Starting phenix.real_space_refine on Fri Mar 1 19:29:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9k_43075/03_2024/8v9k_43075_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9k_43075/03_2024/8v9k_43075.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9k_43075/03_2024/8v9k_43075_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9k_43075/03_2024/8v9k_43075_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9k_43075/03_2024/8v9k_43075_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9k_43075/03_2024/8v9k_43075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9k_43075/03_2024/8v9k_43075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9k_43075/03_2024/8v9k_43075_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v9k_43075/03_2024/8v9k_43075_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.083 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 4786 5.49 5 S 111 5.16 5 C 77258 2.51 5 N 28621 2.21 5 O 42475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c ASP 25": "OD1" <-> "OD2" Residue "c ASP 61": "OD1" <-> "OD2" Residue "c ASP 66": "OD1" <-> "OD2" Residue "c ASP 181": "OD1" <-> "OD2" Residue "c ASP 206": "OD1" <-> "OD2" Residue "d TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 43": "OE1" <-> "OE2" Residue "d TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 147": "OD1" <-> "OD2" Residue "e ASP 188": "OD1" <-> "OD2" Residue "f PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 64": "OD1" <-> "OD2" Residue "f GLU 68": "OE1" <-> "OE2" Residue "f ASP 94": "OD1" <-> "OD2" Residue "i GLU 113": "OE1" <-> "OE2" Residue "i PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 127": "OD1" <-> "OD2" Residue "i GLU 132": "OE1" <-> "OE2" Residue "k GLU 103": "OE1" <-> "OE2" Residue "m ASP 58": "OD1" <-> "OD2" Residue "n PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 10": "OE1" <-> "OE2" Residue "o ASP 19": "OD1" <-> "OD2" Residue "p ASP 52": "OD1" <-> "OD2" Residue "p TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 44": "OE1" <-> "OE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D ASP 45": "OD1" <-> "OD2" Residue "E ASP 97": "OD1" <-> "OD2" Residue "E ASP 193": "OD1" <-> "OD2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "I TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 105": "OD1" <-> "OD2" Residue "L ASP 49": "OD1" <-> "OD2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "N ASP 123": "OD1" <-> "OD2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "P GLU 65": "OE1" <-> "OE2" Residue "P GLU 101": "OE1" <-> "OE2" Residue "P GLU 118": "OE1" <-> "OE2" Residue "Q GLU 34": "OE1" <-> "OE2" Residue "R GLU 56": "OE1" <-> "OE2" Residue "R PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 102": "OD1" <-> "OD2" Residue "T TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 25": "OE1" <-> "OE2" Residue "W ASP 16": "OD1" <-> "OD2" Residue "W ASP 29": "OD1" <-> "OD2" Residue "W TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 53": "OD1" <-> "OD2" Residue "X GLU 72": "OE1" <-> "OE2" Residue "Z ASP 6": "OD1" <-> "OD2" Residue "1 GLU 12": "OE1" <-> "OE2" Residue "3 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 6": "OD1" <-> "OD2" Residue "7 PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 45": "OD1" <-> "OD2" Residue "8 ASP 29": "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: 153253 Number of models: 1 Model: "" Number of chains: 61 Chain: "a" Number of atoms: 32439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1511, 32439 Classifications: {'RNA': 1511} Modifications used: {'rna2p_pur': 114, 'rna2p_pyr': 85, 'rna3p_pur': 735, 'rna3p_pyr': 577} Link IDs: {'rna2p': 199, 'rna3p': 1311} 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: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna3p_pyr': 3} Link IDs: {'rna3p': 2} 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: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2800 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 16, 'TRANS': 347} Chain: "A" Number of atoms: 66171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3081, 66171 Classifications: {'RNA': 3081} Modifications used: {'rna2p_pur': 297, 'rna2p_pyr': 151, 'rna3p_pur': 1468, 'rna3p_pyr': 1165} Link IDs: {'rna2p': 448, 'rna3p': 2632} 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: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1445 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} 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: "K" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 531 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 6, 'TRANS': 95} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 120 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: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 628 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} 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: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 432 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 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: "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 A11XW SG CYS Z 5 186.238 114.226 92.971 1.00 35.34 S ATOM A11YI SG CYS Z 8 184.992 111.815 90.453 1.00 36.60 S ATOM A1280 SG CYS Z 52 185.567 110.644 94.083 1.00 35.90 S ATOM A128J SG CYS Z 55 188.495 111.210 91.915 1.00 38.07 S ATOM A13S3 SG CYS 5 15 146.923 52.914 105.180 1.00 40.67 S ATOM A13SP SG CYS 5 18 148.536 54.580 102.147 1.00 41.76 S ATOM A13YO SG CYS 5 42 144.856 54.320 102.203 1.00 36.83 S ATOM A13Z9 SG CYS 5 45 146.940 51.244 101.646 1.00 40.20 S Time building chain proxies: 56.97, per 1000 atoms: 0.37 Number of scatterers: 153253 At special positions: 0 Unit cell: (256.7, 247.35, 283.9, 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 111 16.00 P 4786 15.00 O 42475 8.00 N 28621 7.00 C 77258 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: 58.78 Conformation dependent library (CDL) restraints added in 8.2 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 52 " 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 " Number of angles added : 12 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11980 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: 193 helices and 82 sheets defined 38.3% alpha, 19.0% beta 1605 base pairs and 2411 stacking pairs defined. Time for finding SS restraints: 71.09 Creating SS restraints... Processing helix chain 'b' and resid 5 through 13 removed outlier: 3.961A pdb=" N GLY b 13 " --> pdb=" O LEU b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 removed outlier: 4.123A pdb=" N LYS b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG b 29 " --> pdb=" O PRO b 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 24 through 29' Processing helix chain 'b' and resid 42 through 64 removed outlier: 3.829A pdb=" N HIS b 63 " --> pdb=" O GLU b 59 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY b 64 " --> pdb=" O THR b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 88 removed outlier: 3.670A pdb=" N GLN b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU b 78 " --> pdb=" O LYS b 74 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER b 79 " --> pdb=" O GLN b 75 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 99 through 104 Processing helix chain 'b' and resid 105 through 124 removed outlier: 5.246A pdb=" N LYS b 109 " --> pdb=" O SER b 105 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ARG b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU b 111 " --> pdb=" O VAL b 107 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY b 124 " --> pdb=" O MET b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 149 removed outlier: 4.071A pdb=" N ARG b 146 " --> pdb=" O ASN b 142 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N SER b 147 " --> pdb=" O LYS b 143 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLY b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 206 through 228 removed outlier: 3.504A pdb=" N ALA b 227 " --> pdb=" O GLU b 223 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG b 228 " --> pdb=" O GLY b 224 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.602A pdb=" N LEU c 12 " --> pdb=" O HIS c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 3.716A pdb=" N LEU c 46 " --> pdb=" O LEU c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.512A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY c 77 " --> pdb=" O GLY c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 94 removed outlier: 3.749A pdb=" N THR c 94 " --> pdb=" O LEU c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.853A pdb=" N ASN c 125 " --> pdb=" O GLU c 121 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 143 removed outlier: 4.115A pdb=" N GLN c 143 " --> pdb=" O SER c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 removed outlier: 4.523A pdb=" N SER d 12 " --> pdb=" O ALA d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 24 through 30 removed outlier: 3.783A pdb=" N LYS d 28 " --> pdb=" O GLN d 24 " (cutoff:3.500A) Proline residue: d 30 - end of helix Processing helix chain 'd' and resid 44 through 61 Processing helix chain 'd' and resid 63 through 78 Proline residue: d 78 - end of helix Processing helix chain 'd' and resid 80 through 92 removed outlier: 3.558A pdb=" N SER d 91 " --> pdb=" O ARG d 87 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 Processing helix chain 'd' and resid 105 through 116 removed outlier: 3.822A pdb=" N GLY d 116 " --> pdb=" O LEU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 141 through 148 removed outlier: 5.788A pdb=" N LEU d 148 " --> pdb=" O SER d 144 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 157 removed outlier: 3.771A pdb=" N ALA d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 182 through 187 Processing helix chain 'd' and resid 192 through 201 removed outlier: 3.588A pdb=" N VAL d 196 " --> pdb=" O GLU d 192 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS d 201 " --> pdb=" O GLU d 197 " (cutoff:3.500A) Processing helix chain 'd' and resid 34 through 39 removed outlier: 3.623A pdb=" N GLY d 37 " --> pdb=" O GLY d 34 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG d 38 " --> pdb=" O GLN d 35 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA d 39 " --> pdb=" O HIS d 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 34 through 39' Processing helix chain 'e' and resid 80 through 96 removed outlier: 3.537A pdb=" N ASN e 95 " --> pdb=" O GLU e 91 " (cutoff:3.500A) removed outlier: 4.752A 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: 3.539A pdb=" N LEU e 171 " --> pdb=" O ALA e 167 " (cutoff:3.500A) removed outlier: 3.733A 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: 3.796A pdb=" N VAL e 189 " --> pdb=" O PRO e 185 " (cutoff:3.500A) Processing helix chain 'e' and resid 191 through 214 removed outlier: 3.674A pdb=" N LEU e 195 " --> pdb=" O PRO e 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 32 removed outlier: 4.022A pdb=" N VAL f 19 " --> pdb=" O ASP f 15 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ALA f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) Proline residue: f 21 - end of helix removed outlier: 4.496A pdb=" N VAL f 29 " --> pdb=" O THR f 25 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 68 through 82 removed outlier: 3.596A pdb=" N LEU f 81 " --> pdb=" O ARG f 77 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN f 82 " --> pdb=" O GLN f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.775A pdb=" N THR g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.676A 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 112 removed outlier: 5.741A pdb=" N ARG g 112 " --> pdb=" O SER g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 4.331A pdb=" N ALA g 121 " --> pdb=" O VAL g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 149 removed outlier: 3.629A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG g 149 " --> pdb=" O ALA g 145 " (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: 4.882A pdb=" N PHE i 59 " --> pdb=" O LEU i 55 " (cutoff:3.500A) Processing helix chain 'i' and resid 61 through 73 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: 4.728A pdb=" N ALA i 117 " --> pdb=" O GLU i 113 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS i 120 " --> pdb=" O PRO i 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.202A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.766A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 60 removed outlier: 3.719A pdb=" N VAL k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) removed outlier: 4.861A 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 68 through 87 removed outlier: 3.541A pdb=" N HIS k 86 " --> pdb=" O LYS k 82 " (cutoff:3.500A) Processing helix chain 'k' and resid 101 through 113 removed outlier: 3.676A 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: 3.886A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.971A pdb=" N THR m 20 " --> pdb=" O GLU m 16 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.729A pdb=" N LEU m 48 " --> pdb=" O ARG m 44 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR m 49 " --> pdb=" O THR m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 Processing helix chain 'm' and resid 67 through 85 removed outlier: 3.869A pdb=" N ARG m 71 " --> pdb=" O GLU m 67 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA m 76 " --> pdb=" O ARG m 72 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP m 77 " --> pdb=" O GLU m 73 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE m 78 " --> pdb=" O VAL m 74 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY m 85 " --> pdb=" O LYS m 81 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 95 Processing helix chain 'm' and resid 107 through 112 Processing helix chain 'n' and resid 3 through 13 removed outlier: 3.934A pdb=" N ASN n 11 " --> pdb=" O VAL n 7 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS n 12 " --> pdb=" O HIS n 8 " (cutoff:3.500A) removed outlier: 5.366A 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: 4.278A pdb=" N VAL o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) removed outlier: 3.513A 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 34 through 43 removed outlier: 4.004A pdb=" N LEU r 38 " --> pdb=" O ASP r 34 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR r 41 " --> pdb=" O LEU r 37 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N SER r 43 " --> pdb=" O ARG r 39 " (cutoff:3.500A) Processing helix chain 'r' and resid 50 through 55 removed outlier: 3.928A pdb=" N THR r 54 " --> pdb=" O ALA r 50 " (cutoff:3.500A) Processing helix chain 'r' and resid 57 through 75 Processing helix chain 's' and resid 12 through 26 removed outlier: 3.749A pdb=" N LEU s 16 " --> pdb=" O ASP s 12 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN s 26 " --> pdb=" O GLN s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 46 removed outlier: 4.381A pdb=" N ILE s 45 " --> pdb=" O ILE s 41 " (cutoff:3.500A) removed outlier: 5.311A 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 't' and resid 4 through 42 Processing helix chain 't' and resid 44 through 65 Processing helix chain 't' and resid 68 through 86 Processing helix chain 'u' and resid 4 through 25 removed outlier: 3.811A pdb=" N THR u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG u 25 " --> pdb=" O LEU u 21 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 33 removed outlier: 3.517A pdb=" N LYS u 33 " --> pdb=" O ARG u 29 " (cutoff:3.500A) Processing helix chain 'z' and resid 6 through 13 removed outlier: 3.565A pdb=" N VAL z 10 " --> pdb=" O LEU z 6 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA z 11 " --> pdb=" O ARG z 7 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N GLU z 13 " --> pdb=" O LEU z 9 " (cutoff:3.500A) Processing helix chain 'z' and resid 27 through 49 removed outlier: 3.865A pdb=" N VAL z 31 " --> pdb=" O THR z 27 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLU z 32 " --> pdb=" O LEU z 28 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ARG z 33 " --> pdb=" O ASP z 29 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG z 34 " --> pdb=" O ALA z 30 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU z 35 " --> pdb=" O VAL z 31 " (cutoff:3.500A) Processing helix chain 'z' and resid 51 through 65 removed outlier: 3.974A pdb=" N ILE z 55 " --> pdb=" O LYS z 51 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU z 60 " --> pdb=" O ASP z 56 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA z 61 " --> pdb=" O SER z 57 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER z 65 " --> pdb=" O ALA z 61 " (cutoff:3.500A) Processing helix chain 'z' and resid 106 through 112 removed outlier: 3.650A pdb=" N ILE z 110 " --> pdb=" O VAL z 106 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP z 111 " --> pdb=" O VAL z 107 " (cutoff:3.500A) Processing helix chain 'z' and resid 165 through 191 removed outlier: 3.672A pdb=" N THR z 169 " --> pdb=" O PHE z 165 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA z 172 " --> pdb=" O THR z 168 " (cutoff:3.500A) Processing helix chain 'z' and resid 202 through 213 removed outlier: 3.715A pdb=" N THR z 206 " --> pdb=" O VAL z 202 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU z 208 " --> pdb=" O SER z 204 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU z 209 " --> pdb=" O ARG z 205 " (cutoff:3.500A) Proline residue: z 213 - end of helix Processing helix chain 'z' and resid 214 through 220 removed outlier: 3.632A pdb=" N VAL z 218 " --> pdb=" O GLN z 214 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG z 219 " --> pdb=" O ARG z 215 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL z 220 " --> pdb=" O VAL z 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 214 through 220' Processing helix chain 'z' and resid 235 through 267 removed outlier: 4.292A pdb=" N ALA z 243 " --> pdb=" O ASP z 239 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU z 244 " --> pdb=" O LEU z 240 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG z 247 " --> pdb=" O ALA z 243 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU z 252 " --> pdb=" O ARG z 248 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE z 253 " --> pdb=" O ARG z 249 " (cutoff:3.500A) Processing helix chain 'z' and resid 274 through 285 removed outlier: 4.077A pdb=" N ALA z 280 " --> pdb=" O ALA z 276 " (cutoff:3.500A) Processing helix chain 'z' and resid 312 through 320 removed outlier: 4.539A pdb=" N GLU z 318 " --> pdb=" O ASP z 314 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LEU z 319 " --> pdb=" O MET z 315 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY z 320 " --> pdb=" O LEU z 316 " (cutoff:3.500A) Processing helix chain 'z' and resid 328 through 341 Proline residue: z 334 - end of helix Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.533A 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: 4.169A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 removed outlier: 3.927A pdb=" N MET C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 5.190A 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: 4.522A pdb=" N LYS C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU C 267 " --> pdb=" O PRO C 263 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 5.945A 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 'C' and resid 198 through 203 removed outlier: 4.233A pdb=" N SER C 202 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.574A pdb=" N GLN D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 96 removed outlier: 4.269A pdb=" N VAL D 92 " --> pdb=" O ASP D 88 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLU D 96 " --> pdb=" O VAL D 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 96' Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.529A pdb=" N ILE D 105 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 47 removed outlier: 4.181A pdb=" N GLN E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLN E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 122 removed outlier: 3.545A pdb=" N ALA E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 149 removed outlier: 3.538A pdb=" N THR E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 171 removed outlier: 3.586A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ASN E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 192 removed outlier: 3.507A pdb=" N VAL E 188 " --> pdb=" O ASN E 184 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASP E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 210 removed outlier: 3.865A pdb=" N ALA E 203 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN E 208 " --> pdb=" O TYR E 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 28 removed outlier: 3.600A pdb=" N ARG F 16 " --> pdb=" O LYS F 12 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU F 17 " --> pdb=" O GLN F 13 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG F 20 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLU F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 removed outlier: 3.677A pdb=" N ASP F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) removed outlier: 3.731A 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: 4.357A pdb=" N GLY F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA F 65 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 117 removed outlier: 4.039A pdb=" N TRP F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA F 114 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 4.936A 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 169 through 181 removed outlier: 3.745A pdb=" N ALA F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 removed outlier: 5.175A pdb=" N MET F 144 " --> pdb=" O GLU F 141 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE F 145 " --> pdb=" O GLN F 142 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N HIS F 146 " --> pdb=" O SER F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 141 through 146' Processing helix chain 'G' and resid 2 through 7 removed outlier: 4.083A pdb=" N GLN G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.717A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 152 removed outlier: 3.844A pdb=" N LEU G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 42 through 60 removed outlier: 4.554A pdb=" N GLN H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL H 58 " --> pdb=" O ARG H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 75 removed outlier: 4.479A pdb=" N GLU H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 108 removed outlier: 3.502A pdb=" N LYS H 105 " --> pdb=" O VAL H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 118 removed outlier: 4.068A pdb=" N VAL H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 5.785A 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 21 removed outlier: 3.678A pdb=" N ALA I 11 " --> pdb=" O ALA I 7 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP I 12 " --> pdb=" O THR I 8 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER I 20 " --> pdb=" O GLN I 16 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N THR I 21 " --> pdb=" O PHE I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 44 Processing helix chain 'I' and resid 53 through 65 removed outlier: 3.810A pdb=" N ALA I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER I 62 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLY I 65 " --> pdb=" O ALA I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 74 removed outlier: 3.975A pdb=" N PHE I 73 " --> pdb=" O LEU I 69 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 69 through 74' Processing helix chain 'I' and resid 85 through 101 removed outlier: 5.697A pdb=" N ALA I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 126 removed outlier: 3.730A pdb=" N GLU I 121 " --> pdb=" O VAL I 117 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS I 122 " --> pdb=" O ALA I 118 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA I 124 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP I 125 " --> pdb=" O GLU I 121 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 31 Proline residue: J 28 - end of helix Processing helix chain 'J' and resid 36 through 49 removed outlier: 4.036A pdb=" N PHE J 40 " --> pdb=" O ASN J 36 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N CYS J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS J 42 " --> pdb=" O MET J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 86 removed outlier: 3.727A pdb=" N LYS J 83 " --> pdb=" O LYS J 79 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA J 85 " --> pdb=" O LEU J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 115 removed outlier: 3.644A pdb=" N VAL J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG J 108 " --> pdb=" O TRP J 104 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU J 109 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE J 110 " --> pdb=" O GLN J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 138 removed outlier: 3.627A pdb=" N LYS J 128 " --> pdb=" O ASP J 124 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE J 129 " --> pdb=" O ALA J 125 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE J 130 " --> pdb=" O ALA J 126 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR J 133 " --> pdb=" O ILE J 129 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG J 135 " --> pdb=" O ALA J 131 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER J 136 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET J 137 " --> pdb=" O THR J 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 200 removed outlier: 3.785A pdb=" N ALA K 186 " --> pdb=" O GLU K 182 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU K 187 " --> pdb=" O THR K 183 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA K 191 " --> pdb=" O GLU K 187 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA K 192 " --> pdb=" O ASN K 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 38 removed outlier: 3.582A pdb=" N THR L 34 " --> pdb=" O SER L 30 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU L 35 " --> pdb=" O ALA L 31 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG L 37 " --> pdb=" O ALA L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 96 removed outlier: 4.020A pdb=" N GLU L 94 " --> pdb=" O GLY L 90 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 97 through 110 removed outlier: 4.277A pdb=" N VAL L 101 " --> pdb=" O PRO L 97 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA L 104 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) Proline residue: L 110 - end of helix Processing helix chain 'L' and resid 112 through 122 removed outlier: 3.541A pdb=" N GLN L 117 " --> pdb=" O LYS L 113 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS L 120 " --> pdb=" O ARG L 116 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS L 121 " --> pdb=" O GLN L 117 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU L 122 " --> pdb=" O ILE L 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 110 removed outlier: 4.095A pdb=" N GLU M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 118 removed outlier: 3.599A pdb=" N LEU M 117 " --> pdb=" O LYS M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 44 removed outlier: 4.220A pdb=" N ARG N 43 " --> pdb=" O GLY N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 3.626A pdb=" N LEU N 61 " --> pdb=" O ILE N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 87 removed outlier: 3.755A pdb=" N ILE N 83 " --> pdb=" O ASN N 79 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN N 84 " --> pdb=" O VAL N 80 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS N 85 " --> pdb=" O GLY N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 102 Processing helix chain 'N' and resid 130 through 141 removed outlier: 3.730A pdb=" N GLU N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA N 140 " --> pdb=" O ALA N 136 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY N 141 " --> pdb=" O ILE N 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 59 removed outlier: 3.582A pdb=" N SER O 49 " --> pdb=" O ARG O 45 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 126 removed outlier: 4.363A pdb=" N ALA O 114 " --> pdb=" O ASP O 110 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS O 123 " --> pdb=" O THR O 119 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS O 124 " --> pdb=" O ARG O 120 " (cutoff:3.500A) removed outlier: 4.006A 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: 3.785A pdb=" N SER P 18 " --> pdb=" O SER P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 58 Proline residue: P 46 - end of helix removed outlier: 3.854A pdb=" N LEU P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE P 52 " --> pdb=" O ALA P 48 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS P 54 " --> pdb=" O LYS P 50 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY P 58 " --> pdb=" O HIS P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 71 removed outlier: 3.704A pdb=" N LYS P 68 " --> pdb=" O ARG P 64 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS P 69 " --> pdb=" O GLU P 65 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG P 71 " --> pdb=" O MET P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 89 removed outlier: 3.630A pdb=" N HIS P 77 " --> pdb=" O LYS P 73 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR P 78 " --> pdb=" O ASP P 74 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLY P 84 " --> pdb=" O PHE P 80 " (cutoff:3.500A) Proline residue: P 85 - end of helix removed outlier: 3.632A pdb=" N ALA P 88 " --> pdb=" O GLY P 84 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP P 89 " --> pdb=" O PRO P 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 29 removed outlier: 3.562A pdb=" N ASN Q 16 " --> pdb=" O GLU Q 12 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG Q 24 " --> pdb=" O ARG Q 20 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU Q 25 " --> pdb=" O ARG Q 21 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS Q 27 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LYS Q 28 " --> pdb=" O ARG Q 24 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL Q 29 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 73 removed outlier: 3.758A pdb=" N ALA Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE Q 73 " --> pdb=" O ASP Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 96 removed outlier: 3.706A pdb=" N ARG Q 83 " --> pdb=" O ALA Q 79 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA Q 89 " --> pdb=" O GLY Q 85 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA Q 95 " --> pdb=" O ARG Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 124 removed outlier: 3.615A pdb=" N GLY Q 124 " --> pdb=" O ALA Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 12 removed outlier: 5.250A pdb=" N ALA R 10 " --> pdb=" O PHE R 6 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER R 11 " --> pdb=" O VAL R 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 103 removed outlier: 4.806A pdb=" N ARG R 100 " --> pdb=" O LEU R 96 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU R 101 " --> pdb=" O TYR R 97 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 5.419A 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: 4.099A pdb=" N LYS S 12 " --> pdb=" O LEU S 8 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS S 13 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG S 14 " --> pdb=" O ALA S 10 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR S 16 " --> pdb=" O LYS S 12 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS S 22 " --> pdb=" O LEU S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 31 removed outlier: 4.122A pdb=" N ARG S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 73 removed outlier: 3.810A pdb=" N HIS S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR S 44 " --> pdb=" O LEU S 40 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR S 47 " --> pdb=" O LEU S 43 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU S 60 " --> pdb=" O GLU S 56 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA S 67 " --> pdb=" O SER S 63 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 Processing helix chain 'S' and resid 91 through 101 removed outlier: 3.819A pdb=" N GLU S 97 " --> pdb=" O LYS S 93 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL S 100 " --> pdb=" O ALA S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 118 removed outlier: 3.625A pdb=" N PHE S 106 " --> pdb=" O ASP S 102 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR S 107 " --> pdb=" O PRO S 103 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL S 112 " --> pdb=" O ALA S 108 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA S 116 " --> pdb=" O VAL S 112 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) Proline residue: S 118 - end of helix Processing helix chain 'T' and resid 51 through 59 removed outlier: 3.709A pdb=" N ALA T 56 " --> pdb=" O ALA T 52 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS T 57 " --> pdb=" O ASP T 53 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL T 58 " --> pdb=" O ASP T 54 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA T 59 " --> pdb=" O LEU T 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 20 through 32 removed outlier: 3.568A pdb=" N ARG U 26 " --> pdb=" O THR U 22 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL U 27 " --> pdb=" O LYS U 23 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU U 30 " --> pdb=" O ARG U 26 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG U 32 " --> pdb=" O ILE U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 46 removed outlier: 3.807A pdb=" N ARG U 44 " --> pdb=" O LEU U 40 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP U 45 " --> pdb=" O ASP U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 50 through 68 removed outlier: 3.585A pdb=" N VAL U 54 " --> pdb=" O ALA U 50 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL U 57 " --> pdb=" O PRO U 53 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA U 59 " --> pdb=" O ALA U 55 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER U 60 " --> pdb=" O LYS U 56 " (cutoff:3.500A) Processing helix chain 'V' and resid 6 through 12 removed outlier: 4.527A pdb=" N ILE V 10 " --> pdb=" O ASP V 6 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE V 11 " --> pdb=" O PRO V 7 " (cutoff:3.500A) removed outlier: 5.013A 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: 3.560A pdb=" N GLU V 25 " --> pdb=" O TYR V 21 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP V 26 " --> pdb=" O GLY V 22 " (cutoff:3.500A) Processing helix chain 'V' and resid 38 through 51 removed outlier: 3.521A pdb=" N LYS V 48 " --> pdb=" O ILE V 44 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 72 removed outlier: 4.457A pdb=" N VAL W 71 " --> pdb=" O HIS W 67 " (cutoff:3.500A) removed outlier: 5.582A 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 removed outlier: 4.012A pdb=" N GLN X 26 " --> pdb=" O GLY X 22 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 61 removed outlier: 3.615A pdb=" N VAL X 57 " --> pdb=" O ASP X 53 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU X 58 " --> pdb=" O PHE X 54 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER X 60 " --> pdb=" O ALA X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 186 through 194 removed outlier: 4.068A pdb=" N GLU X 191 " --> pdb=" O ALA X 187 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU X 192 " --> pdb=" O GLU X 188 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU X 193 " --> pdb=" O ALA X 189 " (cutoff:3.500A) removed outlier: 5.879A 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: 3.917A pdb=" N GLU 1 12 " --> pdb=" O GLY 1 8 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU 1 13 " --> pdb=" O GLU 1 9 " (cutoff:3.500A) Processing helix chain '1' and resid 14 through 39 removed outlier: 4.391A pdb=" N LYS 1 19 " --> pdb=" O ASP 1 15 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP 1 20 " --> pdb=" O ASP 1 16 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE 1 34 " --> pdb=" O PHE 1 30 " (cutoff:3.500A) Processing helix chain '1' and resid 43 through 67 removed outlier: 4.793A pdb=" N LEU 1 47 " --> pdb=" O ASN 1 43 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG 1 48 " --> pdb=" O ASN 1 44 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL 1 57 " --> pdb=" O GLU 1 53 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG 1 64 " --> pdb=" O VAL 1 60 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU 1 65 " --> pdb=" O LEU 1 61 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 removed outlier: 3.739A pdb=" N SER 2 22 " --> pdb=" O LYS 2 18 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU 2 23 " --> pdb=" O GLN 2 19 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 51 removed outlier: 3.762A pdb=" N THR 2 49 " --> pdb=" O GLY 2 45 " (cutoff:3.500A) removed outlier: 3.583A 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 Processing helix chain '4' and resid 9 through 21 removed outlier: 4.080A pdb=" N ARG 4 16 " --> pdb=" O ASN 4 12 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLN 4 19 " --> pdb=" O SER 4 15 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TRP 4 20 " --> pdb=" O ARG 4 16 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS 4 21 " --> pdb=" O ARG 4 17 " (cutoff:3.500A) Processing helix chain '4' and resid 40 through 50 removed outlier: 3.559A pdb=" N LEU 4 44 " --> pdb=" O PRO 4 40 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LYS 4 45 " --> pdb=" O ARG 4 41 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA 4 46 " --> pdb=" O ARG 4 42 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG 4 48 " --> pdb=" O LEU 4 44 " (cutoff:3.500A) removed outlier: 3.707A 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: 3.750A pdb=" N ARG 6 26 " --> pdb=" O ARG 6 22 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR 6 27 " --> pdb=" O LEU 6 23 " (cutoff:3.500A) Processing helix chain '6' and resid 28 through 41 removed outlier: 3.690A pdb=" N ALA 6 32 " --> pdb=" O ARG 6 28 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE 6 33 " --> pdb=" O ALA 6 29 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 14 removed outlier: 3.658A pdb=" N LYS 7 12 " --> pdb=" O SER 7 8 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 45 removed outlier: 4.082A pdb=" N ASP 7 45 " --> pdb=" O THR 7 41 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 64 removed outlier: 4.396A pdb=" N SER 7 56 " --> pdb=" O ALA 7 52 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ARG 7 57 " --> pdb=" O ALA 7 53 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS 7 60 " --> pdb=" O SER 7 56 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU 7 61 " --> pdb=" O ARG 7 57 " (cutoff:3.500A) Processing helix chain '9' and resid 2 through 12 removed outlier: 4.699A pdb=" N LYS 9 12 " --> pdb=" O LYS 9 8 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 68 through 71 removed outlier: 4.228A pdb=" N LEU b 68 " --> pdb=" O ALA b 160 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP b 162 " --> pdb=" O LEU b 68 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA b 185 " --> pdb=" O TYR b 198 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE b 200 " --> pdb=" O ALA b 185 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'c' and resid 53 through 58 removed outlier: 3.908A pdb=" N ASP c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU c 55 " --> pdb=" O ASP c 66 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP c 66 " --> pdb=" O GLU c 55 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 164 through 171 removed outlier: 3.643A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS c 204 " --> pdb=" O ASP c 181 " (cutoff:3.500A) removed outlier: 4.975A 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: 6.822A pdb=" N LEU e 61 " --> pdb=" O VAL e 41 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER e 42 " --> pdb=" O LEU e 61 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 109 through 113 removed outlier: 5.437A pdb=" N VAL e 118 " --> pdb=" O LEU e 153 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA e 124 " --> pdb=" O ASP e 147 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASP e 147 " --> pdb=" O ALA e 124 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 57 through 65 Processing sheet with id= 8, first strand: chain 'f' and resid 37 through 44 removed outlier: 3.832A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR f 93 " --> pdb=" O PRO f 3 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG f 87 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 45 through 48 removed outlier: 7.105A pdb=" N ALA f 56 " --> pdb=" O LEU f 48 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'g' and resid 73 through 79 Processing sheet with id= 11, first strand: chain 'h' and resid 23 through 28 removed outlier: 6.544A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.638A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'i' and resid 26 through 31 removed outlier: 4.891A pdb=" N ILE i 26 " --> pdb=" O LEU i 41 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU i 41 " --> pdb=" O ILE i 26 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN i 47 " --> pdb=" O PHE i 81 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.558A pdb=" N LYS j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'j' and resid 44 through 53 removed outlier: 8.311A pdb=" N SER j 61 " --> pdb=" O ARG j 53 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'k' and resid 38 through 45 removed outlier: 3.632A pdb=" N ASN k 38 " --> pdb=" O THR k 35 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP k 92 " --> pdb=" O GLY k 28 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL k 93 " --> pdb=" O GLY k 117 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'k' and resid 92 through 97 removed outlier: 5.553A pdb=" N GLY k 97 " --> pdb=" O VAL k 122 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'l' and resid 29 through 33 Processing sheet with id= 19, first strand: chain 'l' and resid 35 through 41 removed outlier: 5.193A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'p' and resid 5 through 11 Processing sheet with id= 21, first strand: chain 'q' and resid 21 through 26 removed outlier: 5.008A pdb=" N LYS q 21 " --> pdb=" O GLU q 78 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER q 75 " --> pdb=" O VAL q 91 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'q' and resid 34 through 45 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 's' and resid 30 through 34 removed outlier: 3.638A pdb=" N THR s 33 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS s 52 " --> pdb=" O THR s 33 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'z' and resid 85 through 90 removed outlier: 4.053A pdb=" N ARG z 72 " --> pdb=" O ASP z 23 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'z' and resid 138 through 146 removed outlier: 4.757A pdb=" N THR z 138 " --> pdb=" O GLN z 135 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY z 146 " --> pdb=" O THR z 127 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N THR z 127 " --> pdb=" O GLY z 146 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP z 125 " --> pdb=" O GLY z 128 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL z 195 " --> pdb=" O THR z 118 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'z' and resid 270 through 273 removed outlier: 6.870A pdb=" N LEU z 270 " --> pdb=" O LEU z 361 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY z 356 " --> pdb=" O GLY z 293 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'z' and resid 300 through 303 removed outlier: 3.669A pdb=" N ALA z 310 " --> pdb=" O VAL z 301 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR z 308 " --> pdb=" O GLY z 303 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'C' and resid 2 through 5 removed outlier: 3.751A pdb=" N GLY C 2 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 29 Processing sheet with id= 30, first strand: chain 'C' and resid 81 through 84 removed outlier: 3.851A pdb=" N HIS C 81 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU C 94 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP C 115 " --> pdb=" O VAL C 79 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'C' and resid 163 through 166 removed outlier: 3.512A pdb=" N GLN C 164 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA C 174 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU C 181 " --> pdb=" O MET C 177 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'C' and resid 91 through 97 removed outlier: 5.472A pdb=" N ASN C 91 " --> pdb=" O ALA C 107 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU C 101 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 4 through 8 removed outlier: 5.926A pdb=" N LYS D 4 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP D 173 " --> pdb=" O SER D 118 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'D' and resid 12 through 18 removed outlier: 3.733A pdb=" N GLY D 12 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 16 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS D 184 " --> pdb=" O LEU D 193 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'D' and resid 34 through 37 removed outlier: 6.817A pdb=" N GLN D 51 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR D 47 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR D 42 " --> pdb=" O TYR D 47 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'D' and resid 48 through 54 removed outlier: 4.771A pdb=" N SER D 48 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'E' and resid 2 through 8 removed outlier: 6.865A pdb=" N LEU E 3 " --> pdb=" O GLU E 19 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLU E 19 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL E 5 " --> pdb=" O SER E 17 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N SER E 17 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL E 7 " --> pdb=" O ASP E 15 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'E' and resid 123 through 126 removed outlier: 3.516A pdb=" N ASP E 193 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'F' and resid 40 through 47 removed outlier: 8.462A pdb=" N ILE F 92 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'F' and resid 134 through 140 Processing sheet with id= 41, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 42, first strand: chain 'G' and resid 41 through 46 removed outlier: 3.617A pdb=" N SER G 42 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'G' and resid 83 through 90 removed outlier: 3.501A pdb=" N PHE G 132 " --> pdb=" O MET G 88 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N THR G 130 " --> pdb=" O ILE G 90 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'G' and resid 95 through 99 removed outlier: 3.602A pdb=" N ARG G 96 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN G 98 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'H' and resid 2 through 6 removed outlier: 6.415A pdb=" N LYS H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU H 35 " --> pdb=" O THR H 6 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'H' and resid 77 through 81 removed outlier: 3.636A pdb=" N VAL H 78 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY H 128 " --> pdb=" O VAL H 148 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'I' and resid 47 through 51 removed outlier: 3.557A pdb=" N VAL I 82 " --> pdb=" O ALA I 22 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA I 22 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR I 23 " --> pdb=" O TYR I 109 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL I 25 " --> pdb=" O GLY I 107 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY I 107 " --> pdb=" O VAL I 25 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'J' and resid 10 through 16 removed outlier: 3.716A pdb=" N ILE J 11 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE J 15 " --> pdb=" O ILE J 56 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'K' and resid 44 through 47 removed outlier: 3.560A pdb=" N THR K 213 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS K 211 " --> pdb=" O ARG K 47 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'K' and resid 59 through 64 removed outlier: 6.527A pdb=" N VAL K 59 " --> pdb=" O VAL K 165 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'L' and resid 52 through 57 removed outlier: 4.730A pdb=" N ASP L 19 " --> pdb=" O PHE L 140 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'L' and resid 74 through 78 removed outlier: 7.290A pdb=" N GLY L 83 " --> pdb=" O SER L 78 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'M' and resid 56 through 60 removed outlier: 4.421A pdb=" N ASP M 56 " --> pdb=" O VAL M 43 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL M 40 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER M 6 " --> pdb=" O CYS M 21 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASN M 82 " --> pdb=" O ARG M 7 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU M 81 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL M 66 " --> pdb=" O GLU M 81 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG M 64 " --> pdb=" O ALA M 83 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'M' and resid 68 through 71 removed outlier: 4.399A pdb=" N SER M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'N' and resid 75 through 78 Processing sheet with id= 56, first strand: chain 'N' and resid 122 through 125 Processing sheet with id= 57, first strand: chain 'O' and resid 38 through 41 removed outlier: 6.524A pdb=" N GLU O 38 " --> pdb=" O PRO O 99 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'O' and resid 62 through 66 removed outlier: 3.549A pdb=" N LYS O 63 " --> pdb=" O SER O 107 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE O 104 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS O 128 " --> pdb=" O LEU O 37 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'P' and resid 33 through 37 Processing sheet with id= 60, first strand: chain 'Q' and resid 36 through 42 removed outlier: 3.524A pdb=" N HIS Q 48 " --> pdb=" O ASN Q 41 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ILE Q 47 " --> pdb=" O SER Q 65 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA Q 61 " --> pdb=" O LEU Q 51 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'R' and resid 37 through 44 removed outlier: 6.537A pdb=" N THR R 24 " --> pdb=" O LEU R 86 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS R 82 " --> pdb=" O HIS R 28 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'R' and resid 48 through 51 removed outlier: 3.982A pdb=" N ARG R 48 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N GLU R 56 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'T' and resid 13 through 16 removed outlier: 3.881A pdb=" N LEU T 41 " --> pdb=" O ILE T 6 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'T' and resid 19 through 22 removed outlier: 4.175A pdb=" N ASP T 20 " --> pdb=" O VAL T 99 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL T 96 " --> pdb=" O LEU T 65 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N THR T 61 " --> pdb=" O THR T 100 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA T 33 " --> pdb=" O VAL T 64 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'T' and resid 66 through 70 removed outlier: 3.739A pdb=" N GLU T 66 " --> pdb=" O VAL T 96 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLN T 92 " --> pdb=" O GLY T 70 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'U' and resid 8 through 15 removed outlier: 6.824A pdb=" N ILE U 113 " --> pdb=" O ALA U 79 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N THR U 75 " --> pdb=" O ARG U 117 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'U' and resid 80 through 86 removed outlier: 4.901A pdb=" N THR U 107 " --> pdb=" O GLY U 86 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'V' and resid 28 through 33 removed outlier: 4.547A pdb=" N LYS V 80 " --> pdb=" O VAL V 33 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY V 72 " --> pdb=" O THR V 69 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LYS V 65 " --> pdb=" O ARG V 76 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER V 78 " --> pdb=" O GLN V 63 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLN V 63 " --> pdb=" O SER V 78 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS V 80 " --> pdb=" O ASN V 61 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASN V 61 " --> pdb=" O LYS V 80 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA V 82 " --> pdb=" O THR V 59 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR V 59 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL V 84 " --> pdb=" O VAL V 57 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL V 57 " --> pdb=" O VAL V 84 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'W' and resid 39 through 44 removed outlier: 5.559A pdb=" N ASN W 39 " --> pdb=" O ALA W 64 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'X' and resid 8 through 12 Processing sheet with id= 71, first strand: chain 'X' and resid 44 through 49 removed outlier: 3.527A pdb=" N ALA X 95 " --> pdb=" O PRO X 34 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS X 94 " --> pdb=" O ASP X 84 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA X 82 " --> pdb=" O ASP X 96 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP X 84 " --> pdb=" O GLN X 93 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS X 86 " --> pdb=" O ASN X 91 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASN X 91 " --> pdb=" O HIS X 86 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'X' and resid 121 through 127 removed outlier: 7.909A pdb=" N GLY X 121 " --> pdb=" O ALA X 184 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL X 178 " --> pdb=" O ASP X 127 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'X' and resid 143 through 149 removed outlier: 6.839A pdb=" N GLU X 132 " --> pdb=" O ILE X 171 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU X 134 " --> pdb=" O ASN X 169 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Y' and resid 29 through 32 removed outlier: 4.813A pdb=" N GLN Y 29 " --> pdb=" O VAL Y 67 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY Y 65 " --> pdb=" O VAL Y 31 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE Y 80 " --> pdb=" O GLY Y 48 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Y' and resid 51 through 54 removed outlier: 3.625A pdb=" N PHE Y 60 " --> pdb=" O GLY Y 52 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'Z' and resid 12 through 19 removed outlier: 3.859A pdb=" N THR Z 25 " --> pdb=" O SER Z 17 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain '2' and resid 32 through 38 removed outlier: 4.276A pdb=" N GLN 2 33 " --> pdb=" O GLN 2 8 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLU 2 3 " --> pdb=" O VAL 2 59 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL 2 59 " --> pdb=" O GLU 2 3 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU 2 53 " --> pdb=" O VAL 2 9 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain '3' and resid 20 through 24 removed outlier: 4.192A pdb=" N HIS 3 20 " --> pdb=" O CYS 3 16 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL 3 14 " --> pdb=" O PHE 3 22 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain '4' and resid 28 through 31 Processing sheet with id= 80, first strand: chain '5' and resid 10 through 14 removed outlier: 3.536A pdb=" N TYR 5 23 " --> pdb=" O LEU 5 13 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain '5' and resid 36 through 40 removed outlier: 6.039A pdb=" N LEU 5 36 " --> pdb=" O GLU 5 53 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain '7' and resid 22 through 25 removed outlier: 6.153A pdb=" N ILE 7 22 " --> pdb=" O VAL 7 50 " (cutoff:3.500A) 2008 hydrogen bonds defined for protein. 5952 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4118 hydrogen bonds 6556 hydrogen bond angles 0 basepair planarities 1605 basepair parallelities 2411 stacking parallelities Total time for adding SS restraints: 243.35 Time building geometry restraints manager: 63.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 21857 1.33 - 1.45: 68934 1.45 - 1.57: 65730 1.57 - 1.69: 9568 1.69 - 1.81: 185 Bond restraints: 166274 Sorted by residual: bond pdb=" C4 5MU y 54 " pdb=" C5 5MU y 54 " ideal model delta sigma weight residual 1.802 1.481 0.321 2.00e-02 2.50e+03 2.58e+02 bond pdb=" N1 5MU y 54 " pdb=" C6 5MU y 54 " ideal model delta sigma weight residual 1.635 1.337 0.298 2.00e-02 2.50e+03 2.23e+02 bond pdb=" C5 5MU y 54 " pdb=" C6 5MU y 54 " ideal model delta sigma weight residual 1.155 1.385 -0.230 2.00e-02 2.50e+03 1.33e+02 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 6.66e+01 bond pdb=" N3 5MU y 54 " pdb=" C4 5MU y 54 " ideal model delta sigma weight residual 1.182 1.334 -0.152 2.00e-02 2.50e+03 5.74e+01 ... (remaining 166269 not shown) Histogram of bond angle deviations from ideal: 96.72 - 105.34: 22846 105.34 - 113.95: 109991 113.95 - 122.57: 84326 122.57 - 131.19: 30036 131.19 - 139.81: 1278 Bond angle restraints: 248477 Sorted by residual: angle pdb=" CA PRO L 2 " pdb=" N PRO L 2 " pdb=" CD PRO L 2 " ideal model delta sigma weight residual 112.00 104.05 7.95 1.40e+00 5.10e-01 3.22e+01 angle pdb=" C GLU m 67 " pdb=" CA GLU m 67 " pdb=" CB GLU m 67 " ideal model delta sigma weight residual 115.89 108.98 6.91 1.32e+00 5.74e-01 2.74e+01 angle pdb=" C6 5MU y 54 " pdb=" C5 5MU y 54 " pdb=" C5M 5MU y 54 " ideal model delta sigma weight residual 106.09 120.97 -14.88 3.00e+00 1.11e-01 2.46e+01 angle pdb=" CA ARG m 79 " pdb=" CB ARG m 79 " pdb=" CG ARG m 79 " ideal model delta sigma weight residual 114.10 123.66 -9.56 2.00e+00 2.50e-01 2.28e+01 angle pdb=" C ILE m 78 " pdb=" N ARG m 79 " pdb=" CA ARG m 79 " ideal model delta sigma weight residual 120.72 112.99 7.73 1.67e+00 3.59e-01 2.14e+01 ... (remaining 248472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 94741 35.99 - 71.98: 10795 71.98 - 107.97: 1323 107.97 - 143.96: 33 143.96 - 179.95: 39 Dihedral angle restraints: 106931 sinusoidal: 88306 harmonic: 18625 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 -160.00 19.25 -179.25 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1535 " pdb=" C1' C A1535 " pdb=" N1 C A1535 " pdb=" C2 C A1535 " ideal model delta sinusoidal sigma weight residual -160.00 16.73 -176.73 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 27.00 173.00 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 106928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 28557 0.053 - 0.106: 2655 0.106 - 0.159: 448 0.159 - 0.212: 53 0.212 - 0.265: 12 Chirality restraints: 31725 Sorted by residual: chirality pdb=" C1' U A2804 " pdb=" O4' U A2804 " pdb=" C2' U A2804 " pdb=" N1 U A2804 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.76e+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 -2.48 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C1' G A 784 " pdb=" O4' G A 784 " pdb=" C2' G A 784 " pdb=" N9 G A 784 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 31722 not shown) Planarity restraints: 13780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU y 54 " -0.020 2.00e-02 2.50e+03 5.51e-01 6.83e+03 pdb=" C4' 5MU y 54 " -0.434 2.00e-02 2.50e+03 pdb=" O4' 5MU y 54 " -0.607 2.00e-02 2.50e+03 pdb=" C3' 5MU y 54 " 0.582 2.00e-02 2.50e+03 pdb=" O3' 5MU y 54 " 0.534 2.00e-02 2.50e+03 pdb=" C2' 5MU y 54 " 0.226 2.00e-02 2.50e+03 pdb=" O2' 5MU y 54 " -0.874 2.00e-02 2.50e+03 pdb=" C1' 5MU y 54 " -0.232 2.00e-02 2.50e+03 pdb=" N1 5MU y 54 " 0.825 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG y 46 " 0.766 2.00e-02 2.50e+03 5.40e-01 6.57e+03 pdb=" C4' 7MG y 46 " -0.239 2.00e-02 2.50e+03 pdb=" O4' 7MG y 46 " -0.547 2.00e-02 2.50e+03 pdb=" C3' 7MG y 46 " 0.214 2.00e-02 2.50e+03 pdb=" O3' 7MG y 46 " -0.901 2.00e-02 2.50e+03 pdb=" C2' 7MG y 46 " 0.610 2.00e-02 2.50e+03 pdb=" O2' 7MG y 46 " 0.538 2.00e-02 2.50e+03 pdb=" C1' 7MG y 46 " -0.407 2.00e-02 2.50e+03 pdb=" N9 7MG y 46 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY g 5 " -0.055 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO g 6 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO g 6 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO g 6 " -0.045 5.00e-02 4.00e+02 ... (remaining 13777 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 3336 2.63 - 3.20: 120260 3.20 - 3.76: 283790 3.76 - 4.33: 393548 4.33 - 4.90: 541157 Nonbonded interactions: 1342091 Sorted by model distance: nonbonded pdb=" OE1 GLU F 147 " pdb=" OG1 THR 3 27 " model vdw 2.059 2.440 nonbonded pdb=" O2 U A 329 " pdb=" O6 G A 446 " model vdw 2.077 2.432 nonbonded pdb=" O2 U a 187 " pdb=" O6 G a 201 " model vdw 2.091 2.432 nonbonded pdb=" O2' U a 439 " pdb=" O SER d 114 " model vdw 2.131 2.440 nonbonded pdb=" O2' G a 50 " pdb=" O2' U a 365 " model vdw 2.134 2.440 ... (remaining 1342086 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: 8.050 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: 0.140 Extract box with map and model: 30.900 Check model and map are aligned: 1.610 Set scattering table: 1.010 Process input model: 552.150 Find NCS groups from input model: 3.340 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 600.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 : 0.003 0.321 166274 Z= 0.205 Angle : 0.545 14.880 248477 Z= 0.280 Chirality : 0.033 0.265 31725 Planarity : 0.008 0.551 13780 Dihedral : 23.070 179.948 94951 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % 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: -1.26 (0.10), residues: 6445 helix: -0.51 (0.11), residues: 2014 sheet: -0.41 (0.14), residues: 1293 loop : -1.16 (0.11), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 22 HIS 0.007 0.001 HIS n 8 PHE 0.014 0.001 PHE R 73 TYR 0.046 0.001 TYR d 70 ARG 0.018 0.000 ARG m 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1816 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1816 time to evaluate : 6.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 36 VAL cc_start: 0.9370 (p) cc_final: 0.8845 (m) REVERT: d 110 ARG cc_start: 0.6702 (ptm-80) cc_final: 0.6238 (ptt90) REVERT: d 138 ILE cc_start: 0.8457 (mt) cc_final: 0.8235 (mt) REVERT: d 175 ILE cc_start: 0.9123 (mp) cc_final: 0.8902 (mm) REVERT: g 136 LYS cc_start: 0.8890 (mmtm) cc_final: 0.8558 (mmtt) REVERT: j 69 THR cc_start: 0.8252 (m) cc_final: 0.7553 (m) REVERT: l 39 THR cc_start: 0.8728 (p) cc_final: 0.7812 (p) REVERT: l 77 HIS cc_start: 0.6829 (m-70) cc_final: 0.6538 (m90) REVERT: p 8 THR cc_start: 0.8756 (t) cc_final: 0.8426 (p) REVERT: p 17 GLN cc_start: 0.7866 (mt0) cc_final: 0.7605 (mp10) REVERT: s 53 ASP cc_start: 0.8794 (p0) cc_final: 0.8341 (p0) REVERT: z 134 TYR cc_start: 0.7852 (m-80) cc_final: 0.7550 (m-80) REVERT: G 57 ASP cc_start: 0.7456 (m-30) cc_final: 0.6633 (m-30) REVERT: H 11 HIS cc_start: 0.8563 (m-70) cc_final: 0.7272 (m-70) REVERT: H 121 LYS cc_start: 0.9087 (mmmm) cc_final: 0.8469 (mptt) REVERT: I 96 PHE cc_start: 0.7867 (t80) cc_final: 0.7361 (t80) REVERT: J 33 HIS cc_start: 0.7967 (m-70) cc_final: 0.7660 (m90) REVERT: M 92 ASP cc_start: 0.7261 (m-30) cc_final: 0.6240 (m-30) REVERT: V 6 ASP cc_start: 0.7070 (t0) cc_final: 0.6817 (t70) REVERT: 1 21 LYS cc_start: 0.7654 (ttmm) cc_final: 0.7310 (ttmm) REVERT: 3 1 MET cc_start: 0.7099 (tpp) cc_final: 0.6883 (tpp) REVERT: 3 8 GLU cc_start: 0.7075 (pm20) cc_final: 0.6647 (pm20) outliers start: 0 outliers final: 0 residues processed: 1816 average time/residue: 1.4439 time to fit residues: 4468.2600 Evaluate side-chains 1398 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1398 time to evaluate : 6.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 935 optimal weight: 10.0000 chunk 839 optimal weight: 7.9990 chunk 465 optimal weight: 10.0000 chunk 286 optimal weight: 20.0000 chunk 566 optimal weight: 10.0000 chunk 448 optimal weight: 10.0000 chunk 868 optimal weight: 0.8980 chunk 336 optimal weight: 20.0000 chunk 528 optimal weight: 10.0000 chunk 646 optimal weight: 10.0000 chunk 1006 optimal weight: 6.9990 overall best weight: 7.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 108 HIS b 155 GLN d 35 GLN ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 HIS ** d 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 153 HIS h 63 GLN ** i 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 146 GLN j 64 HIS k 49 ASN k 128 ASN l 6 GLN l 72 HIS ** m 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 88 GLN ** m 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 18 HIS o 28 GLN q 46 HIS ** q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 HIS t 7 GLN ** t 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 176 ASN z 222 GLN z 258 GLN C 109 GLN C 113 GLN C 129 ASN ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN E 76 GLN E 134 GLN E 151 ASN E 202 ASN F 25 GLN G 23 ASN G 112 HIS H 118 GLN J 121 ASN L 77 HIS L 103 ASN ** L 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 HIS M 13 ASN M 82 ASN M 89 ASN N 58 HIS N 76 GLN O 35 GLN O 57 HIS P 62 ASN Q 8 GLN S 41 HIS S 72 ASN S 94 ASN S 122 ASN T 67 HIS W 67 HIS W 70 ASN X 46 HIS X 93 GLN X 94 HIS ** X 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 129 ASN X 156 GLN X 169 ASN Y 3 HIS Y 12 ASN Y 29 GLN Y 79 ASN Z 30 ASN ** 2 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 36 GLN 5 20 HIS 5 48 HIS 7 31 HIS Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 166274 Z= 0.325 Angle : 0.623 14.219 248477 Z= 0.323 Chirality : 0.037 0.280 31725 Planarity : 0.005 0.124 13780 Dihedral : 23.553 179.255 82568 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.90 % Favored : 95.08 % Rotamer: Outliers : 2.72 % Allowed : 13.46 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % 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: -0.87 (0.10), residues: 6445 helix: 0.17 (0.11), residues: 2089 sheet: -0.30 (0.14), residues: 1340 loop : -1.19 (0.11), residues: 3016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP z 38 HIS 0.008 0.001 HIS i 64 PHE 0.024 0.002 PHE s 44 TYR 0.018 0.002 TYR h 49 ARG 0.010 0.001 ARG N 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1585 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1443 time to evaluate : 6.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 120 MET cc_start: -0.1848 (mpp) cc_final: -0.2641 (mtt) REVERT: c 36 VAL cc_start: 0.9355 (p) cc_final: 0.8946 (p) REVERT: d 110 ARG cc_start: 0.7050 (ptm-80) cc_final: 0.6750 (ptt90) REVERT: d 175 ILE cc_start: 0.9149 (mp) cc_final: 0.8876 (mm) REVERT: g 44 TYR cc_start: 0.7955 (m-80) cc_final: 0.7137 (m-80) REVERT: g 151 PHE cc_start: 0.7162 (m-80) cc_final: 0.6626 (m-80) REVERT: j 97 ASP cc_start: 0.7409 (p0) cc_final: 0.7075 (p0) REVERT: l 35 THR cc_start: 0.8970 (m) cc_final: 0.8751 (p) REVERT: l 77 HIS cc_start: 0.7017 (m-70) cc_final: 0.6710 (m90) REVERT: o 15 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.6729 (t80) REVERT: p 8 THR cc_start: 0.8749 (t) cc_final: 0.8524 (p) REVERT: p 60 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8322 (mm) REVERT: s 18 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7802 (mptt) REVERT: t 17 ARG cc_start: 0.8504 (ptm160) cc_final: 0.8040 (ptm160) REVERT: z 40 ASP cc_start: 0.8387 (m-30) cc_final: 0.8135 (m-30) REVERT: z 82 GLN cc_start: 0.7119 (pm20) cc_final: 0.6904 (pm20) REVERT: H 10 GLU cc_start: 0.8016 (pt0) cc_final: 0.7803 (pt0) REVERT: I 1 MET cc_start: 0.1227 (OUTLIER) cc_final: -0.0419 (pmm) REVERT: J 13 LEU cc_start: 0.9047 (tp) cc_final: 0.8747 (tt) REVERT: J 15 ILE cc_start: 0.9178 (mp) cc_final: 0.8855 (mp) REVERT: J 33 HIS cc_start: 0.7995 (m-70) cc_final: 0.7783 (m90) outliers start: 142 outliers final: 93 residues processed: 1491 average time/residue: 1.3399 time to fit residues: 3429.2363 Evaluate side-chains 1448 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1351 time to evaluate : 6.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain e residue 140 LEU Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain h residue 9 ASP Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 71 LYS Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 128 ASN Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain m residue 86 CYS Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain n residue 47 MET Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 15 TYR Chi-restraints excluded: chain o residue 45 VAL Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain p residue 53 SER Chi-restraints excluded: chain p residue 60 LEU Chi-restraints excluded: chain q residue 38 VAL Chi-restraints excluded: chain q residue 45 SER Chi-restraints excluded: chain s residue 18 LYS Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain u residue 4 VAL Chi-restraints excluded: chain u residue 13 SER Chi-restraints excluded: chain u residue 20 LEU Chi-restraints excluded: chain u residue 24 THR Chi-restraints excluded: chain z residue 216 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain P residue 97 ILE Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 172 SER Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain 1 residue 44 ASN Chi-restraints excluded: chain 1 residue 61 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 4 residue 15 SER Chi-restraints excluded: chain 5 residue 34 ASP Chi-restraints excluded: chain 5 residue 54 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 8 residue 28 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 559 optimal weight: 10.0000 chunk 312 optimal weight: 2.9990 chunk 837 optimal weight: 5.9990 chunk 685 optimal weight: 10.0000 chunk 277 optimal weight: 7.9990 chunk 1007 optimal weight: 8.9990 chunk 1088 optimal weight: 9.9990 chunk 897 optimal weight: 0.9990 chunk 999 optimal weight: 4.9990 chunk 343 optimal weight: 7.9990 chunk 808 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 117 GLN ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 185 GLN d 193 GLN i 111 GLN i 146 GLN ** m 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 106 ASN o 46 HIS q 65 ASN ** t 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN I 35 ASN J 14 GLN J 19 GLN L 119 GLN Q 8 GLN R 50 GLN S 27 GLN X 126 GLN X 156 GLN 2 19 GLN 2 52 HIS 9 18 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 166274 Z= 0.171 Angle : 0.555 12.612 248477 Z= 0.289 Chirality : 0.033 0.259 31725 Planarity : 0.005 0.120 13780 Dihedral : 23.555 179.627 82568 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.08 % Favored : 95.90 % Rotamer: Outliers : 2.26 % Allowed : 16.64 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % 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: -0.58 (0.10), residues: 6445 helix: 0.53 (0.11), residues: 2084 sheet: -0.15 (0.14), residues: 1331 loop : -1.10 (0.11), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP O 92 HIS 0.019 0.001 HIS X 86 PHE 0.022 0.001 PHE s 44 TYR 0.039 0.002 TYR d 70 ARG 0.020 0.000 ARG g 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1573 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1455 time to evaluate : 6.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 120 MET cc_start: -0.1881 (OUTLIER) cc_final: -0.2181 (mtm) REVERT: c 94 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8177 (p) REVERT: d 58 PHE cc_start: 0.8764 (m-80) cc_final: 0.7858 (m-80) REVERT: d 110 ARG cc_start: 0.7020 (ptm-80) cc_final: 0.6205 (ppt170) REVERT: g 36 LYS cc_start: 0.8499 (mtmm) cc_final: 0.8276 (mtmt) REVERT: g 136 LYS cc_start: 0.9309 (pptt) cc_final: 0.8835 (mmtt) REVERT: l 77 HIS cc_start: 0.6969 (m-70) cc_final: 0.6683 (m90) REVERT: o 15 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.6461 (t80) REVERT: p 8 THR cc_start: 0.8763 (t) cc_final: 0.8549 (p) REVERT: p 52 ASP cc_start: 0.8388 (t0) cc_final: 0.8156 (t0) REVERT: r 62 ARG cc_start: 0.7087 (ppt170) cc_final: 0.6859 (ptt90) REVERT: s 37 ARG cc_start: 0.7763 (ptm160) cc_final: 0.7409 (ptm160) REVERT: D 186 ASP cc_start: 0.7098 (t0) cc_final: 0.6755 (t0) REVERT: G 88 MET cc_start: 0.7572 (mmm) cc_final: 0.7358 (mmm) REVERT: I 1 MET cc_start: 0.1030 (OUTLIER) cc_final: -0.0601 (pmm) REVERT: I 101 LYS cc_start: 0.8633 (mptt) cc_final: 0.8419 (mmmt) REVERT: J 33 HIS cc_start: 0.8067 (m-70) cc_final: 0.7835 (m90) REVERT: R 33 GLU cc_start: 0.6310 (pt0) cc_final: 0.6073 (pt0) outliers start: 118 outliers final: 77 residues processed: 1496 average time/residue: 1.3416 time to fit residues: 3457.7471 Evaluate side-chains 1424 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1343 time to evaluate : 6.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain e residue 47 SER Chi-restraints excluded: chain f residue 11 ASP Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 45 ASP Chi-restraints excluded: chain k residue 114 LEU Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 47 SER Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain m residue 86 CYS Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain n residue 47 MET Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 15 TYR Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 56 LYS Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain u residue 4 VAL Chi-restraints excluded: chain u residue 13 SER Chi-restraints excluded: chain u residue 20 LEU Chi-restraints excluded: chain z residue 216 VAL Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 63 GLU Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 172 SER Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 1 residue 44 ASN Chi-restraints excluded: chain 1 residue 61 LEU Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 4 residue 51 LEU Chi-restraints excluded: chain 8 residue 28 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 995 optimal weight: 7.9990 chunk 757 optimal weight: 5.9990 chunk 523 optimal weight: 10.0000 chunk 111 optimal weight: 40.0000 chunk 481 optimal weight: 10.0000 chunk 676 optimal weight: 10.0000 chunk 1011 optimal weight: 2.9990 chunk 1070 optimal weight: 6.9990 chunk 528 optimal weight: 10.0000 chunk 958 optimal weight: 5.9990 chunk 288 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 113 GLN ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 110 GLN i 146 GLN m 75 GLN o 7 GLN q 65 ASN ** t 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN ** C 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 189 ASN H 118 GLN I 35 ASN J 19 GLN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 ASN M 82 ASN Q 8 GLN R 50 GLN X 126 GLN 6 11 ASN 7 59 ASN 7 63 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 166274 Z= 0.274 Angle : 0.583 12.680 248477 Z= 0.302 Chirality : 0.035 0.269 31725 Planarity : 0.005 0.119 13780 Dihedral : 23.506 179.866 82568 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.70 % Favored : 95.28 % Rotamer: Outliers : 3.33 % Allowed : 18.01 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % 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: -0.48 (0.10), residues: 6445 helix: 0.69 (0.11), residues: 2095 sheet: -0.14 (0.14), residues: 1326 loop : -1.09 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP q 88 HIS 0.008 0.001 HIS 7 31 PHE 0.022 0.001 PHE e 97 TYR 0.059 0.002 TYR g 44 ARG 0.014 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1530 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1356 time to evaluate : 6.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 120 MET cc_start: -0.1573 (OUTLIER) cc_final: -0.1842 (mtm) REVERT: c 94 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8256 (p) REVERT: d 58 PHE cc_start: 0.8812 (m-80) cc_final: 0.7896 (m-80) REVERT: d 110 ARG cc_start: 0.7145 (ptm-80) cc_final: 0.6405 (ppt170) REVERT: i 58 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7422 (t80) REVERT: j 13 TYR cc_start: 0.8301 (m-80) cc_final: 0.7932 (m-80) REVERT: j 97 ASP cc_start: 0.7505 (p0) cc_final: 0.7172 (p0) REVERT: n 9 LYS cc_start: 0.9399 (ttpp) cc_final: 0.9101 (mttt) REVERT: p 52 ASP cc_start: 0.8434 (t0) cc_final: 0.8158 (t0) REVERT: p 60 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8261 (mm) REVERT: s 37 ARG cc_start: 0.7894 (ptm160) cc_final: 0.7484 (ptm160) REVERT: t 17 ARG cc_start: 0.8515 (ptp-110) cc_final: 0.8009 (ptp-170) REVERT: z 52 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8252 (tp-100) REVERT: z 82 GLN cc_start: 0.7099 (pm20) cc_final: 0.6895 (pm20) REVERT: F 155 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7927 (ttp80) REVERT: I 1 MET cc_start: 0.0817 (OUTLIER) cc_final: -0.0703 (pmm) REVERT: I 101 LYS cc_start: 0.8594 (mptt) cc_final: 0.8381 (mmmt) REVERT: J 33 HIS cc_start: 0.8099 (m-70) cc_final: 0.7823 (m90) outliers start: 174 outliers final: 125 residues processed: 1423 average time/residue: 1.3574 time to fit residues: 3338.5119 Evaluate side-chains 1439 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1308 time to evaluate : 5.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 161 GLU Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain e residue 47 SER Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain f residue 11 ASP Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain i residue 58 TYR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain k residue 109 LEU Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 103 ASP Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain m residue 86 CYS Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain n residue 47 MET Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain p residue 60 LEU Chi-restraints excluded: chain q residue 22 THR Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 70 ASN Chi-restraints excluded: chain u residue 4 VAL Chi-restraints excluded: chain u residue 13 SER Chi-restraints excluded: chain z residue 216 VAL Chi-restraints excluded: chain z residue 247 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 13 ASN Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 110 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain Q residue 56 ASN Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 63 GLU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 43 ASP Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 1 residue 44 ASN Chi-restraints excluded: chain 1 residue 61 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 4 residue 51 LEU Chi-restraints excluded: chain 5 residue 34 ASP Chi-restraints excluded: chain 5 residue 54 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 8 residue 28 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 891 optimal weight: 50.0000 chunk 607 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 797 optimal weight: 9.9990 chunk 441 optimal weight: 10.0000 chunk 913 optimal weight: 8.9990 chunk 740 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 546 optimal weight: 20.0000 chunk 961 optimal weight: 20.0000 chunk 270 optimal weight: 50.0000 overall best weight: 9.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 121 ASN g 25 GLN h 93 ASN ** i 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 61 GLN s 69 HIS t 84 ASN D 145 HIS D 202 ASN H 137 HIS J 19 GLN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 GLN M 82 ASN N 127 ASN P 17 GLN Q 8 GLN X 61 HIS 7 59 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 166274 Z= 0.427 Angle : 0.672 14.053 248477 Z= 0.345 Chirality : 0.040 0.405 31725 Planarity : 0.005 0.121 13780 Dihedral : 23.578 179.669 82568 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.48 % Favored : 94.51 % Rotamer: Outliers : 4.15 % Allowed : 18.97 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % 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: -0.63 (0.10), residues: 6445 helix: 0.57 (0.11), residues: 2108 sheet: -0.27 (0.14), residues: 1332 loop : -1.17 (0.11), residues: 3005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP q 88 HIS 0.014 0.001 HIS 7 31 PHE 0.022 0.002 PHE F 145 TYR 0.028 0.002 TYR z 250 ARG 0.011 0.001 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1524 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1307 time to evaluate : 6.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 120 MET cc_start: -0.1833 (OUTLIER) cc_final: -0.2060 (mtm) REVERT: c 66 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6940 (p0) REVERT: c 94 THR cc_start: 0.8580 (OUTLIER) cc_final: 0.8348 (p) REVERT: d 110 ARG cc_start: 0.7295 (ptm-80) cc_final: 0.6545 (ppt170) REVERT: g 44 TYR cc_start: 0.8194 (m-80) cc_final: 0.7941 (m-80) REVERT: g 136 LYS cc_start: 0.9401 (pptt) cc_final: 0.8896 (mmtt) REVERT: j 13 TYR cc_start: 0.8424 (m-80) cc_final: 0.8155 (m-80) REVERT: l 94 ARG cc_start: 0.8008 (ptp-170) cc_final: 0.7736 (ptp-170) REVERT: p 15 ASN cc_start: 0.8688 (p0) cc_final: 0.8384 (p0) REVERT: r 18 ARG cc_start: 0.6850 (mmp80) cc_final: 0.6533 (mmp80) REVERT: r 61 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8049 (tp40) REVERT: s 37 ARG cc_start: 0.7940 (ptm160) cc_final: 0.7544 (ptm160) REVERT: u 25 ARG cc_start: 0.8299 (ttm170) cc_final: 0.8031 (ttm170) REVERT: z 52 GLN cc_start: 0.8625 (tp-100) cc_final: 0.8355 (tp-100) REVERT: I 1 MET cc_start: 0.1341 (OUTLIER) cc_final: 0.1089 (ptp) REVERT: I 101 LYS cc_start: 0.8625 (mptt) cc_final: 0.8420 (mmmt) REVERT: J 13 LEU cc_start: 0.8955 (tp) cc_final: 0.8740 (tt) REVERT: J 33 HIS cc_start: 0.8116 (m-70) cc_final: 0.7823 (m90) REVERT: R 36 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7738 (mtmm) outliers start: 217 outliers final: 168 residues processed: 1400 average time/residue: 1.3420 time to fit residues: 3252.3357 Evaluate side-chains 1435 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1262 time to evaluate : 6.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 66 ASP Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 161 GLU Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain e residue 47 SER Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain f residue 11 ASP Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 52 ILE Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 106 ASN Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 9 ASP Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 48 PHE Chi-restraints excluded: chain i residue 50 LEU Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 44 THR Chi-restraints excluded: chain k residue 73 GLN Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain k residue 109 LEU Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 90 LEU Chi-restraints excluded: chain l residue 103 ASP Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 15 MET Chi-restraints excluded: chain m residue 17 ILE Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain m residue 86 CYS Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 8 THR Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain r residue 61 GLN Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain t residue 24 VAL Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 70 ASN Chi-restraints excluded: chain u residue 24 THR Chi-restraints excluded: chain z residue 177 CYS Chi-restraints excluded: chain z residue 216 VAL Chi-restraints excluded: chain z residue 247 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 119 ASP Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain M residue 80 ASP Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 110 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 97 ILE Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 56 ASN Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain R residue 5 ASP Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 63 GLU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 5 THR Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 1 residue 44 ASN Chi-restraints excluded: chain 1 residue 61 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 2 residue 38 GLU Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 4 residue 15 SER Chi-restraints excluded: chain 4 residue 51 LEU Chi-restraints excluded: chain 5 residue 34 ASP Chi-restraints excluded: chain 5 residue 38 ILE Chi-restraints excluded: chain 5 residue 53 GLU Chi-restraints excluded: chain 5 residue 54 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 8 residue 28 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 360 optimal weight: 10.0000 chunk 964 optimal weight: 8.9990 chunk 211 optimal weight: 0.9990 chunk 628 optimal weight: 10.0000 chunk 264 optimal weight: 7.9990 chunk 1072 optimal weight: 7.9990 chunk 889 optimal weight: 50.0000 chunk 496 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 354 optimal weight: 40.0000 chunk 562 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 25 GLN ** g 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 93 ASN ** i 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 61 GLN z 222 GLN J 19 GLN J 21 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 ASN Q 8 GLN X 126 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 166274 Z= 0.306 Angle : 0.612 12.916 248477 Z= 0.317 Chirality : 0.037 0.390 31725 Planarity : 0.005 0.119 13780 Dihedral : 23.597 179.511 82568 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.70 % Favored : 95.25 % Rotamer: Outliers : 3.81 % Allowed : 20.85 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % 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: -0.49 (0.10), residues: 6445 helix: 0.76 (0.11), residues: 2106 sheet: -0.23 (0.14), residues: 1313 loop : -1.12 (0.11), residues: 3026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP O 92 HIS 0.010 0.001 HIS P 31 PHE 0.021 0.001 PHE i 59 TYR 0.029 0.002 TYR i 58 ARG 0.010 0.000 ARG K 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1519 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1320 time to evaluate : 6.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 100 MET cc_start: 0.1086 (mmt) cc_final: 0.0533 (mmp) REVERT: b 120 MET cc_start: -0.1562 (OUTLIER) cc_final: -0.1782 (mtm) REVERT: b 136 MET cc_start: 0.6233 (pmm) cc_final: 0.5926 (pmm) REVERT: c 94 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8371 (p) REVERT: d 58 PHE cc_start: 0.8838 (m-80) cc_final: 0.7993 (m-80) REVERT: d 110 ARG cc_start: 0.7280 (ptm-80) cc_final: 0.6557 (ppt170) REVERT: g 44 TYR cc_start: 0.8285 (m-80) cc_final: 0.7842 (m-80) REVERT: h 93 ASN cc_start: 0.8196 (m-40) cc_final: 0.7965 (m110) REVERT: j 13 TYR cc_start: 0.8404 (m-80) cc_final: 0.8165 (m-80) REVERT: l 76 GLU cc_start: 0.8361 (tm-30) cc_final: 0.7622 (tm-30) REVERT: m 59 TYR cc_start: 0.8240 (t80) cc_final: 0.7997 (t80) REVERT: n 52 GLU cc_start: 0.8335 (mp0) cc_final: 0.7873 (mp0) REVERT: p 15 ASN cc_start: 0.8529 (p0) cc_final: 0.8198 (p0) REVERT: p 65 GLN cc_start: 0.8567 (mm110) cc_final: 0.8356 (mm110) REVERT: p 79 ASP cc_start: 0.8007 (t0) cc_final: 0.7802 (t70) REVERT: z 52 GLN cc_start: 0.8610 (tp-100) cc_final: 0.8381 (tp-100) REVERT: I 1 MET cc_start: 0.1408 (OUTLIER) cc_final: 0.0087 (pmm) REVERT: J 33 HIS cc_start: 0.8066 (m-70) cc_final: 0.7765 (m90) REVERT: L 106 ILE cc_start: 0.8722 (mm) cc_final: 0.8040 (mm) REVERT: M 88 LYS cc_start: 0.8107 (ptpp) cc_final: 0.7853 (ptpp) REVERT: R 36 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7645 (mtmm) REVERT: 3 8 GLU cc_start: 0.7075 (pm20) cc_final: 0.6607 (pm20) outliers start: 199 outliers final: 161 residues processed: 1407 average time/residue: 1.3202 time to fit residues: 3221.4168 Evaluate side-chains 1438 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1274 time to evaluate : 6.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 161 GLU Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain e residue 47 SER Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain f residue 11 ASP Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 106 ASN Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 74 THR Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 73 GLN Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain k residue 109 LEU Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 57 LEU Chi-restraints excluded: chain l residue 79 MET Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain m residue 86 CYS Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 4 LYS Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain q residue 53 ILE Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain r residue 26 LYS Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 70 ASN Chi-restraints excluded: chain u residue 13 SER Chi-restraints excluded: chain z residue 1 MET Chi-restraints excluded: chain z residue 216 VAL Chi-restraints excluded: chain z residue 247 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 58 ASN Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 110 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 56 ASN Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 63 GLU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 43 ASP Chi-restraints excluded: chain X residue 110 VAL Chi-restraints excluded: chain X residue 172 SER Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 1 residue 44 ASN Chi-restraints excluded: chain 1 residue 61 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 4 residue 15 SER Chi-restraints excluded: chain 4 residue 51 LEU Chi-restraints excluded: chain 5 residue 34 ASP Chi-restraints excluded: chain 5 residue 38 ILE Chi-restraints excluded: chain 5 residue 53 GLU Chi-restraints excluded: chain 5 residue 54 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 28 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 1033 optimal weight: 20.0000 chunk 120 optimal weight: 30.0000 chunk 610 optimal weight: 10.0000 chunk 782 optimal weight: 5.9990 chunk 606 optimal weight: 10.0000 chunk 902 optimal weight: 6.9990 chunk 598 optimal weight: 10.0000 chunk 1067 optimal weight: 0.6980 chunk 668 optimal weight: 10.0000 chunk 651 optimal weight: 10.0000 chunk 493 optimal weight: 10.0000 overall best weight: 6.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 173 GLN g 25 GLN ** g 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 31 HIS l 77 HIS ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN J 21 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 ASN ** X 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 126 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 166274 Z= 0.301 Angle : 0.611 14.162 248477 Z= 0.316 Chirality : 0.036 0.343 31725 Planarity : 0.005 0.119 13780 Dihedral : 23.584 179.655 82568 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 3.86 % Allowed : 22.05 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % 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: -0.45 (0.10), residues: 6445 helix: 0.81 (0.11), residues: 2108 sheet: -0.22 (0.14), residues: 1307 loop : -1.10 (0.11), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP z 38 HIS 0.015 0.001 HIS l 77 PHE 0.030 0.001 PHE t 35 TYR 0.022 0.001 TYR c 187 ARG 0.018 0.001 ARG r 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1517 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1315 time to evaluate : 5.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 120 MET cc_start: -0.1539 (OUTLIER) cc_final: -0.1838 (mtm) REVERT: c 40 LYS cc_start: 0.8751 (ptpp) cc_final: 0.8488 (ptpp) REVERT: c 66 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6888 (p0) REVERT: c 94 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8385 (p) REVERT: d 58 PHE cc_start: 0.8828 (m-80) cc_final: 0.8018 (m-80) REVERT: d 110 ARG cc_start: 0.7239 (ptm-80) cc_final: 0.6573 (ppt170) REVERT: g 44 TYR cc_start: 0.8193 (m-80) cc_final: 0.7617 (m-80) REVERT: j 13 TYR cc_start: 0.8392 (m-80) cc_final: 0.8170 (m-80) REVERT: n 36 LYS cc_start: 0.9248 (tptp) cc_final: 0.9029 (tptt) REVERT: p 8 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8340 (p) REVERT: p 79 ASP cc_start: 0.8003 (t0) cc_final: 0.7801 (t70) REVERT: s 70 LYS cc_start: 0.8547 (mmtp) cc_final: 0.8081 (mmtp) REVERT: t 17 ARG cc_start: 0.8507 (ptp-110) cc_final: 0.7940 (ptp-170) REVERT: I 1 MET cc_start: 0.1357 (OUTLIER) cc_final: 0.0040 (pmm) REVERT: M 88 LYS cc_start: 0.8035 (ptpp) cc_final: 0.7768 (ptpp) REVERT: 3 1 MET cc_start: 0.7121 (tpp) cc_final: 0.6874 (tpp) outliers start: 202 outliers final: 172 residues processed: 1408 average time/residue: 1.3176 time to fit residues: 3209.7144 Evaluate side-chains 1464 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1287 time to evaluate : 6.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 66 ASP Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 161 GLU Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain e residue 47 SER Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain f residue 11 ASP Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 25 GLN Chi-restraints excluded: chain g residue 106 ASN Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 74 THR Chi-restraints excluded: chain j residue 29 VAL Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 73 GLN Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain k residue 109 LEU Chi-restraints excluded: chain l residue 18 LYS Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 79 MET Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 103 ASP Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 17 ILE Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain m residue 86 CYS Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 8 THR Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain q residue 53 ILE Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 70 ASN Chi-restraints excluded: chain u residue 24 THR Chi-restraints excluded: chain u residue 31 LEU Chi-restraints excluded: chain z residue 1 MET Chi-restraints excluded: chain z residue 216 VAL Chi-restraints excluded: chain z residue 247 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 110 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 56 ASN Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 111 GLU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 63 GLU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 43 ASP Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 1 residue 44 ASN Chi-restraints excluded: chain 1 residue 61 LEU Chi-restraints excluded: chain 1 residue 66 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 32 THR Chi-restraints excluded: chain 4 residue 15 SER Chi-restraints excluded: chain 4 residue 51 LEU Chi-restraints excluded: chain 5 residue 34 ASP Chi-restraints excluded: chain 5 residue 38 ILE Chi-restraints excluded: chain 5 residue 53 GLU Chi-restraints excluded: chain 5 residue 54 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 7 residue 51 SER Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 28 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 660 optimal weight: 30.0000 chunk 426 optimal weight: 10.0000 chunk 637 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 chunk 678 optimal weight: 10.0000 chunk 727 optimal weight: 10.0000 chunk 527 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 839 optimal weight: 10.0000 overall best weight: 6.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN J 21 ASN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 ASN X 126 GLN Y 46 HIS 3 15 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 166274 Z= 0.297 Angle : 0.612 15.907 248477 Z= 0.316 Chirality : 0.036 0.449 31725 Planarity : 0.005 0.119 13780 Dihedral : 23.583 179.795 82568 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.93 % Favored : 94.99 % Rotamer: Outliers : 4.04 % Allowed : 22.51 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % 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: -0.42 (0.10), residues: 6445 helix: 0.86 (0.11), residues: 2107 sheet: -0.24 (0.14), residues: 1321 loop : -1.08 (0.11), residues: 3017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP z 8 HIS 0.007 0.001 HIS H 11 PHE 0.023 0.001 PHE s 44 TYR 0.023 0.001 TYR c 187 ARG 0.010 0.001 ARG z 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1519 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1308 time to evaluate : 6.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 100 MET cc_start: 0.0954 (mmt) cc_final: 0.0235 (mmp) REVERT: b 120 MET cc_start: -0.1526 (OUTLIER) cc_final: -0.1847 (mtm) REVERT: b 136 MET cc_start: 0.6329 (pmm) cc_final: 0.6034 (pmm) REVERT: b 144 LEU cc_start: 0.4618 (OUTLIER) cc_final: 0.4297 (tt) REVERT: c 66 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6885 (p0) REVERT: c 94 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8415 (p) REVERT: d 58 PHE cc_start: 0.8836 (m-80) cc_final: 0.8025 (m-80) REVERT: d 110 ARG cc_start: 0.7234 (ptm-80) cc_final: 0.6574 (ppt170) REVERT: f 87 ARG cc_start: 0.8287 (mtt180) cc_final: 0.8076 (mtt180) REVERT: g 44 TYR cc_start: 0.8246 (m-80) cc_final: 0.7680 (m-80) REVERT: n 9 LYS cc_start: 0.9377 (ttpp) cc_final: 0.9074 (mttm) REVERT: p 8 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8313 (p) REVERT: s 70 LYS cc_start: 0.8560 (mmtp) cc_final: 0.8080 (mmtp) REVERT: t 17 ARG cc_start: 0.8511 (ptp-110) cc_final: 0.7870 (ptp-170) REVERT: z 259 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8198 (mm-40) REVERT: I 1 MET cc_start: 0.1390 (OUTLIER) cc_final: 0.0086 (pmm) REVERT: M 88 LYS cc_start: 0.7998 (ptpp) cc_final: 0.7708 (ptpp) REVERT: 3 8 GLU cc_start: 0.7050 (pm20) cc_final: 0.6784 (pm20) outliers start: 211 outliers final: 181 residues processed: 1404 average time/residue: 1.4046 time to fit residues: 3421.2078 Evaluate side-chains 1467 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1280 time to evaluate : 6.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain b residue 144 LEU Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 66 ASP Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 161 GLU Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain e residue 47 SER Chi-restraints excluded: chain e residue 142 CYS Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain f residue 11 ASP Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 106 ASN Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 74 THR Chi-restraints excluded: chain j residue 8 ILE Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 73 GLN Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain k residue 109 LEU Chi-restraints excluded: chain l residue 18 LYS Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 79 MET Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 103 ASP Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 17 ILE Chi-restraints excluded: chain m residue 39 ILE Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain m residue 86 CYS Chi-restraints excluded: chain n residue 11 ASN Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain o residue 11 ILE Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 8 THR Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain q residue 53 ILE Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 70 ASN Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain u residue 24 THR Chi-restraints excluded: chain u residue 31 LEU Chi-restraints excluded: chain z residue 216 VAL Chi-restraints excluded: chain z residue 223 LEU Chi-restraints excluded: chain z residue 247 ARG Chi-restraints excluded: chain z residue 300 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 110 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 56 ASN Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 63 GLU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 79 THR Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 43 ASP Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain Y residue 9 SER Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 1 residue 44 ASN Chi-restraints excluded: chain 1 residue 61 LEU Chi-restraints excluded: chain 1 residue 66 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 32 THR Chi-restraints excluded: chain 4 residue 15 SER Chi-restraints excluded: chain 4 residue 51 LEU Chi-restraints excluded: chain 5 residue 34 ASP Chi-restraints excluded: chain 5 residue 38 ILE Chi-restraints excluded: chain 5 residue 53 GLU Chi-restraints excluded: chain 5 residue 54 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 7 residue 51 SER Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 28 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 971 optimal weight: 8.9990 chunk 1023 optimal weight: 8.9990 chunk 933 optimal weight: 10.0000 chunk 995 optimal weight: 9.9990 chunk 1022 optimal weight: 20.0000 chunk 598 optimal weight: 10.0000 chunk 433 optimal weight: 10.0000 chunk 781 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 chunk 899 optimal weight: 6.9990 chunk 941 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 117 GLN ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 95 HIS ** L 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 ASN X 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 166274 Z= 0.258 Angle : 0.601 14.385 248477 Z= 0.311 Chirality : 0.035 0.490 31725 Planarity : 0.005 0.118 13780 Dihedral : 23.577 179.801 82568 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.03 % Rotamer: Outliers : 3.60 % Allowed : 23.43 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % 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: -0.35 (0.10), residues: 6445 helix: 0.90 (0.12), residues: 2104 sheet: -0.17 (0.14), residues: 1308 loop : -1.04 (0.11), residues: 3033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP z 38 HIS 0.006 0.001 HIS H 11 PHE 0.021 0.001 PHE s 44 TYR 0.035 0.001 TYR m 59 ARG 0.009 0.000 ARG k 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1497 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1309 time to evaluate : 6.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 120 MET cc_start: -0.1454 (OUTLIER) cc_final: -0.1721 (mtm) REVERT: b 136 MET cc_start: 0.6469 (pmm) cc_final: 0.6138 (pmm) REVERT: b 144 LEU cc_start: 0.4642 (OUTLIER) cc_final: 0.4314 (tt) REVERT: c 66 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6876 (p0) REVERT: c 94 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8386 (p) REVERT: d 58 PHE cc_start: 0.8825 (m-80) cc_final: 0.7987 (m-80) REVERT: d 110 ARG cc_start: 0.7203 (ptm-80) cc_final: 0.6599 (ppt170) REVERT: f 87 ARG cc_start: 0.8284 (mtt180) cc_final: 0.8055 (mtt180) REVERT: g 44 TYR cc_start: 0.8142 (m-80) cc_final: 0.7629 (m-80) REVERT: n 9 LYS cc_start: 0.9363 (ttpp) cc_final: 0.9056 (mttm) REVERT: n 46 GLU cc_start: 0.8332 (pp20) cc_final: 0.7651 (pp20) REVERT: n 47 MET cc_start: 0.8173 (mmm) cc_final: 0.7853 (mmp) REVERT: s 70 LYS cc_start: 0.8586 (mmtp) cc_final: 0.8091 (mmtp) REVERT: t 17 ARG cc_start: 0.8496 (ptp-110) cc_final: 0.7800 (ptp-170) REVERT: z 52 GLN cc_start: 0.8609 (tp-100) cc_final: 0.8286 (tp-100) REVERT: I 1 MET cc_start: 0.1259 (mpp) cc_final: 0.0722 (ptp) REVERT: M 88 LYS cc_start: 0.7903 (ptpp) cc_final: 0.7619 (ptpp) REVERT: R 36 LYS cc_start: 0.7863 (mtmm) cc_final: 0.7610 (mtmm) outliers start: 188 outliers final: 168 residues processed: 1390 average time/residue: 1.3410 time to fit residues: 3232.9572 Evaluate side-chains 1455 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1283 time to evaluate : 6.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 111 LEU Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain b residue 144 LEU Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 66 ASP Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 161 GLU Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 139 ASP Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain d residue 155 GLU Chi-restraints excluded: chain e residue 47 SER Chi-restraints excluded: chain e residue 140 LEU Chi-restraints excluded: chain e residue 142 CYS Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain f residue 11 ASP Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 106 ASN Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 74 THR Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 29 VAL Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 73 GLN Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain k residue 109 LEU Chi-restraints excluded: chain l residue 18 LYS Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 79 MET Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 90 LEU Chi-restraints excluded: chain l residue 103 ASP Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 70 ASN Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain u residue 4 VAL Chi-restraints excluded: chain u residue 24 THR Chi-restraints excluded: chain u residue 31 LEU Chi-restraints excluded: chain z residue 216 VAL Chi-restraints excluded: chain z residue 247 ARG Chi-restraints excluded: chain z residue 300 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 95 HIS Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 110 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 56 ASN Chi-restraints excluded: chain Q residue 69 ASP Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 63 GLU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 43 ASP Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain X residue 172 SER Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 1 residue 44 ASN Chi-restraints excluded: chain 1 residue 61 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 32 THR Chi-restraints excluded: chain 4 residue 15 SER Chi-restraints excluded: chain 4 residue 51 LEU Chi-restraints excluded: chain 5 residue 34 ASP Chi-restraints excluded: chain 5 residue 38 ILE Chi-restraints excluded: chain 5 residue 54 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 7 residue 51 SER Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 8 residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 991 optimal weight: 0.9980 chunk 653 optimal weight: 20.0000 chunk 1052 optimal weight: 7.9990 chunk 642 optimal weight: 10.0000 chunk 499 optimal weight: 10.0000 chunk 731 optimal weight: 10.0000 chunk 1103 optimal weight: 9.9990 chunk 1015 optimal weight: 10.0000 chunk 879 optimal weight: 0.9990 chunk 91 optimal weight: 20.0000 chunk 678 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 117 GLN ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 80 ASN ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 110 GLN ** k 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 166 GLN D 135 GLN ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 82 ASN X 126 GLN X 129 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 166274 Z= 0.275 Angle : 0.612 13.494 248477 Z= 0.316 Chirality : 0.036 0.529 31725 Planarity : 0.005 0.118 13780 Dihedral : 23.565 179.861 82568 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 3.63 % Allowed : 23.60 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % 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: -0.37 (0.10), residues: 6445 helix: 0.88 (0.11), residues: 2106 sheet: -0.21 (0.14), residues: 1329 loop : -1.04 (0.11), residues: 3010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP z 38 HIS 0.008 0.001 HIS H 11 PHE 0.021 0.001 PHE s 44 TYR 0.035 0.002 TYR m 59 ARG 0.012 0.000 ARG t 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12890 Ramachandran restraints generated. 6445 Oldfield, 0 Emsley, 6445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1301 time to evaluate : 6.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 120 MET cc_start: -0.1647 (OUTLIER) cc_final: -0.1879 (mtm) REVERT: b 136 MET cc_start: 0.6491 (pmm) cc_final: 0.6154 (pmm) REVERT: b 144 LEU cc_start: 0.4725 (OUTLIER) cc_final: 0.4374 (tt) REVERT: c 66 ASP cc_start: 0.7159 (OUTLIER) cc_final: 0.6881 (p0) REVERT: c 94 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8409 (p) REVERT: d 110 ARG cc_start: 0.7241 (ptm-80) cc_final: 0.6640 (ppt170) REVERT: f 87 ARG cc_start: 0.8280 (mtt180) cc_final: 0.8078 (mtt180) REVERT: g 44 TYR cc_start: 0.8093 (m-80) cc_final: 0.7642 (m-80) REVERT: n 9 LYS cc_start: 0.9351 (ttpp) cc_final: 0.9037 (mttm) REVERT: n 46 GLU cc_start: 0.8337 (pp20) cc_final: 0.7672 (pp20) REVERT: n 47 MET cc_start: 0.8269 (mmm) cc_final: 0.7800 (mmp) REVERT: s 70 LYS cc_start: 0.8589 (mmtp) cc_final: 0.8090 (mmtp) REVERT: t 17 ARG cc_start: 0.8463 (ptp-110) cc_final: 0.7725 (ptp-170) REVERT: I 1 MET cc_start: 0.1261 (mpp) cc_final: 0.0741 (ptp) REVERT: I 101 LYS cc_start: 0.8686 (mmmt) cc_final: 0.8394 (mmmt) REVERT: M 88 LYS cc_start: 0.7930 (ptpp) cc_final: 0.7649 (ptpp) outliers start: 190 outliers final: 171 residues processed: 1378 average time/residue: 1.3273 time to fit residues: 3170.8120 Evaluate side-chains 1462 residues out of total 5344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1287 time to evaluate : 6.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 120 MET Chi-restraints excluded: chain b residue 144 LEU Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 59 THR Chi-restraints excluded: chain c residue 66 ASP Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 121 GLU Chi-restraints excluded: chain c residue 139 SER Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 161 GLU Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain d residue 9 THR Chi-restraints excluded: chain d residue 73 GLU Chi-restraints excluded: chain d residue 120 VAL Chi-restraints excluded: chain d residue 139 ASP Chi-restraints excluded: chain d residue 140 VAL Chi-restraints excluded: chain e residue 47 SER Chi-restraints excluded: chain e residue 140 LEU Chi-restraints excluded: chain e residue 142 CYS Chi-restraints excluded: chain e residue 155 SER Chi-restraints excluded: chain e residue 159 ILE Chi-restraints excluded: chain f residue 11 ASP Chi-restraints excluded: chain f residue 22 SER Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 106 ASN Chi-restraints excluded: chain g residue 108 SER Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 74 THR Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 29 VAL Chi-restraints excluded: chain j residue 35 SER Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 48 VAL Chi-restraints excluded: chain k residue 41 VAL Chi-restraints excluded: chain k residue 91 VAL Chi-restraints excluded: chain k residue 109 LEU Chi-restraints excluded: chain l residue 18 LYS Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 79 MET Chi-restraints excluded: chain l residue 89 ASP Chi-restraints excluded: chain l residue 90 LEU Chi-restraints excluded: chain l residue 103 ASP Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 42 ASN Chi-restraints excluded: chain m residue 51 ASP Chi-restraints excluded: chain n residue 25 ASN Chi-restraints excluded: chain o residue 70 VAL Chi-restraints excluded: chain p residue 13 ILE Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain q residue 53 ILE Chi-restraints excluded: chain q residue 65 ASN Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 19 LEU Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 50 LEU Chi-restraints excluded: chain t residue 70 ASN Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain u residue 4 VAL Chi-restraints excluded: chain u residue 24 THR Chi-restraints excluded: chain u residue 31 LEU Chi-restraints excluded: chain z residue 216 VAL Chi-restraints excluded: chain z residue 247 ARG Chi-restraints excluded: chain z residue 300 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 122 ASP Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 140 ASN Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain F residue 151 ASP Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain I residue 26 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 110 MET Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 72 LEU Chi-restraints excluded: chain J residue 81 LEU Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 124 ASP Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 96 HIS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain M residue 4 GLN Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 82 ASP Chi-restraints excluded: chain N residue 96 ASP Chi-restraints excluded: chain N residue 108 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain O residue 92 TRP Chi-restraints excluded: chain O residue 110 ASP Chi-restraints excluded: chain O residue 119 THR Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 56 ASN Chi-restraints excluded: chain Q residue 99 THR Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 55 SER Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 110 LYS Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 37 LEU Chi-restraints excluded: chain T residue 50 SER Chi-restraints excluded: chain T residue 63 GLU Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 84 ASP Chi-restraints excluded: chain U residue 108 SER Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 20 SER Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 43 ASP Chi-restraints excluded: chain X residue 158 THR Chi-restraints excluded: chain X residue 172 SER Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 26 SER Chi-restraints excluded: chain Z residue 33 ILE Chi-restraints excluded: chain Z residue 39 VAL Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain 1 residue 44 ASN Chi-restraints excluded: chain 1 residue 61 LEU Chi-restraints excluded: chain 1 residue 66 LEU Chi-restraints excluded: chain 2 residue 12 THR Chi-restraints excluded: chain 3 residue 5 ILE Chi-restraints excluded: chain 3 residue 32 THR Chi-restraints excluded: chain 4 residue 15 SER Chi-restraints excluded: chain 4 residue 51 LEU Chi-restraints excluded: chain 5 residue 34 ASP Chi-restraints excluded: chain 5 residue 38 ILE Chi-restraints excluded: chain 5 residue 54 SER Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 39 SER Chi-restraints excluded: chain 7 residue 51 SER Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 7 residue 56 SER Chi-restraints excluded: chain 8 residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1108 random chunks: chunk 538 optimal weight: 10.0000 chunk 698 optimal weight: 10.0000 chunk 936 optimal weight: 4.9990 chunk 269 optimal weight: 8.9990 chunk 810 optimal weight: 2.9990 chunk 129 optimal weight: 30.0000 chunk 244 optimal weight: 7.9990 chunk 880 optimal weight: 10.0000 chunk 368 optimal weight: 10.0000 chunk 904 optimal weight: 20.0000 chunk 111 optimal weight: 40.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 126 GLN 1 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.054460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.036945 restraints weight = 789474.237| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 2.67 r_work: 0.2477 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.222 166274 Z= 0.309 Angle : 0.632 59.200 248477 Z= 0.331 Chirality : 0.036 0.509 31725 Planarity : 0.005 0.118 13780 Dihedral : 23.564 179.852 82568 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.04 % Favored : 94.88 % Rotamer: Outliers : 3.61 % Allowed : 24.13 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % 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: -0.38 (0.10), residues: 6445 helix: 0.87 (0.11), residues: 2106 sheet: -0.21 (0.14), residues: 1329 loop : -1.05 (0.11), residues: 3010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP z 38 HIS 0.010 0.001 HIS l 72 PHE 0.019 0.001 PHE s 44 TYR 0.029 0.001 TYR m 59 ARG 0.033 0.000 ARG c 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47513.59 seconds wall clock time: 827 minutes 11.91 seconds (49631.91 seconds total)