) cc_final: 0.8386 (mt) REVERT: C 101 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: C 265 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8098 (m-30) REVERT: D 4 LYS cc_start: 0.8102 (mttm) cc_final: 0.7879 (mttp) REVERT: F 105 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7486 (mt-10) REVERT: F 108 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7280 (t70) REVERT: I 3 LYS cc_start: 0.5349 (OUTLIER) cc_final: 0.3540 (mptt) REVERT: L 37 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7932 (ttt90) REVERT: L 135 GLN cc_start: 0.9338 (OUTLIER) cc_final: 0.7811 (mm110) REVERT: M 12 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7277 (m-30) REVERT: P 117 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7315 (mmp80) REVERT: Q 126 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7536 (ptmt) REVERT: R 111 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7606 (tt0) REVERT: T 54 ASP cc_start: 0.8722 (m-30) cc_final: 0.8328 (m-30) REVERT: U 41 ASP cc_start: 0.8317 (m-30) cc_final: 0.8062 (m-30) REVERT: U 74 SER cc_start: 0.8920 (p) cc_final: 0.8650 (p) REVERT: X 66 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8508 (tp) REVERT: Z 33 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8239 (pp) REVERT: 1 40 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8353 (pm20) REVERT: 3 24 THR cc_start: 0.8841 (t) cc_final: 0.8538 (p) REVERT: 3 40 GLN cc_start: 0.8311 (mp10) cc_final: 0.8012 (mp10) REVERT: 4 6 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.6199 (mmt180) REVERT: 5 38 ILE cc_start: 0.8470 (tt) cc_final: 0.8152 (pt) REVERT: 5 39 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8268 (mttm) outliers start: 205 outliers final: 127 residues processed: 850 average time/residue: 2.1970 time to fit residues: 2706.6950 Evaluate side-chains 858 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 707 time to evaluate : 6.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain d residue 48 GLN Chi-restraints excluded: chain d residue 88 ILE Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain e residue 104 SER Chi-restraints excluded: chain e residue 200 GLU Chi-restraints excluded: chain f residue 31 ARG Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain f residue 52 ILE Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 117 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 45 ASP Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain m residue 8 ASP Chi-restraints excluded: chain m residue 43 MET Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain o residue 47 LYS Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 77 THR Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain p residue 110 LEU Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 70 ILE Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain t residue 20 ARG Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain x residue 13 VAL Chi-restraints excluded: chain x residue 54 ASN Chi-restraints excluded: chain x residue 65 ILE Chi-restraints excluded: chain x residue 172 VAL Chi-restraints excluded: chain x residue 227 THR Chi-restraints excluded: chain x residue 229 VAL Chi-restraints excluded: chain x residue 282 ARG Chi-restraints excluded: chain x residue 360 ASP Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain z residue 50 LEU Chi-restraints excluded: chain z residue 123 HIS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 38 LYS Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain P residue 117 ARG Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 126 LYS Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 6 ASP Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 96 ASP Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain X residue 192 GLU Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain 1 residue 40 GLN Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 4 residue 6 ARG Chi-restraints excluded: chain 5 residue 39 LYS Chi-restraints excluded: chain 6 residue 23 LEU Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 8 residue 24 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1135 random chunks: chunk 369 optimal weight: 20.0000 chunk 987 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 644 optimal weight: 7.9990 chunk 270 optimal weight: 20.0000 chunk 1098 optimal weight: 2.9990 chunk 911 optimal weight: 0.9980 chunk 508 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 chunk 363 optimal weight: 20.0000 chunk 576 optimal weight: 8.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 51 GLN ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 HIS ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 54 ASN ** x 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN F 28 ASN F 34 GLN F 62 ASN ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 HIS ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 36 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 168698 Z= 0.309 Angle : 0.613 13.266 251717 Z= 0.315 Chirality : 0.038 0.312 32077 Planarity : 0.005 0.116 14232 Dihedral : 23.260 179.677 82804 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.45 % Favored : 95.52 % Rotamer: Outliers : 3.84 % Allowed : 18.19 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % 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: -0.29 (0.10), residues: 6737 helix: 0.96 (0.11), residues: 2207 sheet: -0.30 (0.13), residues: 1447 loop : -0.94 (0.11), residues: 3083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP c 22 HIS 0.007 0.001 HIS Y 44 PHE 0.021 0.002 PHE J 70 TYR 0.017 0.001 TYR x 90 ARG 0.009 0.000 ARG t 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 725 time to evaluate : 6.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 74 LYS cc_start: 0.6503 (OUTLIER) cc_final: 0.5368 (tptp) REVERT: b 136 MET cc_start: 0.3872 (pmm) cc_final: 0.3450 (pmm) REVERT: b 154 MET cc_start: 0.4461 (ppp) cc_final: 0.2923 (OUTLIER) REVERT: f 31 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7665 (mpp80) REVERT: g 59 VAL cc_start: 0.6103 (OUTLIER) cc_final: 0.5722 (t) REVERT: k 85 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: o 41 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: o 44 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8453 (mttp) REVERT: z 50 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8573 (mp) REVERT: z 202 LEU cc_start: 0.8587 (mt) cc_final: 0.8377 (mt) REVERT: C 101 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: C 265 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: D 4 LYS cc_start: 0.8104 (mttm) cc_final: 0.7876 (mttp) REVERT: F 105 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: F 108 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7285 (t70) REVERT: F 130 ASP cc_start: 0.6927 (t0) cc_final: 0.6693 (t0) REVERT: F 142 GLN cc_start: 0.8212 (pm20) cc_final: 0.7996 (pm20) REVERT: I 3 LYS cc_start: 0.5361 (OUTLIER) cc_final: 0.3554 (mptt) REVERT: L 37 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7952 (ttt90) REVERT: P 117 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7302 (mmp80) REVERT: R 111 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: T 54 ASP cc_start: 0.8725 (m-30) cc_final: 0.8327 (m-30) REVERT: U 41 ASP cc_start: 0.8319 (m-30) cc_final: 0.8088 (m-30) REVERT: U 74 SER cc_start: 0.8943 (p) cc_final: 0.8676 (p) REVERT: X 66 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8506 (tp) REVERT: Z 33 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8264 (pp) REVERT: 1 40 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8362 (pm20) REVERT: 3 24 THR cc_start: 0.8864 (t) cc_final: 0.8603 (p) REVERT: 3 40 GLN cc_start: 0.8340 (mp10) cc_final: 0.8065 (mp10) REVERT: 3 42 HIS cc_start: 0.7376 (t-90) cc_final: 0.6997 (t-90) REVERT: 4 6 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.6188 (mmt180) REVERT: 5 38 ILE cc_start: 0.8478 (tt) cc_final: 0.8138 (pt) REVERT: 5 39 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8247 (mttm) outliers start: 213 outliers final: 140 residues processed: 842 average time/residue: 2.2093 time to fit residues: 2706.4037 Evaluate side-chains 868 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 709 time to evaluate : 7.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain d residue 48 GLN Chi-restraints excluded: chain d residue 88 ILE Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 104 SER Chi-restraints excluded: chain e residue 200 GLU Chi-restraints excluded: chain f residue 31 ARG Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain f residue 52 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 117 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 45 ASP Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 85 GLU Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain m residue 8 ASP Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 77 THR Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain p residue 110 LEU Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 70 ILE Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain u residue 20 LEU Chi-restraints excluded: chain x residue 13 VAL Chi-restraints excluded: chain x residue 54 ASN Chi-restraints excluded: chain x residue 65 ILE Chi-restraints excluded: chain x residue 172 VAL Chi-restraints excluded: chain x residue 193 LEU Chi-restraints excluded: chain x residue 227 THR Chi-restraints excluded: chain x residue 229 VAL Chi-restraints excluded: chain x residue 272 GLN Chi-restraints excluded: chain x residue 360 ASP Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain z residue 50 LEU Chi-restraints excluded: chain z residue 123 HIS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 38 LYS Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain P residue 117 ARG Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 6 ASP Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 96 ASP Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain X residue 192 GLU Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain 1 residue 40 GLN Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 34 VAL Chi-restraints excluded: chain 4 residue 6 ARG Chi-restraints excluded: chain 5 residue 39 LYS Chi-restraints excluded: chain 6 residue 23 LEU Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 8 residue 24 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1135 random chunks: chunk 1058 optimal weight: 10.0000 chunk 123 optimal weight: 50.0000 chunk 625 optimal weight: 10.0000 chunk 801 optimal weight: 0.6980 chunk 621 optimal weight: 50.0000 chunk 924 optimal weight: 6.9990 chunk 613 optimal weight: 7.9990 chunk 1093 optimal weight: 6.9990 chunk 684 optimal weight: 7.9990 chunk 666 optimal weight: 10.0000 chunk 505 optimal weight: 10.0000 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 122 GLN d 36 HIS ** d 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 HIS m 75 GLN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 54 ASN x 69 HIS ** x 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 34 GLN ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 HIS ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 29 GLN 4 36 GLN 9 17 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 168698 Z= 0.422 Angle : 0.691 13.307 251717 Z= 0.352 Chirality : 0.043 0.347 32077 Planarity : 0.006 0.116 14232 Dihedral : 23.298 179.883 82804 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.20 % Favored : 94.76 % Rotamer: Outliers : 4.14 % Allowed : 18.68 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % 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: -0.47 (0.10), residues: 6737 helix: 0.79 (0.11), residues: 2204 sheet: -0.40 (0.13), residues: 1448 loop : -1.03 (0.11), residues: 3085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 23 HIS 0.009 0.001 HIS Y 44 PHE 0.026 0.002 PHE t 35 TYR 0.017 0.002 TYR x 90 ARG 0.009 0.001 ARG t 17 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 722 time to evaluate : 7.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 74 LYS cc_start: 0.6516 (OUTLIER) cc_final: 0.5417 (tptp) REVERT: b 136 MET cc_start: 0.4074 (pmm) cc_final: 0.3818 (pmm) REVERT: b 154 MET cc_start: 0.4468 (ppp) cc_final: 0.2985 (OUTLIER) REVERT: c 121 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: e 79 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8121 (tptt) REVERT: g 59 VAL cc_start: 0.6055 (OUTLIER) cc_final: 0.5673 (t) REVERT: i 55 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.4527 (mp) REVERT: k 85 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7483 (tp30) REVERT: m 15 MET cc_start: 0.4096 (OUTLIER) cc_final: 0.3564 (mpp) REVERT: m 43 MET cc_start: 0.3826 (OUTLIER) cc_final: 0.2320 (mpt) REVERT: o 41 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: o 44 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8465 (mttp) REVERT: z 50 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8555 (mp) REVERT: C 101 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7763 (tt0) REVERT: C 265 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: D 4 LYS cc_start: 0.8142 (mttm) cc_final: 0.7909 (mttp) REVERT: D 19 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: F 105 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: F 108 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7450 (t70) REVERT: F 142 GLN cc_start: 0.8254 (pm20) cc_final: 0.8047 (pm20) REVERT: F 170 ASP cc_start: 0.6159 (m-30) cc_final: 0.5722 (m-30) REVERT: I 3 LYS cc_start: 0.5267 (OUTLIER) cc_final: 0.3474 (mptt) REVERT: L 37 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8018 (ttt90) REVERT: N 70 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.7994 (mtp85) REVERT: P 117 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7409 (mmp80) REVERT: R 111 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: T 54 ASP cc_start: 0.8741 (m-30) cc_final: 0.8347 (m-30) REVERT: U 41 ASP cc_start: 0.8349 (m-30) cc_final: 0.8137 (m-30) REVERT: W 40 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7700 (mpp80) REVERT: X 66 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8524 (tp) REVERT: Z 33 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8315 (pp) REVERT: 1 40 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: 3 40 GLN cc_start: 0.8389 (mp10) cc_final: 0.8120 (mp10) REVERT: 3 42 HIS cc_start: 0.7497 (t-90) cc_final: 0.7075 (t-90) REVERT: 4 6 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.6145 (mmt180) REVERT: 5 39 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8306 (mttm) outliers start: 230 outliers final: 145 residues processed: 853 average time/residue: 2.1980 time to fit residues: 2742.6675 Evaluate side-chains 866 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 695 time to evaluate : 6.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain d residue 48 GLN Chi-restraints excluded: chain d residue 88 ILE Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain e residue 104 SER Chi-restraints excluded: chain e residue 200 GLU Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain f residue 52 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 117 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 45 ASP Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 85 GLU Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain m residue 8 ASP Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 43 MET Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 44 LYS Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 36 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 77 THR Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain p residue 110 LEU Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 70 ILE Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 85 LYS Chi-restraints excluded: chain u residue 20 LEU Chi-restraints excluded: chain x residue 13 VAL Chi-restraints excluded: chain x residue 54 ASN Chi-restraints excluded: chain x residue 65 ILE Chi-restraints excluded: chain x residue 193 LEU Chi-restraints excluded: chain x residue 227 THR Chi-restraints excluded: chain x residue 229 VAL Chi-restraints excluded: chain x residue 360 ASP Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain z residue 50 LEU Chi-restraints excluded: chain z residue 123 HIS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 105 GLU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 7 GLN Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 101 LYS Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 38 LYS Chi-restraints excluded: chain N residue 70 ARG Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain P residue 117 ARG Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 64 SER Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 6 ASP Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 40 ARG Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 96 ASP Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain X residue 192 GLU Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain 1 residue 40 GLN Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 34 VAL Chi-restraints excluded: chain 4 residue 6 ARG Chi-restraints excluded: chain 5 residue 39 LYS Chi-restraints excluded: chain 6 residue 23 LEU Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 8 residue 6 SER Chi-restraints excluded: chain 8 residue 24 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1135 random chunks: chunk 676 optimal weight: 6.9990 chunk 436 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 329 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 695 optimal weight: 50.0000 chunk 745 optimal weight: 7.9990 chunk 540 optimal weight: 10.0000 chunk 101 optimal weight: 50.0000 chunk 859 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 HIS ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 31 ASN F 34 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 168698 Z= 0.487 Angle : 0.740 13.857 251717 Z= 0.375 Chirality : 0.046 0.368 32077 Planarity : 0.006 0.117 14232 Dihedral : 23.354 179.958 82804 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.37 % Favored : 94.58 % Rotamer: Outliers : 4.20 % Allowed : 19.42 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % Cis-general : 0.00 % Twisted Proline : 0.33 % 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: 6737 helix: 0.56 (0.11), residues: 2207 sheet: -0.49 (0.13), residues: 1430 loop : -1.20 (0.11), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP b 23 HIS 0.007 0.002 HIS C 38 PHE 0.025 0.002 PHE h 10 TYR 0.024 0.002 TYR d 70 ARG 0.009 0.001 ARG m 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 707 time to evaluate : 6.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 74 LYS cc_start: 0.6571 (OUTLIER) cc_final: 0.5471 (tptp) REVERT: b 136 MET cc_start: 0.4283 (OUTLIER) cc_final: 0.4020 (pmm) REVERT: b 154 MET cc_start: 0.4360 (ppp) cc_final: 0.2903 (mtp) REVERT: c 121 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6937 (pm20) REVERT: d 102 LEU cc_start: 0.6965 (mp) cc_final: 0.6626 (tt) REVERT: e 79 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8113 (tptt) REVERT: e 177 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: g 59 VAL cc_start: 0.5986 (OUTLIER) cc_final: 0.5601 (t) REVERT: h 120 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7275 (mmt-90) REVERT: i 55 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.4618 (mp) REVERT: i 77 ARG cc_start: 0.6342 (ttp-110) cc_final: 0.4837 (tmt-80) REVERT: k 85 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: m 15 MET cc_start: 0.4505 (OUTLIER) cc_final: 0.3525 (mpp) REVERT: m 43 MET cc_start: 0.3721 (OUTLIER) cc_final: 0.2394 (mpt) REVERT: o 41 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: p 17 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7321 (mp10) REVERT: z 50 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8547 (mp) REVERT: C 101 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: C 265 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8166 (m-30) REVERT: D 4 LYS cc_start: 0.8168 (mttm) cc_final: 0.7943 (mttp) REVERT: D 96 GLU cc_start: 0.7795 (tt0) cc_final: 0.7418 (tt0) REVERT: F 88 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7294 (tm-30) REVERT: F 108 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7344 (t70) REVERT: F 142 GLN cc_start: 0.8283 (pm20) cc_final: 0.8002 (pm20) REVERT: I 3 LYS cc_start: 0.5188 (OUTLIER) cc_final: 0.3369 (mptt) REVERT: L 37 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8008 (ttt90) REVERT: N 70 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8012 (mtp85) REVERT: P 117 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7382 (mmp80) REVERT: R 111 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: T 54 ASP cc_start: 0.8751 (m-30) cc_final: 0.8366 (m-30) REVERT: W 40 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7690 (mpp80) REVERT: X 66 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8551 (tp) REVERT: Z 33 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8358 (pp) REVERT: 3 40 GLN cc_start: 0.8421 (mp10) cc_final: 0.8126 (mp10) REVERT: 3 42 HIS cc_start: 0.7542 (t-90) cc_final: 0.7163 (t-90) REVERT: 4 6 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.6156 (mmt180) REVERT: 5 39 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8304 (mttm) outliers start: 233 outliers final: 155 residues processed: 845 average time/residue: 2.2428 time to fit residues: 2758.6108 Evaluate side-chains 874 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 692 time to evaluate : 6.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 136 MET Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain d residue 48 GLN Chi-restraints excluded: chain d residue 88 ILE Chi-restraints excluded: chain d residue 91 SER Chi-restraints excluded: chain d residue 96 VAL Chi-restraints excluded: chain d residue 112 LEU Chi-restraints excluded: chain e residue 59 THR Chi-restraints excluded: chain e residue 71 VAL Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain e residue 104 SER Chi-restraints excluded: chain e residue 177 GLU Chi-restraints excluded: chain e residue 200 GLU Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain g residue 117 VAL Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 120 ARG Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain k residue 23 LYS Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 45 ASP Chi-restraints excluded: chain k residue 74 LEU Chi-restraints excluded: chain k residue 85 GLU Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 35 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain m residue 8 ASP Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 43 MET Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 72 GLN Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 17 GLN Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 77 THR Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain p residue 110 LEU Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 70 ILE Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 27 SER Chi-restraints excluded: chain t residue 48 SER Chi-restraints excluded: chain t residue 85 LYS Chi-restraints excluded: chain u residue 20 LEU Chi-restraints excluded: chain x residue 13 VAL Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 227 THR Chi-restraints excluded: chain x residue 229 VAL Chi-restraints excluded: chain x residue 311 VAL Chi-restraints excluded: chain x residue 346 LEU Chi-restraints excluded: chain x residue 360 ASP Chi-restraints excluded: chain z residue 2 ASP Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 37 LEU Chi-restraints excluded: chain z residue 50 LEU Chi-restraints excluded: chain z residue 66 VAL Chi-restraints excluded: chain z residue 123 HIS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain G residue 7 GLN Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 101 LYS Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 83 LYS Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain J residue 113 THR Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 90 ASP Chi-restraints excluded: chain N residue 22 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 38 LYS Chi-restraints excluded: chain N residue 70 ARG Chi-restraints excluded: chain N residue 95 VAL Chi-restraints excluded: chain O residue 81 THR Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain P residue 117 ARG Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 39 ILE Chi-restraints excluded: chain R residue 64 SER Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 82 THR Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 6 ASP Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 40 ARG Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain X residue 192 GLU Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 61 VAL Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 34 VAL Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 4 residue 6 ARG Chi-restraints excluded: chain 5 residue 39 LYS Chi-restraints excluded: chain 6 residue 23 LEU Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 41 THR Chi-restraints excluded: chain 8 residue 6 SER Chi-restraints excluded: chain 8 residue 24 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1135 random chunks: chunk 995 optimal weight: 5.9990 chunk 1048 optimal weight: 0.9990 chunk 956 optimal weight: 0.9990 chunk 1019 optimal weight: 1.9990 chunk 1047 optimal weight: 5.9990 chunk 613 optimal weight: 5.9990 chunk 444 optimal weight: 6.9990 chunk 800 optimal weight: 1.9990 chunk 312 optimal weight: 6.9990 chunk 921 optimal weight: 3.9990 chunk 964 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN ** i 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 HIS ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 41 HIS ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 54 ASN ** x 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 121 HIS ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN F 28 ASN F 31 ASN F 34 GLN ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 GLN M 3 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 32 HIS 9 17 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 168698 Z= 0.136 Angle : 0.553 14.039 251717 Z= 0.286 Chirality : 0.033 0.252 32077 Planarity : 0.005 0.116 14232 Dihedral : 23.283 179.707 82804 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 2.50 % Allowed : 21.33 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % 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: -0.20 (0.10), residues: 6737 helix: 1.08 (0.11), residues: 2215 sheet: -0.22 (0.13), residues: 1423 loop : -0.94 (0.11), residues: 3099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP z 375 HIS 0.004 0.001 HIS p 41 PHE 0.025 0.001 PHE x 220 TYR 0.023 0.001 TYR d 70 ARG 0.022 0.000 ARG m 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 734 time to evaluate : 6.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 74 LYS cc_start: 0.6510 (OUTLIER) cc_final: 0.5274 (mttp) REVERT: b 136 MET cc_start: 0.4187 (OUTLIER) cc_final: 0.3955 (pmm) REVERT: b 154 MET cc_start: 0.4352 (ppp) cc_final: 0.2910 (mtp) REVERT: e 79 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8140 (tptt) REVERT: g 59 VAL cc_start: 0.6054 (OUTLIER) cc_final: 0.5664 (t) REVERT: h 18 ASN cc_start: 0.8275 (t0) cc_final: 0.8054 (t0) REVERT: h 78 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7266 (ptm-80) REVERT: i 55 LEU cc_start: 0.5719 (OUTLIER) cc_final: 0.4638 (mp) REVERT: i 77 ARG cc_start: 0.6200 (ttp-110) cc_final: 0.4866 (tmt-80) REVERT: k 82 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8334 (mtmm) REVERT: k 85 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7372 (tp30) REVERT: m 15 MET cc_start: 0.3948 (OUTLIER) cc_final: 0.3628 (mpp) REVERT: z 50 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8561 (mp) REVERT: C 265 ASP cc_start: 0.8514 (t0) cc_final: 0.8088 (m-30) REVERT: D 4 LYS cc_start: 0.8031 (mttm) cc_final: 0.7791 (mttp) REVERT: D 127 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8649 (mmt) REVERT: F 25 GLN cc_start: 0.8090 (mm-40) cc_final: 0.6910 (mm-40) REVERT: F 88 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6901 (tm-30) REVERT: I 3 LYS cc_start: 0.5338 (OUTLIER) cc_final: 0.3565 (mptt) REVERT: L 37 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7896 (ttt90) REVERT: T 54 ASP cc_start: 0.8695 (m-30) cc_final: 0.8300 (m-30) REVERT: W 40 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7724 (mpp80) REVERT: X 66 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8489 (tp) REVERT: Z 33 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8101 (pp) REVERT: 3 40 GLN cc_start: 0.8352 (mp10) cc_final: 0.7959 (mp10) REVERT: 3 42 HIS cc_start: 0.7351 (t-90) cc_final: 0.6968 (t-90) outliers start: 139 outliers final: 81 residues processed: 815 average time/residue: 2.2476 time to fit residues: 2657.4132 Evaluate side-chains 801 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 704 time to evaluate : 6.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 136 MET Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain d residue 48 GLN Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain e residue 104 SER Chi-restraints excluded: chain e residue 200 GLU Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 82 LYS Chi-restraints excluded: chain k residue 85 GLU Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 57 ARG Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain p residue 110 LEU Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 70 ILE Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain x residue 54 ASN Chi-restraints excluded: chain x residue 160 LEU Chi-restraints excluded: chain x residue 227 THR Chi-restraints excluded: chain x residue 229 VAL Chi-restraints excluded: chain x residue 360 ASP Chi-restraints excluded: chain z residue 2 ASP Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 50 LEU Chi-restraints excluded: chain z residue 123 HIS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 119 ARG Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 101 LYS Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain P residue 117 ARG Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain W residue 40 ARG Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 192 GLU Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 34 VAL Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1135 random chunks: chunk 1015 optimal weight: 0.9990 chunk 669 optimal weight: 10.0000 chunk 1077 optimal weight: 9.9990 chunk 657 optimal weight: 10.0000 chunk 511 optimal weight: 10.0000 chunk 749 optimal weight: 10.0000 chunk 1130 optimal weight: 3.9990 chunk 1040 optimal weight: 0.0060 chunk 900 optimal weight: 8.9990 chunk 93 optimal weight: 40.0000 chunk 695 optimal weight: 50.0000 overall best weight: 4.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 54 ASN ** x 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 121 HIS ** z 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 34 GLN ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 GLN N 89 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 36 GLN 7 55 ASN 9 17 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 168698 Z= 0.333 Angle : 0.628 13.557 251717 Z= 0.322 Chirality : 0.039 0.318 32077 Planarity : 0.005 0.116 14232 Dihedral : 23.244 179.827 82804 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.76 % Favored : 95.21 % Rotamer: Outliers : 2.20 % Allowed : 22.06 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.33 % 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: -0.33 (0.10), residues: 6737 helix: 0.97 (0.11), residues: 2214 sheet: -0.35 (0.13), residues: 1451 loop : -0.99 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP k 53 HIS 0.005 0.001 HIS x 20 PHE 0.023 0.002 PHE J 70 TYR 0.025 0.002 TYR d 70 ARG 0.009 0.000 ARG m 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13474 Ramachandran restraints generated. 6737 Oldfield, 0 Emsley, 6737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 702 time to evaluate : 6.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 74 LYS cc_start: 0.6508 (OUTLIER) cc_final: 0.5393 (tptp) REVERT: b 136 MET cc_start: 0.4184 (OUTLIER) cc_final: 0.3946 (pmm) REVERT: b 154 MET cc_start: 0.4382 (ppp) cc_final: 0.3167 (mtm) REVERT: d 102 LEU cc_start: 0.6830 (mp) cc_final: 0.6514 (tt) REVERT: d 135 TYR cc_start: 0.6480 (m-10) cc_final: 0.6151 (m-10) REVERT: e 79 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8151 (tptt) REVERT: e 201 SER cc_start: 0.8519 (t) cc_final: 0.8261 (p) REVERT: g 59 VAL cc_start: 0.6168 (OUTLIER) cc_final: 0.5784 (t) REVERT: i 55 LEU cc_start: 0.5704 (OUTLIER) cc_final: 0.4608 (mp) REVERT: i 77 ARG cc_start: 0.6289 (ttp-110) cc_final: 0.4848 (tmt-80) REVERT: k 85 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7499 (tp30) REVERT: m 15 MET cc_start: 0.4022 (OUTLIER) cc_final: 0.3452 (mpp) REVERT: p 32 ARG cc_start: 0.8131 (tpp80) cc_final: 0.7929 (mmt180) REVERT: z 1 MET cc_start: 0.5518 (mtp) cc_final: 0.5173 (ptp) REVERT: z 50 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8534 (mp) REVERT: D 4 LYS cc_start: 0.8117 (mttm) cc_final: 0.7890 (mttp) REVERT: F 25 GLN cc_start: 0.8222 (mm-40) cc_final: 0.6993 (mm-40) REVERT: F 88 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7005 (tm-30) REVERT: F 108 ASP cc_start: 0.7699 (OUTLIER) cc_final: 0.7434 (t70) REVERT: I 3 LYS cc_start: 0.5328 (OUTLIER) cc_final: 0.3535 (mptt) REVERT: L 37 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7971 (ttt90) REVERT: L 135 GLN cc_start: 0.9382 (OUTLIER) cc_final: 0.7500 (mm110) REVERT: P 117 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7295 (mmp80) REVERT: T 54 ASP cc_start: 0.8741 (m-30) cc_final: 0.8332 (m-30) REVERT: W 40 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7677 (mpp80) REVERT: X 66 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8514 (tp) REVERT: Z 33 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8252 (pp) REVERT: 3 40 GLN cc_start: 0.8276 (mp10) cc_final: 0.8003 (mp10) REVERT: 3 42 HIS cc_start: 0.7429 (t-90) cc_final: 0.7052 (t-90) outliers start: 122 outliers final: 89 residues processed: 774 average time/residue: 2.2100 time to fit residues: 2481.3564 Evaluate side-chains 799 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 694 time to evaluate : 6.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 136 MET Chi-restraints excluded: chain b residue 157 VAL Chi-restraints excluded: chain b residue 189 THR Chi-restraints excluded: chain c residue 169 ARG Chi-restraints excluded: chain d residue 48 GLN Chi-restraints excluded: chain d residue 88 ILE Chi-restraints excluded: chain e residue 79 LYS Chi-restraints excluded: chain e residue 104 SER Chi-restraints excluded: chain e residue 200 GLU Chi-restraints excluded: chain f residue 36 THR Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 116 MET Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 53 ASP Chi-restraints excluded: chain h residue 78 ARG Chi-restraints excluded: chain i residue 55 LEU Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 23 LYS Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 45 ASP Chi-restraints excluded: chain k residue 85 GLU Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 106 ILE Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain p residue 103 LEU Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain p residue 110 LEU Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 70 ILE Chi-restraints excluded: chain s residue 66 MET Chi-restraints excluded: chain u residue 20 LEU Chi-restraints excluded: chain x residue 54 ASN Chi-restraints excluded: chain x residue 205 VAL Chi-restraints excluded: chain x residue 223 THR Chi-restraints excluded: chain x residue 227 THR Chi-restraints excluded: chain x residue 229 VAL Chi-restraints excluded: chain x residue 360 ASP Chi-restraints excluded: chain z residue 3 VAL Chi-restraints excluded: chain z residue 50 LEU Chi-restraints excluded: chain z residue 123 HIS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 101 LYS Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 15 ILE Chi-restraints excluded: chain J residue 48 THR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain P residue 82 GLU Chi-restraints excluded: chain P residue 117 ARG Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 9 THR Chi-restraints excluded: chain T residue 51 LYS Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 91 ARG Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 80 THR Chi-restraints excluded: chain V residue 71 THR Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 40 ARG Chi-restraints excluded: chain W residue 60 VAL Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 192 GLU Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain 3 residue 10 VAL Chi-restraints excluded: chain 3 residue 34 VAL Chi-restraints excluded: chain 7 residue 34 GLU Chi-restraints excluded: chain 7 residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1135 random chunks: chunk 552 optimal weight: 6.9990 chunk 715 optimal weight: 10.0000 chunk 959 optimal weight: 4.9990 chunk 275 optimal weight: 30.0000 chunk 830 optimal weight: 0.4980 chunk 132 optimal weight: 30.0000 chunk 250 optimal weight: 8.9990 chunk 901 optimal weight: 10.0000 chunk 377 optimal weight: 8.9990 chunk 926 optimal weight: 3.9990 chunk 114 optimal weight: 30.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 41 HIS ** s 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 69 HIS ** t 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 121 HIS ** z 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 34 GLN ** F 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 ASN ** 3 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 36 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.168310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115150 restraints weight = 205374.380| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.06 r_work: 0.3299 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.209 168698 Z= 0.349 Angle : 0.654 59.199 251717 Z= 0.343 Chirality : 0.040 0.575 32077 Planarity : 0.006 0.194 14232 Dihedral : 23.245 179.817 82804 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.22 % Rotamer: Outliers : 2.43 % Allowed : 22.06 % Favored : 75.50 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.33 % 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: -0.34 (0.10), residues: 6737 helix: 0.95 (0.11), residues: 2214 sheet: -0.34 (0.13), residues: 1441 loop : -1.00 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP k 53 HIS 0.005 0.001 HIS 7 35 PHE 0.023 0.002 PHE J 70 TYR 0.023 0.002 TYR d 70 ARG 0.047 0.000 ARG g 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42696.36 seconds wall clock time: 744 minutes 41.06 seconds (44681.06 seconds total)