Starting phenix.real_space_refine on Tue Feb 20 17:28:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8k_27250/02_2024/8d8k_27250_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8k_27250/02_2024/8d8k_27250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8k_27250/02_2024/8d8k_27250.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8k_27250/02_2024/8d8k_27250.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8k_27250/02_2024/8d8k_27250_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d8k_27250/02_2024/8d8k_27250_neut_updated.pdb" } resolution = 3.13 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= 0.010 sd= 1.048 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 1541 5.49 5 Mg 72 5.21 5 S 222 5.16 5 C 50541 2.51 5 N 15754 2.21 5 O 20843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 114": "OE1" <-> "OE2" Residue "0 PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 331": "OE1" <-> "OE2" Residue "0 TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 457": "OE1" <-> "OE2" Residue "0 GLU 468": "OE1" <-> "OE2" Residue "0 ASP 482": "OD1" <-> "OD2" Residue "0 ASP 500": "OD1" <-> "OD2" Residue "0 GLU 518": "OE1" <-> "OE2" Residue "5 GLU 42": "OE1" <-> "OE2" Residue "5 ASP 49": "OD1" <-> "OD2" Residue "5 GLU 50": "OE1" <-> "OE2" Residue "5 GLU 115": "OE1" <-> "OE2" Residue "5 GLU 122": "OE1" <-> "OE2" Residue "5 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 257": "OD1" <-> "OD2" Residue "5 ASP 269": "OD1" <-> "OD2" Residue "5 PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 310": "OE1" <-> "OE2" Residue "5 ASP 316": "OD1" <-> "OD2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "d ASP 167": "OD1" <-> "OD2" Residue "d TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 256": "OE1" <-> "OE2" Residue "d GLU 370": "OE1" <-> "OE2" Residue "d TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 500": "OE1" <-> "OE2" Residue "d PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 619": "OE1" <-> "OE2" Residue "d PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 661": "OE1" <-> "OE2" Residue "d ASP 737": "OD1" <-> "OD2" Residue "d GLU 742": "OE1" <-> "OE2" Residue "d GLU 754": "OE1" <-> "OE2" Residue "d GLU 832": "OE1" <-> "OE2" Residue "d ASP 835": "OD1" <-> "OD2" Residue "d GLU 840": "OE1" <-> "OE2" Residue "M GLU 14": "OE1" <-> "OE2" Residue "M GLU 33": "OE1" <-> "OE2" Residue "M GLU 52": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M ASP 77": "OD1" <-> "OD2" Residue "N GLU 33": "OE1" <-> "OE2" Residue "O GLU 96": "OE1" <-> "OE2" Residue "O GLU 97": "OE1" <-> "OE2" Residue "O ASP 99": "OD1" <-> "OD2" Residue "O GLU 106": "OE1" <-> "OE2" Residue "O ASP 127": "OD1" <-> "OD2" Residue "O ASP 254": "OD1" <-> "OD2" Residue "O GLU 256": "OE1" <-> "OE2" Residue "P ASP 68": "OD1" <-> "OD2" Residue "P ASP 70": "OD1" <-> "OD2" Residue "P GLU 84": "OE1" <-> "OE2" Residue "Q ASP 42": "OD1" <-> "OD2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q GLU 76": "OE1" <-> "OE2" Residue "Q GLU 159": "OE1" <-> "OE2" Residue "Q ASP 168": "OD1" <-> "OD2" Residue "Q GLU 192": "OE1" <-> "OE2" Residue "Q ASP 197": "OD1" <-> "OD2" Residue "R ASP 42": "OD1" <-> "OD2" Residue "R ASP 113": "OD1" <-> "OD2" Residue "T ASP 171": "OD1" <-> "OD2" Residue "U GLU 65": "OE1" <-> "OE2" Residue "U ASP 83": "OD1" <-> "OD2" Residue "U ASP 129": "OD1" <-> "OD2" Residue "U TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 164": "OD1" <-> "OD2" Residue "U GLU 186": "OE1" <-> "OE2" Residue "U ASP 218": "OD1" <-> "OD2" Residue "U GLU 226": "OE1" <-> "OE2" Residue "V ASP 72": "OD1" <-> "OD2" Residue "V GLU 81": "OE1" <-> "OE2" Residue "V GLU 133": "OE1" <-> "OE2" Residue "V GLU 141": "OE1" <-> "OE2" Residue "V GLU 171": "OE1" <-> "OE2" Residue "V GLU 198": "OE1" <-> "OE2" Residue "V GLU 230": "OE1" <-> "OE2" Residue "V ASP 233": "OD1" <-> "OD2" Residue "W GLU 117": "OE1" <-> "OE2" Residue "W ASP 257": "OD1" <-> "OD2" Residue "W TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 388": "OE1" <-> "OE2" Residue "W GLU 390": "OE1" <-> "OE2" Residue "W GLU 398": "OE1" <-> "OE2" Residue "W GLU 423": "OE1" <-> "OE2" Residue "X PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 70": "OD1" <-> "OD2" Residue "X GLU 72": "OE1" <-> "OE2" Residue "Y GLU 55": "OE1" <-> "OE2" Residue "Y PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 135": "OD1" <-> "OD2" Residue "Y GLU 161": "OE1" <-> "OE2" Residue "Y GLU 171": "OE1" <-> "OE2" Residue "Y TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 212": "OE1" <-> "OE2" Residue "Y GLU 242": "OE1" <-> "OE2" Residue "Y GLU 261": "OE1" <-> "OE2" Residue "Y ASP 264": "OD1" <-> "OD2" Residue "Y GLU 296": "OE1" <-> "OE2" Residue "Z TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 57": "OE1" <-> "OE2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "2 PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 60": "OE1" <-> "OE2" Residue "2 ASP 70": "OD1" <-> "OD2" Residue "2 GLU 114": "OE1" <-> "OE2" Residue "3 ASP 40": "OD1" <-> "OD2" Residue "3 TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 47": "OD1" <-> "OD2" Residue "3 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 114": "OE1" <-> "OE2" Residue "3 GLU 133": "OE1" <-> "OE2" Residue "3 TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 144": "OE1" <-> "OE2" Residue "3 PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 202": "OE1" <-> "OE2" Residue "3 ASP 234": "OD1" <-> "OD2" Residue "3 TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 35": "OD1" <-> "OD2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D ASP 470": "OD1" <-> "OD2" Residue "D GLU 475": "OE1" <-> "OE2" Residue "D TYR 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 20": "OE1" <-> "OE2" Residue "4 GLU 35": "OE1" <-> "OE2" Residue "4 GLU 106": "OE1" <-> "OE2" Residue "4 ASP 121": "OD1" <-> "OD2" Residue "4 ASP 194": "OD1" <-> "OD2" Residue "4 PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 254": "OE1" <-> "OE2" Residue "4 PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 264": "OE1" <-> "OE2" Residue "4 TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 294": "OE1" <-> "OE2" Residue "E TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 183": "OE1" <-> "OE2" Residue "E GLU 188": "OE1" <-> "OE2" Residue "E GLU 251": "OE1" <-> "OE2" Residue "E ASP 299": "OD1" <-> "OD2" Residue "F ASP 41": "OD1" <-> "OD2" Residue "F TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 70": "OE1" <-> "OE2" Residue "6 ASP 112": "OD1" <-> "OD2" Residue "6 PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 204": "OD1" <-> "OD2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 148": "OD1" <-> "OD2" Residue "G PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 228": "OE1" <-> "OE2" Residue "H ASP 66": "OD1" <-> "OD2" Residue "H ASP 137": "OD1" <-> "OD2" Residue "H GLU 140": "OE1" <-> "OE2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I GLU 59": "OE1" <-> "OE2" Residue "I TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I GLU 175": "OE1" <-> "OE2" Residue "I GLU 225": "OE1" <-> "OE2" Residue "I GLU 260": "OE1" <-> "OE2" Residue "J GLU 25": "OE1" <-> "OE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J GLU 84": "OE1" <-> "OE2" Residue "J PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 103": "OE1" <-> "OE2" Residue "J GLU 189": "OE1" <-> "OE2" Residue "K ASP 97": "OD1" <-> "OD2" Residue "K TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 153": "OE1" <-> "OE2" Residue "L ASP 101": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 88977 Number of models: 1 Model: "" Number of chains: 41 Chain: "0" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3471 Classifications: {'peptide': 429} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 403} Chain breaks: 3 Chain: "5" Number of atoms: 2199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2199 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 13, 'TRANS': 256} Chain breaks: 2 Chain: "C" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 2014 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 236} Chain breaks: 5 Chain: "d" Number of atoms: 5497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5497 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 15, 'TRANS': 644} Chain breaks: 3 Chain: "M" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "N" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 931 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "O" Number of atoms: 1724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1724 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 5, 'TRANS': 204} Chain breaks: 1 Chain: "P" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 919 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain breaks: 1 Chain: "Q" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1690 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 2, 'TRANS': 202} Chain breaks: 4 Chain: "R" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 738 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "S" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 595 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 7, 'TRANS': 67} Chain: "T" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 760 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "U" Number of atoms: 1907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1907 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain: "V" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1872 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 223} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "W" Number of atoms: 3174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3174 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain: "X" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 6, 'TRANS': 89} Chain: "Y" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2208 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 16, 'TRANS': 246} Chain breaks: 1 Chain: "Z" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 660 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 6, 'TRANS': 77} Chain breaks: 1 Chain: "A" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1585 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 3 Chain: "B" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2085 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 16, 'TRANS': 249} Chain: "2" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 833 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "3" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1953 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2567 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 22, 'TRANS': 285} Chain breaks: 2 Chain: "4" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2182 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 12, 'TRANS': 258} Chain breaks: 2 Chain: "E" Number of atoms: 2321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2321 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 16, 'TRANS': 274} Chain breaks: 1 Chain: "F" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1054 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "6" Number of atoms: 2071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2071 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 18, 'TRANS': 232} Chain breaks: 1 Chain: "G" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1185 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain breaks: 1 Chain: "H" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1221 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 146} Chain: "I" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1667 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "a" Number of atoms: 32666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1538, 32666 Classifications: {'RNA': 1538} Modifications used: {'rna2p_pur': 142, 'rna2p_pyr': 103, 'rna3p_pur': 707, 'rna3p_pyr': 586} Link IDs: {'rna2p': 244, 'rna3p': 1293} Chain breaks: 13 Chain: "J" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1186 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 10, 'TRANS': 133} Chain breaks: 2 Chain: "K" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1113 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain breaks: 1 Chain: "c" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 470 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'TRANS': 93} Chain breaks: 3 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 94 Planarities with less than four sites: {'UNK:plan-1': 94} Unresolved non-hydrogen planarities: 94 Chain: "L" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 926 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 112} Chain: "0" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Unusual residues: {' MG': 69} Classifications: {'undetermined': 69} Link IDs: {None: 68} Chain: "W" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2256 SG CYS 0 400 43.541 68.193 130.186 1.00 34.98 S ATOM 2033 SG CYS 0 373 39.093 67.279 134.598 1.00 31.85 S ATOM 3068 SG CYS 0 513 44.073 63.009 134.013 1.00 30.98 S ATOM 2085 SG CYS 0 379 45.078 68.696 136.377 1.00 38.78 S Time building chain proxies: 34.33, per 1000 atoms: 0.39 Number of scatterers: 88977 At special positions: 0 Unit cell: (186.032, 220.913, 329.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 222 16.00 P 1541 15.00 Mg 72 11.99 O 20843 8.00 N 15754 7.00 C 50541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS Z 40 " - pdb=" SG CYS Z 51 " distance=2.03 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: 32.73 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 0 701 " pdb="FE2 SF4 0 701 " - pdb=" SG CYS 0 373 " pdb="FE1 SF4 0 701 " - pdb=" SG CYS 0 400 " pdb="FE3 SF4 0 701 " - pdb=" SG CYS 0 513 " pdb="FE4 SF4 0 701 " - pdb=" SG CYS 0 379 " Number of angles added : 12 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13244 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 305 helices and 37 sheets defined 48.6% alpha, 8.3% beta 453 base pairs and 788 stacking pairs defined. Time for finding SS restraints: 30.86 Creating SS restraints... Processing helix chain '0' and resid 66 through 71 Processing helix chain '0' and resid 82 through 91 Processing helix chain '0' and resid 98 through 112 Processing helix chain '0' and resid 125 through 134 Processing helix chain '0' and resid 136 through 154 Processing helix chain '0' and resid 173 through 181 Processing helix chain '0' and resid 200 through 210 Processing helix chain '0' and resid 288 through 299 removed outlier: 4.484A pdb=" N ILE 0 299 " --> pdb=" O HIS 0 295 " (cutoff:3.500A) Processing helix chain '0' and resid 314 through 328 Processing helix chain '0' and resid 330 through 333 Processing helix chain '0' and resid 386 through 390 Processing helix chain '0' and resid 410 through 415 Processing helix chain '0' and resid 463 through 474 Processing helix chain '0' and resid 491 through 493 No H-bonds generated for 'chain '0' and resid 491 through 493' Processing helix chain '0' and resid 530 through 538 removed outlier: 3.736A pdb=" N LYS 0 538 " --> pdb=" O HIS 0 534 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 56 removed outlier: 3.689A pdb=" N LYS 5 47 " --> pdb=" O ILE 5 43 " (cutoff:3.500A) Processing helix chain '5' and resid 62 through 66 Processing helix chain '5' and resid 68 through 76 removed outlier: 4.359A pdb=" N GLN 5 72 " --> pdb=" O LYS 5 69 " (cutoff:3.500A) Processing helix chain '5' and resid 99 through 105 removed outlier: 3.504A pdb=" N ASP 5 104 " --> pdb=" O GLN 5 100 " (cutoff:3.500A) Processing helix chain '5' and resid 116 through 124 Processing helix chain '5' and resid 131 through 136 Processing helix chain '5' and resid 139 through 151 removed outlier: 3.774A pdb=" N PHE 5 150 " --> pdb=" O LEU 5 146 " (cutoff:3.500A) Processing helix chain '5' and resid 156 through 172 removed outlier: 4.889A pdb=" N HIS 5 168 " --> pdb=" O TYR 5 164 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS 5 169 " --> pdb=" O GLY 5 165 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU 5 171 " --> pdb=" O GLU 5 167 " (cutoff:3.500A) Processing helix chain '5' and resid 176 through 178 No H-bonds generated for 'chain '5' and resid 176 through 178' Processing helix chain '5' and resid 184 through 198 removed outlier: 3.782A pdb=" N ASN 5 188 " --> pdb=" O PHE 5 184 " (cutoff:3.500A) Processing helix chain '5' and resid 204 through 217 removed outlier: 3.730A pdb=" N LYS 5 216 " --> pdb=" O GLN 5 212 " (cutoff:3.500A) Processing helix chain '5' and resid 227 through 239 Processing helix chain '5' and resid 264 through 287 removed outlier: 4.987A pdb=" N GLY 5 276 " --> pdb=" O SER 5 272 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ILE 5 277 " --> pdb=" O LYS 5 273 " (cutoff:3.500A) Processing helix chain '5' and resid 295 through 309 Processing helix chain '5' and resid 314 through 326 removed outlier: 3.919A pdb=" N LEU 5 322 " --> pdb=" O HIS 5 318 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU 5 324 " --> pdb=" O LYS 5 320 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU 5 325 " --> pdb=" O ALA 5 321 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU 5 326 " --> pdb=" O LEU 5 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 59 Processing helix chain 'C' and resid 89 through 92 Processing helix chain 'C' and resid 102 through 123 removed outlier: 3.627A pdb=" N MET C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 191 through 199 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 254 through 280 Processing helix chain 'C' and resid 302 through 305 No H-bonds generated for 'chain 'C' and resid 302 through 305' Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'd' and resid 149 through 153 Processing helix chain 'd' and resid 163 through 171 Processing helix chain 'd' and resid 181 through 191 Processing helix chain 'd' and resid 197 through 210 Processing helix chain 'd' and resid 220 through 232 Processing helix chain 'd' and resid 246 through 269 Processing helix chain 'd' and resid 284 through 297 Processing helix chain 'd' and resid 300 through 314 Processing helix chain 'd' and resid 320 through 332 Processing helix chain 'd' and resid 336 through 349 Processing helix chain 'd' and resid 357 through 370 Processing helix chain 'd' and resid 373 through 385 Processing helix chain 'd' and resid 392 through 407 removed outlier: 3.817A pdb=" N SER d 407 " --> pdb=" O ALA d 403 " (cutoff:3.500A) Processing helix chain 'd' and resid 409 through 412 No H-bonds generated for 'chain 'd' and resid 409 through 412' Processing helix chain 'd' and resid 416 through 432 Processing helix chain 'd' and resid 439 through 455 removed outlier: 4.691A pdb=" N LEU d 443 " --> pdb=" O LYS d 439 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 479 Processing helix chain 'd' and resid 489 through 496 Processing helix chain 'd' and resid 499 through 510 Processing helix chain 'd' and resid 519 through 521 No H-bonds generated for 'chain 'd' and resid 519 through 521' Processing helix chain 'd' and resid 524 through 542 Processing helix chain 'd' and resid 565 through 580 Processing helix chain 'd' and resid 593 through 613 removed outlier: 4.717A pdb=" N GLN d 612 " --> pdb=" O ASP d 608 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU d 613 " --> pdb=" O SER d 609 " (cutoff:3.500A) Processing helix chain 'd' and resid 617 through 635 Processing helix chain 'd' and resid 643 through 656 Proline residue: d 653 - end of helix Processing helix chain 'd' and resid 659 through 669 Processing helix chain 'd' and resid 673 through 688 Processing helix chain 'd' and resid 719 through 732 removed outlier: 4.680A pdb=" N ARG d 731 " --> pdb=" O ILE d 727 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N HIS d 732 " --> pdb=" O THR d 728 " (cutoff:3.500A) Processing helix chain 'd' and resid 738 through 751 Processing helix chain 'd' and resid 754 through 769 removed outlier: 3.801A pdb=" N THR d 769 " --> pdb=" O GLY d 765 " (cutoff:3.500A) Processing helix chain 'd' and resid 771 through 775 Processing helix chain 'd' and resid 778 through 798 Processing helix chain 'd' and resid 802 through 811 Processing helix chain 'd' and resid 824 through 833 Processing helix chain 'd' and resid 836 through 847 Processing helix chain 'M' and resid 16 through 23 removed outlier: 4.219A pdb=" N ALA M 21 " --> pdb=" O LYS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 39 Processing helix chain 'M' and resid 47 through 49 No H-bonds generated for 'chain 'M' and resid 47 through 49' Processing helix chain 'M' and resid 52 through 64 Processing helix chain 'M' and resid 69 through 83 Processing helix chain 'N' and resid 19 through 46 removed outlier: 5.131A pdb=" N ILE N 36 " --> pdb=" O LYS N 32 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU N 37 " --> pdb=" O GLU N 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 64 Processing helix chain 'N' and resid 67 through 69 No H-bonds generated for 'chain 'N' and resid 67 through 69' Processing helix chain 'N' and resid 95 through 104 Processing helix chain 'O' and resid 35 through 60 Processing helix chain 'O' and resid 74 through 84 Processing helix chain 'O' and resid 95 through 110 Processing helix chain 'O' and resid 128 through 142 Processing helix chain 'O' and resid 144 through 146 No H-bonds generated for 'chain 'O' and resid 144 through 146' Processing helix chain 'O' and resid 149 through 164 Processing helix chain 'O' and resid 174 through 194 Processing helix chain 'O' and resid 199 through 222 Processing helix chain 'O' and resid 224 through 234 Processing helix chain 'O' and resid 238 through 242 Processing helix chain 'O' and resid 249 through 254 Processing helix chain 'P' and resid 52 through 57 Processing helix chain 'P' and resid 69 through 78 Processing helix chain 'P' and resid 84 through 93 Processing helix chain 'P' and resid 98 through 100 No H-bonds generated for 'chain 'P' and resid 98 through 100' Processing helix chain 'Q' and resid 81 through 116 removed outlier: 3.893A pdb=" N ALA Q 86 " --> pdb=" O GLY Q 82 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU Q 87 " --> pdb=" O GLN Q 83 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU Q 89 " --> pdb=" O PHE Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 134 Processing helix chain 'Q' and resid 141 through 149 Processing helix chain 'Q' and resid 160 through 164 Processing helix chain 'Q' and resid 168 through 195 Processing helix chain 'Q' and resid 197 through 207 Processing helix chain 'Q' and resid 219 through 230 Processing helix chain 'R' and resid 43 through 45 No H-bonds generated for 'chain 'R' and resid 43 through 45' Processing helix chain 'R' and resid 57 through 60 Processing helix chain 'R' and resid 62 through 70 Processing helix chain 'R' and resid 89 through 93 Processing helix chain 'R' and resid 96 through 102 removed outlier: 4.003A pdb=" N TYR R 102 " --> pdb=" O ILE R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 115 No H-bonds generated for 'chain 'R' and resid 112 through 115' Processing helix chain 'R' and resid 119 through 134 Processing helix chain 'S' and resid 12 through 14 No H-bonds generated for 'chain 'S' and resid 12 through 14' Processing helix chain 'S' and resid 23 through 28 Processing helix chain 'S' and resid 44 through 46 No H-bonds generated for 'chain 'S' and resid 44 through 46' Processing helix chain 'S' and resid 66 through 68 No H-bonds generated for 'chain 'S' and resid 66 through 68' Processing helix chain 'S' and resid 73 through 76 Processing helix chain 'T' and resid 87 through 99 removed outlier: 4.535A pdb=" N GLU T 94 " --> pdb=" O ARG T 90 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASN T 95 " --> pdb=" O SER T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 113 through 126 Processing helix chain 'T' and resid 129 through 137 Processing helix chain 'T' and resid 142 through 175 Processing helix chain 'U' and resid 10 through 20 Processing helix chain 'U' and resid 28 through 35 removed outlier: 4.537A pdb=" N VAL U 32 " --> pdb=" O ALA U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 84 No H-bonds generated for 'chain 'U' and resid 82 through 84' Processing helix chain 'U' and resid 88 through 92 Processing helix chain 'U' and resid 100 through 111 removed outlier: 3.568A pdb=" N LEU U 104 " --> pdb=" O VAL U 100 " (cutoff:3.500A) Processing helix chain 'U' and resid 113 through 117 Processing helix chain 'U' and resid 146 through 159 Processing helix chain 'U' and resid 165 through 196 Processing helix chain 'U' and resid 205 through 232 Processing helix chain 'V' and resid 4 through 8 Processing helix chain 'V' and resid 30 through 37 Processing helix chain 'V' and resid 71 through 78 Processing helix chain 'V' and resid 91 through 147 removed outlier: 4.172A pdb=" N VAL V 95 " --> pdb=" O SER V 91 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS V 145 " --> pdb=" O GLU V 141 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU V 146 " --> pdb=" O LYS V 142 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 161 removed outlier: 4.522A pdb=" N SER V 161 " --> pdb=" O ASP V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 170 through 205 Processing helix chain 'V' and resid 213 through 223 Processing helix chain 'W' and resid 60 through 66 Processing helix chain 'W' and resid 69 through 72 removed outlier: 3.967A pdb=" N THR W 72 " --> pdb=" O LEU W 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 69 through 72' Processing helix chain 'W' and resid 86 through 89 No H-bonds generated for 'chain 'W' and resid 86 through 89' Processing helix chain 'W' and resid 98 through 107 removed outlier: 3.551A pdb=" N LYS W 102 " --> pdb=" O ASN W 98 " (cutoff:3.500A) Processing helix chain 'W' and resid 131 through 139 Processing helix chain 'W' and resid 156 through 169 Processing helix chain 'W' and resid 180 through 183 Processing helix chain 'W' and resid 202 through 215 removed outlier: 3.522A pdb=" N LYS W 207 " --> pdb=" O MET W 203 " (cutoff:3.500A) Processing helix chain 'W' and resid 218 through 223 Processing helix chain 'W' and resid 255 through 260 Processing helix chain 'W' and resid 267 through 281 removed outlier: 3.622A pdb=" N MET W 272 " --> pdb=" O GLY W 269 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS W 273 " --> pdb=" O LYS W 270 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA W 274 " --> pdb=" O LEU W 271 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP W 277 " --> pdb=" O ALA W 274 " (cutoff:3.500A) Processing helix chain 'W' and resid 294 through 299 Processing helix chain 'W' and resid 319 through 329 Processing helix chain 'W' and resid 354 through 358 Processing helix chain 'W' and resid 375 through 383 Processing helix chain 'W' and resid 396 through 408 Processing helix chain 'W' and resid 414 through 417 No H-bonds generated for 'chain 'W' and resid 414 through 417' Processing helix chain 'W' and resid 422 through 432 Processing helix chain 'W' and resid 438 through 446 Processing helix chain 'X' and resid 5 through 18 Processing helix chain 'X' and resid 32 through 36 Processing helix chain 'X' and resid 41 through 45 Processing helix chain 'X' and resid 56 through 62 removed outlier: 3.955A pdb=" N LYS X 60 " --> pdb=" O ARG X 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 71 through 85 Processing helix chain 'Y' and resid 54 through 56 No H-bonds generated for 'chain 'Y' and resid 54 through 56' Processing helix chain 'Y' and resid 62 through 79 removed outlier: 6.630A pdb=" N SER Y 78 " --> pdb=" O ALA Y 74 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU Y 79 " --> pdb=" O ARG Y 75 " (cutoff:3.500A) Processing helix chain 'Y' and resid 84 through 94 removed outlier: 3.782A pdb=" N THR Y 92 " --> pdb=" O ASN Y 88 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR Y 93 " --> pdb=" O ALA Y 89 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 101 through 117 removed outlier: 7.748A pdb=" N GLU Y 112 " --> pdb=" O TYR Y 108 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N GLN Y 113 " --> pdb=" O HIS Y 109 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA Y 115 " --> pdb=" O GLY Y 111 " (cutoff:3.500A) Processing helix chain 'Y' and resid 139 through 160 Processing helix chain 'Y' and resid 162 through 168 removed outlier: 3.809A pdb=" N ALA Y 166 " --> pdb=" O PRO Y 163 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN Y 167 " --> pdb=" O LEU Y 164 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR Y 168 " --> pdb=" O LEU Y 165 " (cutoff:3.500A) Processing helix chain 'Y' and resid 195 through 198 Processing helix chain 'Y' and resid 213 through 226 removed outlier: 3.592A pdb=" N ARG Y 224 " --> pdb=" O ARG Y 220 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N SER Y 225 " --> pdb=" O ILE Y 221 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ARG Y 226 " --> pdb=" O LEU Y 222 " (cutoff:3.500A) Processing helix chain 'Y' and resid 244 through 263 Processing helix chain 'Y' and resid 278 through 285 Processing helix chain 'Y' and resid 301 through 303 No H-bonds generated for 'chain 'Y' and resid 301 through 303' Processing helix chain 'Y' and resid 311 through 317 Processing helix chain 'Z' and resid 29 through 43 Processing helix chain 'Z' and resid 52 through 61 Processing helix chain 'Z' and resid 78 through 89 removed outlier: 4.893A pdb=" N ASP Z 87 " --> pdb=" O ALA Z 83 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ARG Z 88 " --> pdb=" O ARG Z 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 11 through 14 No H-bonds generated for 'chain 'A' and resid 11 through 14' Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 82 through 93 removed outlier: 3.617A pdb=" N ASN A 86 " --> pdb=" O GLY A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 273 removed outlier: 6.752A pdb=" N ASP A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N PHE A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE A 271 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ARG A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N MET A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 Processing helix chain 'B' and resid 170 through 175 removed outlier: 4.052A pdb=" N ILE B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'B' and resid 204 through 209 removed outlier: 4.940A pdb=" N SER B 208 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 241 Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 283 through 286 No H-bonds generated for 'chain 'B' and resid 283 through 286' Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 329 through 338 Processing helix chain 'B' and resid 352 through 354 No H-bonds generated for 'chain 'B' and resid 352 through 354' Processing helix chain 'B' and resid 366 through 391 Processing helix chain '2' and resid 41 through 48 Processing helix chain '2' and resid 53 through 59 removed outlier: 4.668A pdb=" N ASP 2 57 " --> pdb=" O GLU 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 63 through 68 Processing helix chain '2' and resid 71 through 77 Processing helix chain '2' and resid 81 through 95 Processing helix chain '2' and resid 114 through 127 removed outlier: 4.465A pdb=" N LYS 2 118 " --> pdb=" O GLU 2 114 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ALA 2 119 " --> pdb=" O ARG 2 115 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 22 Processing helix chain '3' and resid 31 through 37 Processing helix chain '3' and resid 41 through 53 Processing helix chain '3' and resid 57 through 60 Processing helix chain '3' and resid 63 through 70 Processing helix chain '3' and resid 74 through 96 removed outlier: 5.167A pdb=" N ASN 3 78 " --> pdb=" O LEU 3 75 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASN 3 89 " --> pdb=" O ILE 3 86 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 126 Processing helix chain '3' and resid 132 through 145 Processing helix chain '3' and resid 177 through 179 No H-bonds generated for 'chain '3' and resid 177 through 179' Processing helix chain '3' and resid 191 through 206 Processing helix chain '3' and resid 228 through 235 removed outlier: 5.516A pdb=" N HIS 3 233 " --> pdb=" O HIS 3 229 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASP 3 234 " --> pdb=" O ALA 3 230 " (cutoff:3.500A) Processing helix chain '3' and resid 240 through 249 Processing helix chain '3' and resid 253 through 259 Processing helix chain 'D' and resid 22 through 31 Processing helix chain 'D' and resid 41 through 55 Processing helix chain 'D' and resid 62 through 68 Processing helix chain 'D' and resid 93 through 103 removed outlier: 4.335A pdb=" N PHE D 98 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL D 100 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS D 103 " --> pdb=" O VAL D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'D' and resid 118 through 126 Processing helix chain 'D' and resid 154 through 161 Processing helix chain 'D' and resid 168 through 191 Processing helix chain 'D' and resid 193 through 204 Processing helix chain 'D' and resid 374 through 379 Processing helix chain 'D' and resid 388 through 391 No H-bonds generated for 'chain 'D' and resid 388 through 391' Processing helix chain 'D' and resid 395 through 401 Processing helix chain 'D' and resid 471 through 483 removed outlier: 3.764A pdb=" N ARG D 483 " --> pdb=" O MET D 479 " (cutoff:3.500A) Processing helix chain '4' and resid 34 through 55 removed outlier: 4.217A pdb=" N ASP 4 43 " --> pdb=" O LYS 4 39 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG 4 44 " --> pdb=" O ALA 4 40 " (cutoff:3.500A) Processing helix chain '4' and resid 58 through 60 No H-bonds generated for 'chain '4' and resid 58 through 60' Processing helix chain '4' and resid 64 through 71 Processing helix chain '4' and resid 78 through 95 Processing helix chain '4' and resid 113 through 117 Processing helix chain '4' and resid 130 through 133 No H-bonds generated for 'chain '4' and resid 130 through 133' Processing helix chain '4' and resid 136 through 146 Processing helix chain '4' and resid 149 through 162 Processing helix chain '4' and resid 215 through 229 Processing helix chain '4' and resid 245 through 257 removed outlier: 3.508A pdb=" N ILE 4 252 " --> pdb=" O LYS 4 248 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN 4 257 " --> pdb=" O TYR 4 253 " (cutoff:3.500A) Processing helix chain '4' and resid 277 through 280 No H-bonds generated for 'chain '4' and resid 277 through 280' Processing helix chain '4' and resid 289 through 298 Processing helix chain '4' and resid 302 through 308 Processing helix chain 'E' and resid 18 through 24 removed outlier: 3.559A pdb=" N TYR E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 39 removed outlier: 3.938A pdb=" N LYS E 31 " --> pdb=" O GLU E 27 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N SER E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'E' and resid 137 through 143 Processing helix chain 'E' and resid 190 through 203 Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 244 through 253 Processing helix chain 'E' and resid 268 through 281 Processing helix chain 'E' and resid 286 through 293 Processing helix chain 'E' and resid 297 through 300 No H-bonds generated for 'chain 'E' and resid 297 through 300' Processing helix chain 'F' and resid 18 through 34 Processing helix chain 'F' and resid 75 through 87 Processing helix chain 'F' and resid 110 through 115 Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain '6' and resid 53 through 62 Processing helix chain '6' and resid 90 through 93 No H-bonds generated for 'chain '6' and resid 90 through 93' Processing helix chain '6' and resid 123 through 126 No H-bonds generated for 'chain '6' and resid 123 through 126' Processing helix chain '6' and resid 130 through 134 removed outlier: 3.842A pdb=" N LEU 6 134 " --> pdb=" O LYS 6 130 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 130 through 134' Processing helix chain '6' and resid 151 through 162 Processing helix chain '6' and resid 168 through 174 Processing helix chain '6' and resid 179 through 197 Processing helix chain '6' and resid 203 through 214 Processing helix chain 'G' and resid 92 through 102 Processing helix chain 'G' and resid 112 through 121 Processing helix chain 'G' and resid 127 through 145 Processing helix chain 'G' and resid 149 through 160 Processing helix chain 'G' and resid 185 through 201 Processing helix chain 'G' and resid 208 through 220 Processing helix chain 'G' and resid 225 through 239 Processing helix chain 'G' and resid 241 through 243 No H-bonds generated for 'chain 'G' and resid 241 through 243' Processing helix chain 'H' and resid 3 through 19 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 68 through 70 No H-bonds generated for 'chain 'H' and resid 68 through 70' Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'H' and resid 138 through 143 Processing helix chain 'I' and resid 49 through 64 Processing helix chain 'I' and resid 86 through 92 removed outlier: 3.727A pdb=" N ILE I 92 " --> pdb=" O GLU I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 97 No H-bonds generated for 'chain 'I' and resid 95 through 97' Processing helix chain 'I' and resid 100 through 115 Processing helix chain 'I' and resid 118 through 120 No H-bonds generated for 'chain 'I' and resid 118 through 120' Processing helix chain 'I' and resid 123 through 132 removed outlier: 4.070A pdb=" N GLN I 131 " --> pdb=" O SER I 127 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR I 132 " --> pdb=" O GLU I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 186 No H-bonds generated for 'chain 'I' and resid 183 through 186' Processing helix chain 'I' and resid 190 through 202 Proline residue: I 199 - end of helix Processing helix chain 'I' and resid 220 through 238 removed outlier: 3.960A pdb=" N VAL I 237 " --> pdb=" O LYS I 233 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE I 238 " --> pdb=" O ALA I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 249 removed outlier: 4.423A pdb=" N SER I 244 " --> pdb=" O LEU I 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 28 removed outlier: 3.513A pdb=" N VAL J 27 " --> pdb=" O ASN J 23 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR J 28 " --> pdb=" O VAL J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 68 Processing helix chain 'J' and resid 118 through 130 Processing helix chain 'J' and resid 182 through 192 Processing helix chain 'J' and resid 197 through 199 No H-bonds generated for 'chain 'J' and resid 197 through 199' Processing helix chain 'K' and resid 108 through 116 Processing helix chain 'K' and resid 128 through 131 Processing helix chain 'K' and resid 135 through 139 Processing helix chain 'K' and resid 141 through 157 Processing helix chain 'K' and resid 175 through 184 Processing helix chain 'K' and resid 189 through 192 No H-bonds generated for 'chain 'K' and resid 189 through 192' Processing helix chain 'c' and resid 3 through 19 Processing helix chain 'c' and resid 23 through 36 removed outlier: 3.980A pdb=" N UNK c 28 " --> pdb=" O UNK c 24 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N UNK c 29 " --> pdb=" O UNK c 25 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 57 Processing helix chain 'c' and resid 77 through 92 Processing helix chain 'c' and resid 106 through 123 Processing helix chain 'L' and resid 31 through 35 Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'L' and resid 142 through 145 Processing sheet with id= A, first strand: chain '0' and resid 367 through 371 removed outlier: 7.014A pdb=" N ILE 0 455 " --> pdb=" O ILE 0 370 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU 0 190 " --> pdb=" O ILE 0 164 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASP 0 166 " --> pdb=" O LEU 0 190 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASP 0 192 " --> pdb=" O ASP 0 166 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N GLY 0 168 " --> pdb=" O ASP 0 192 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL 0 194 " --> pdb=" O GLY 0 168 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN 0 258 " --> pdb=" O ALA 0 193 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE 0 195 " --> pdb=" O ASN 0 258 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG 0 260 " --> pdb=" O ILE 0 195 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '0' and resid 402 through 407 Processing sheet with id= C, first strand: chain '0' and resid 502 through 504 Processing sheet with id= D, first strand: chain 'C' and resid 124 through 126 Processing sheet with id= E, first strand: chain 'C' and resid 141 through 144 Processing sheet with id= F, first strand: chain 'C' and resid 323 through 328 removed outlier: 6.853A pdb=" N ASN C 396 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TRP C 327 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS C 394 " --> pdb=" O TRP C 327 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'M' and resid 3 through 5 Processing sheet with id= H, first strand: chain 'P' and resid 6 through 15 removed outlier: 3.554A pdb=" N ARG P 15 " --> pdb=" O SER P 18 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL P 25 " --> pdb=" O VAL P 39 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N VAL P 39 " --> pdb=" O VAL P 25 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP P 64 " --> pdb=" O VAL P 44 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'Q' and resid 72 through 74 removed outlier: 13.932A pdb=" N ASN Q 5 " --> pdb=" O LYS Q 27 " (cutoff:3.500A) removed outlier: 10.703A pdb=" N LYS Q 27 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU Q 7 " --> pdb=" O GLU Q 25 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU Q 25 " --> pdb=" O LEU Q 7 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS Q 21 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 33 through 35 Processing sheet with id= K, first strand: chain 'W' and resid 93 through 95 Processing sheet with id= L, first strand: chain 'W' and resid 387 through 390 removed outlier: 6.176A pdb=" N THR W 341 " --> pdb=" O PHE W 146 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE W 148 " --> pdb=" O THR W 341 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU W 343 " --> pdb=" O ILE W 148 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE W 173 " --> pdb=" O MET W 288 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N THR W 290 " --> pdb=" O ILE W 173 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE W 175 " --> pdb=" O THR W 290 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'W' and resid 191 through 193 Processing sheet with id= N, first strand: chain 'W' and resid 230 through 233 removed outlier: 3.544A pdb=" N TYR W 230 " --> pdb=" O LEU W 248 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'Y' and resid 183 through 186 Processing sheet with id= P, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.540A pdb=" N HIS A 294 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA A 283 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER A 292 " --> pdb=" O ALA A 283 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL A 251 " --> pdb=" O MET A 293 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ALA A 295 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP A 253 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU A 297 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL A 255 " --> pdb=" O LEU A 297 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 64 through 67 removed outlier: 6.835A pdb=" N THR A 76 " --> pdb=" O ASN A 66 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 269 through 271 removed outlier: 6.589A pdb=" N LEU B 319 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU B 249 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 321 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR B 357 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE B 346 " --> pdb=" O TYR B 357 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE B 359 " --> pdb=" O ILE B 346 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 210 through 214 removed outlier: 6.694A pdb=" N ILE B 219 " --> pdb=" O TYR B 211 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU B 213 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '3' and resid 163 through 169 removed outlier: 6.690A pdb=" N GLU 3 157 " --> pdb=" O PRO 3 220 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 130 through 132 removed outlier: 3.895A pdb=" N ASP D 148 " --> pdb=" O TYR D 452 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '4' and resid 196 through 202 removed outlier: 3.514A pdb=" N LEU 4 271 " --> pdb=" O LEU 4 171 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA 4 173 " --> pdb=" O PRO 4 269 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG 4 175 " --> pdb=" O TYR 4 267 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N TYR 4 267 " --> pdb=" O ARG 4 175 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 179 through 186 removed outlier: 6.384A pdb=" N VAL E 171 " --> pdb=" O PRO E 148 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLY E 173 " --> pdb=" O MET E 146 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N MET E 146 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 220 through 224 Processing sheet with id= Y, first strand: chain 'F' and resid 47 through 49 removed outlier: 4.168A pdb=" N LEU F 2 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG F 93 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG F 10 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL F 91 " --> pdb=" O ARG F 10 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 54 through 56 Processing sheet with id= AA, first strand: chain 'F' and resid 38 through 43 removed outlier: 6.687A pdb=" N LEU F 70 " --> pdb=" O ARG F 40 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE F 42 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU F 68 " --> pdb=" O ILE F 42 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '6' and resid 294 through 296 Processing sheet with id= AC, first strand: chain '6' and resid 334 through 336 Processing sheet with id= AD, first strand: chain 'G' and resid 164 through 167 Processing sheet with id= AE, first strand: chain 'H' and resid 23 through 27 removed outlier: 3.676A pdb=" N SER H 47 " --> pdb=" O GLY H 76 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 89 through 91 removed outlier: 6.731A pdb=" N LEU H 128 " --> pdb=" O LEU H 151 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG H 153 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU H 126 " --> pdb=" O ARG H 153 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 154 through 160 Processing sheet with id= AH, first strand: chain 'J' and resid 136 through 142 removed outlier: 6.633A pdb=" N ALA J 113 " --> pdb=" O VAL J 42 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP J 44 " --> pdb=" O ILE J 111 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE J 111 " --> pdb=" O ASP J 44 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN J 46 " --> pdb=" O ARG J 109 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG J 109 " --> pdb=" O GLN J 46 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG J 48 " --> pdb=" O HIS J 107 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS J 107 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS J 108 " --> pdb=" O LEU J 79 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 82 through 88 Processing sheet with id= AJ, first strand: chain 'K' and resid 120 through 127 removed outlier: 6.688A pdb=" N PHE K 91 " --> pdb=" O LYS K 123 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER K 125 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU K 89 " --> pdb=" O SER K 125 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N SER K 127 " --> pdb=" O THR K 87 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR K 87 " --> pdb=" O SER K 127 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS K 75 " --> pdb=" O VAL K 94 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU K 96 " --> pdb=" O VAL K 73 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL K 73 " --> pdb=" O GLU K 96 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL K 167 " --> pdb=" O VAL K 196 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE K 198 " --> pdb=" O VAL K 167 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET K 169 " --> pdb=" O ILE K 198 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ASP K 200 " --> pdb=" O MET K 169 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 123 through 125 removed outlier: 6.817A pdb=" N ARG L 82 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL L 65 " --> pdb=" O ALA L 80 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ALA L 80 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL L 67 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG L 78 " --> pdb=" O VAL L 67 " (cutoff:3.500A) 2387 hydrogen bonds defined for protein. 6786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1013 hydrogen bonds 1746 hydrogen bond angles 0 basepair planarities 453 basepair parallelities 788 stacking parallelities Total time for adding SS restraints: 53.01 Time building geometry restraints manager: 35.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.33: 12924 1.33 - 1.57: 77530 1.57 - 1.82: 3459 1.82 - 2.07: 0 2.07 - 2.32: 12 Bond restraints: 93925 Sorted by residual: bond pdb=" CG PRO 4 310 " pdb=" CD PRO 4 310 " ideal model delta sigma weight residual 1.503 1.080 0.423 3.40e-02 8.65e+02 1.55e+02 bond pdb=" N PRO 4 310 " pdb=" CD PRO 4 310 " ideal model delta sigma weight residual 1.473 1.557 -0.084 1.40e-02 5.10e+03 3.58e+01 bond pdb=" CB PRO 4 310 " pdb=" CG PRO 4 310 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.55e+00 bond pdb=" N PRO 4 310 " pdb=" CA PRO 4 310 " ideal model delta sigma weight residual 1.481 1.438 0.043 1.85e-02 2.92e+03 5.47e+00 bond pdb=" CB VAL V 44 " pdb=" CG2 VAL V 44 " ideal model delta sigma weight residual 1.521 1.595 -0.074 3.30e-02 9.18e+02 4.98e+00 ... (remaining 93920 not shown) Histogram of bond angle deviations from ideal: 72.00 - 85.56: 13 85.56 - 99.13: 5 99.13 - 112.70: 60043 112.70 - 126.27: 68324 126.27 - 139.83: 5746 Bond angle restraints: 134131 Sorted by residual: angle pdb=" N PRO 4 310 " pdb=" CD PRO 4 310 " pdb=" CG PRO 4 310 " ideal model delta sigma weight residual 103.20 82.27 20.93 1.50e+00 4.44e-01 1.95e+02 angle pdb=" CA PRO 4 310 " pdb=" N PRO 4 310 " pdb=" CD PRO 4 310 " ideal model delta sigma weight residual 112.00 98.37 13.63 1.40e+00 5.10e-01 9.47e+01 angle pdb=" CA PRO 4 310 " pdb=" CB PRO 4 310 " pdb=" CG PRO 4 310 " ideal model delta sigma weight residual 104.50 89.32 15.18 1.90e+00 2.77e-01 6.39e+01 angle pdb=" C GLY V 43 " pdb=" N VAL V 44 " pdb=" CA VAL V 44 " ideal model delta sigma weight residual 120.55 132.14 -11.59 1.60e+00 3.91e-01 5.25e+01 angle pdb=" CA PRO W 237 " pdb=" N PRO W 237 " pdb=" CD PRO W 237 " ideal model delta sigma weight residual 112.00 102.96 9.04 1.40e+00 5.10e-01 4.17e+01 ... (remaining 134126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 53738 35.88 - 71.76: 3648 71.76 - 107.64: 295 107.64 - 143.52: 13 143.52 - 179.40: 20 Dihedral angle restraints: 57714 sinusoidal: 37313 harmonic: 20401 Sorted by residual: dihedral pdb=" O4' U a1130 " pdb=" C1' U a1130 " pdb=" N1 U a1130 " pdb=" C2 U a1130 " ideal model delta sinusoidal sigma weight residual -160.00 18.50 -178.50 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U a1448 " pdb=" C1' U a1448 " pdb=" N1 U a1448 " pdb=" C2 U a1448 " ideal model delta sinusoidal sigma weight residual -160.00 8.98 -168.98 1 1.50e+01 4.44e-03 8.45e+01 dihedral pdb=" O4' U a1416 " pdb=" C1' U a1416 " pdb=" N1 U a1416 " pdb=" C2 U a1416 " ideal model delta sinusoidal sigma weight residual -160.00 -9.07 -150.93 1 1.50e+01 4.44e-03 8.00e+01 ... (remaining 57711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.215: 16173 4.215 - 8.430: 0 8.430 - 12.645: 0 12.645 - 16.860: 0 16.860 - 21.075: 4 Chirality restraints: 16177 Sorted by residual: chirality pdb="FE3 SF4 0 701 " pdb=" S1 SF4 0 701 " pdb=" S2 SF4 0 701 " pdb=" S4 SF4 0 701 " both_signs ideal model delta sigma weight residual False -10.55 10.52 -21.08 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE4 SF4 0 701 " pdb=" S1 SF4 0 701 " pdb=" S2 SF4 0 701 " pdb=" S3 SF4 0 701 " both_signs ideal model delta sigma weight residual False 10.55 -10.42 20.97 2.00e-01 2.50e+01 1.10e+04 chirality pdb="FE1 SF4 0 701 " pdb=" S2 SF4 0 701 " pdb=" S3 SF4 0 701 " pdb=" S4 SF4 0 701 " both_signs ideal model delta sigma weight residual False -10.55 10.40 -20.95 2.00e-01 2.50e+01 1.10e+04 ... (remaining 16174 not shown) Planarity restraints: 11387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS Y 53 " 0.061 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO Y 54 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO Y 54 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO Y 54 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP X 70 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" CG ASP X 70 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASP X 70 " -0.023 2.00e-02 2.50e+03 pdb=" OD2 ASP X 70 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN W 236 " -0.064 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO W 237 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO W 237 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO W 237 " -0.051 5.00e-02 4.00e+02 ... (remaining 11384 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 505 2.52 - 3.11: 63975 3.11 - 3.71: 156854 3.71 - 4.30: 226536 4.30 - 4.90: 332630 Nonbonded interactions: 780500 Sorted by model distance: nonbonded pdb=" OG SER E 265 " pdb=" OP1 U a 26 " model vdw 1.924 2.440 nonbonded pdb=" O6 G a1254 " pdb="MG MG a1768 " model vdw 1.957 2.170 nonbonded pdb=" O LEU d 666 " pdb=" OG1 THR d 670 " model vdw 1.971 2.440 nonbonded pdb=" OP2 A a 312 " pdb="MG MG a1754 " model vdw 1.971 2.170 nonbonded pdb=" O ASP U 145 " pdb=" OG SER U 148 " model vdw 1.981 2.440 ... (remaining 780495 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: 5.040 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: 0.070 Extract box with map and model: 18.680 Check model and map are aligned: 1.000 Set scattering table: 0.590 Process input model: 227.170 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.240 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: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 257.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 0.423 93925 Z= 0.202 Angle : 0.624 20.927 134131 Z= 0.328 Chirality : 0.332 21.075 16177 Planarity : 0.005 0.093 11387 Dihedral : 19.828 179.400 44467 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.05 % Allowed : 0.18 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.10), residues: 6722 helix: 1.60 (0.09), residues: 3295 sheet: 0.06 (0.20), residues: 625 loop : -0.03 (0.12), residues: 2802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Y 57 HIS 0.012 0.001 HIS 4 21 PHE 0.038 0.002 PHE d 176 TYR 0.024 0.001 TYR F 128 ARG 0.012 0.001 ARG J 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1175 time to evaluate : 5.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 136 PHE cc_start: 0.5867 (t80) cc_final: 0.5546 (t80) REVERT: 0 288 GLN cc_start: 0.4954 (tm-30) cc_final: 0.4653 (tm-30) REVERT: 0 289 VAL cc_start: 0.5150 (t) cc_final: 0.4611 (p) REVERT: 0 300 LEU cc_start: 0.4564 (tp) cc_final: 0.3958 (tp) REVERT: 5 91 ARG cc_start: 0.5739 (mtt90) cc_final: 0.5425 (mtt90) REVERT: C 53 MET cc_start: 0.7208 (mmt) cc_final: 0.6849 (mmt) REVERT: C 217 SER cc_start: 0.8123 (p) cc_final: 0.7856 (p) REVERT: d 207 LEU cc_start: 0.7151 (mt) cc_final: 0.6937 (mt) REVERT: d 482 LYS cc_start: 0.5127 (ptpt) cc_final: 0.4834 (mptt) REVERT: P 55 LEU cc_start: 0.6646 (mt) cc_final: 0.6342 (mt) REVERT: U 215 GLU cc_start: 0.7215 (mt-10) cc_final: 0.7001 (mt-10) REVERT: W 252 LYS cc_start: 0.7337 (ttpp) cc_final: 0.7113 (tmtt) REVERT: Y 130 ARG cc_start: 0.6922 (ptm160) cc_final: 0.6600 (ttm170) REVERT: Z 17 LYS cc_start: 0.8164 (tttp) cc_final: 0.7880 (tttp) REVERT: B 364 ASP cc_start: 0.7799 (m-30) cc_final: 0.7571 (m-30) REVERT: 3 142 ARG cc_start: 0.6771 (mmm-85) cc_final: 0.6524 (mmm160) REVERT: D 188 GLU cc_start: 0.7317 (tp30) cc_final: 0.6982 (mm-30) REVERT: F 35 ASN cc_start: 0.8002 (m-40) cc_final: 0.7712 (m110) REVERT: 6 331 ASP cc_start: 0.6373 (m-30) cc_final: 0.6125 (m-30) REVERT: G 165 MET cc_start: 0.6795 (ttt) cc_final: 0.6477 (ttt) REVERT: G 227 PHE cc_start: 0.7043 (m-80) cc_final: 0.6759 (m-80) REVERT: I 50 ASN cc_start: 0.7744 (m-40) cc_final: 0.7538 (m-40) REVERT: I 57 ARG cc_start: 0.7445 (mtp85) cc_final: 0.7223 (mtp-110) REVERT: K 76 TYR cc_start: 0.8445 (m-80) cc_final: 0.8162 (m-80) REVERT: L 57 GLN cc_start: 0.8046 (pt0) cc_final: 0.7683 (pt0) outliers start: 3 outliers final: 2 residues processed: 1176 average time/residue: 0.8320 time to fit residues: 1675.0605 Evaluate side-chains 871 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 869 time to evaluate : 6.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 90 ARG Chi-restraints excluded: chain X residue 22 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 835 random chunks: chunk 705 optimal weight: 10.0000 chunk 632 optimal weight: 0.7980 chunk 351 optimal weight: 0.0870 chunk 216 optimal weight: 3.9990 chunk 426 optimal weight: 4.9990 chunk 338 optimal weight: 7.9990 chunk 654 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 397 optimal weight: 10.0000 chunk 487 optimal weight: 3.9990 chunk 758 optimal weight: 10.0000 overall best weight: 2.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 91 ASN 0 305 HIS 5 194 HIS ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 249 GLN C 259 ASN C 296 ASN ** C 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 484 ASN ** M 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 GLN P 27 ASN Q 30 ASN Q 34 ASN Q 227 HIS U 80 ASN U 136 HIS V 29 GLN V 93 GLN V 120 HIS V 192 HIS V 215 GLN ** W 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 58 HIS ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 142 GLN Y 148 HIS Y 229 HIS Y 252 HIS ** Z 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 HIS A 33 HIS A 233 ASN 2 62 ASN 2 83 GLN 2 92 HIS 3 65 HIS 3 199 GLN D 383 HIS D 403 ASN D 449 HIS 4 21 HIS 4 71 ASN 4 160 ASN ** 4 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 ASN E 157 GLN E 198 HIS F 13 ASN F 34 GLN F 112 HIS G 198 GLN ** G 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 GLN I 114 HIS ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.251 93925 Z= 0.288 Angle : 0.751 50.388 134131 Z= 0.440 Chirality : 0.106 6.447 16177 Planarity : 0.005 0.062 11387 Dihedral : 20.206 179.001 30032 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.35 % Allowed : 7.52 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: 1.14 (0.10), residues: 6722 helix: 1.60 (0.09), residues: 3319 sheet: 0.23 (0.20), residues: 610 loop : -0.06 (0.11), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 57 HIS 0.006 0.001 HIS A 33 PHE 0.025 0.002 PHE d 176 TYR 0.023 0.002 TYR 4 202 ARG 0.008 0.001 ARG J 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 908 time to evaluate : 6.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 53 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7658 (mp) REVERT: 5 95 LYS cc_start: 0.5597 (mmtm) cc_final: 0.5372 (mmtt) REVERT: 5 170 PHE cc_start: 0.6171 (m-80) cc_final: 0.5755 (m-80) REVERT: C 53 MET cc_start: 0.7290 (mmt) cc_final: 0.6933 (mmt) REVERT: C 123 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7245 (mmp) REVERT: C 176 MET cc_start: 0.6915 (tmm) cc_final: 0.6599 (tmm) REVERT: C 217 SER cc_start: 0.8335 (p) cc_final: 0.8095 (p) REVERT: d 482 LYS cc_start: 0.5128 (ptpt) cc_final: 0.4858 (mptt) REVERT: R 59 ASP cc_start: 0.8091 (m-30) cc_final: 0.7861 (m-30) REVERT: U 223 LYS cc_start: 0.7985 (tppt) cc_final: 0.7673 (mptt) REVERT: X 71 LEU cc_start: 0.8869 (mt) cc_final: 0.8662 (mp) REVERT: Y 130 ARG cc_start: 0.6882 (ptm160) cc_final: 0.6573 (ttm110) REVERT: Z 17 LYS cc_start: 0.8325 (tttp) cc_final: 0.7930 (tttp) REVERT: A 199 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: B 392 ASN cc_start: 0.7259 (t0) cc_final: 0.7012 (t0) REVERT: F 35 ASN cc_start: 0.7949 (m-40) cc_final: 0.7580 (m110) REVERT: 6 331 ASP cc_start: 0.6429 (m-30) cc_final: 0.6176 (m-30) REVERT: K 76 TYR cc_start: 0.8476 (m-80) cc_final: 0.8216 (m-80) REVERT: K 134 ARG cc_start: 0.7503 (mmt-90) cc_final: 0.7026 (mpt180) outliers start: 83 outliers final: 58 residues processed: 951 average time/residue: 0.8177 time to fit residues: 1339.0355 Evaluate side-chains 890 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 829 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 370 ILE Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 5 residue 258 ILE Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain d residue 519 VAL Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain T residue 123 ILE Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain U residue 203 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 113 LYS Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain W residue 194 ASP Chi-restraints excluded: chain W residue 225 GLU Chi-restraints excluded: chain W residue 254 THR Chi-restraints excluded: chain W residue 324 MET Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 46 SER Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain 3 residue 97 LEU Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain 4 residue 103 THR Chi-restraints excluded: chain 4 residue 286 VAL Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain 6 residue 293 LYS Chi-restraints excluded: chain 6 residue 334 ILE Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 106 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 835 random chunks: chunk 421 optimal weight: 4.9990 chunk 235 optimal weight: 10.0000 chunk 631 optimal weight: 7.9990 chunk 516 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 759 optimal weight: 10.0000 chunk 820 optimal weight: 20.0000 chunk 676 optimal weight: 20.0000 chunk 753 optimal weight: 10.0000 chunk 258 optimal weight: 8.9990 chunk 609 optimal weight: 5.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 212 GLN ** 0 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 168 HIS 5 196 ASN ** C 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 ASN C 174 ASN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN C 304 ASN d 753 ASN ** M 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 HIS ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 GLN R 66 HIS T 136 GLN T 154 HIS U 188 GLN V 93 GLN V 204 HIS ** W 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 310 ASN W 449 HIS ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 142 GLN Y 180 HIS Y 247 ASN Z 28 ASN Z 94 HIS A 233 ASN B 386 ASN 3 9 HIS 3 186 ASN 3 199 GLN D 139 HIS D 203 ASN 4 38 GLN 4 69 HIS 4 229 GLN ** 4 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN 6 46 HIS G 234 HIS H 14 GLN H 34 GLN H 67 ASN I 50 ASN I 114 HIS J 101 ASN J 144 GLN K 79 HIS ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 57 GLN L 77 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.241 93925 Z= 0.514 Angle : 0.905 50.584 134131 Z= 0.507 Chirality : 0.110 6.393 16177 Planarity : 0.006 0.086 11387 Dihedral : 20.414 179.370 30028 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.67 % Allowed : 11.31 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.10), residues: 6722 helix: 0.75 (0.09), residues: 3309 sheet: -0.07 (0.20), residues: 610 loop : -0.44 (0.11), residues: 2803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP 0 344 HIS 0.026 0.002 HIS A 19 PHE 0.029 0.003 PHE d 176 TYR 0.036 0.003 TYR 4 202 ARG 0.009 0.001 ARG Q 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 850 time to evaluate : 5.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 49 ASP cc_start: 0.5715 (m-30) cc_final: 0.5041 (t0) REVERT: 5 53 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7591 (mp) REVERT: 5 159 MET cc_start: 0.5950 (mmm) cc_final: 0.5185 (mtp) REVERT: 5 164 TYR cc_start: 0.5783 (m-80) cc_final: 0.5543 (m-80) REVERT: 5 223 ASN cc_start: 0.2330 (t0) cc_final: 0.2114 (p0) REVERT: 5 320 LYS cc_start: 0.4343 (mtpp) cc_final: 0.3994 (tppt) REVERT: C 53 MET cc_start: 0.7384 (mmt) cc_final: 0.6957 (mmt) REVERT: d 535 ARG cc_start: 0.6936 (mtp-110) cc_final: 0.6363 (mtm-85) REVERT: P 38 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7608 (mt-10) REVERT: R 117 LEU cc_start: 0.8807 (mt) cc_final: 0.8606 (mt) REVERT: U 193 GLU cc_start: 0.7668 (tt0) cc_final: 0.7442 (tt0) REVERT: U 223 LYS cc_start: 0.8059 (tppt) cc_final: 0.7720 (tptt) REVERT: X 54 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7032 (tt) REVERT: Y 50 LEU cc_start: 0.7364 (tp) cc_final: 0.7131 (tp) REVERT: Y 161 GLU cc_start: 0.6977 (tt0) cc_final: 0.6751 (tt0) REVERT: E 105 ILE cc_start: 0.8100 (tp) cc_final: 0.7864 (tp) REVERT: F 36 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7188 (ttm-80) REVERT: I 256 TYR cc_start: 0.8630 (t80) cc_final: 0.8360 (t80) REVERT: K 76 TYR cc_start: 0.8555 (m-80) cc_final: 0.8283 (m-80) REVERT: K 134 ARG cc_start: 0.7573 (mmt-90) cc_final: 0.6997 (mpt180) REVERT: L 54 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7419 (mt0) outliers start: 164 outliers final: 109 residues processed: 953 average time/residue: 0.8150 time to fit residues: 1343.1360 Evaluate side-chains 890 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 777 time to evaluate : 5.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 63 ARG Chi-restraints excluded: chain 0 residue 307 VAL Chi-restraints excluded: chain 0 residue 370 ILE Chi-restraints excluded: chain 0 residue 545 TRP Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 178 VAL Chi-restraints excluded: chain 5 residue 194 HIS Chi-restraints excluded: chain 5 residue 230 ILE Chi-restraints excluded: chain 5 residue 232 VAL Chi-restraints excluded: chain 5 residue 310 GLU Chi-restraints excluded: chain 5 residue 324 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain d residue 301 HIS Chi-restraints excluded: chain d residue 519 VAL Chi-restraints excluded: chain d residue 639 ASN Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 59 VAL Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 43 TYR Chi-restraints excluded: chain Q residue 188 THR Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain T residue 136 GLN Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 138 LEU Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain U residue 203 VAL Chi-restraints excluded: chain V residue 17 THR Chi-restraints excluded: chain V residue 27 THR Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 113 LYS Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 217 LEU Chi-restraints excluded: chain W residue 84 ASP Chi-restraints excluded: chain W residue 194 ASP Chi-restraints excluded: chain W residue 242 VAL Chi-restraints excluded: chain W residue 254 THR Chi-restraints excluded: chain W residue 324 MET Chi-restraints excluded: chain W residue 418 THR Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 46 SER Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 266 THR Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 62 THR Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain 3 residue 70 THR Chi-restraints excluded: chain 3 residue 97 LEU Chi-restraints excluded: chain 3 residue 125 ASP Chi-restraints excluded: chain 3 residue 247 VAL Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain 4 residue 103 THR Chi-restraints excluded: chain 4 residue 198 ILE Chi-restraints excluded: chain 4 residue 199 LEU Chi-restraints excluded: chain 4 residue 286 VAL Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 124 ASP Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain 6 residue 293 LYS Chi-restraints excluded: chain 6 residue 334 ILE Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 205 SER Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 259 VAL Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 140 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 835 random chunks: chunk 750 optimal weight: 8.9990 chunk 571 optimal weight: 3.9990 chunk 394 optimal weight: 0.0270 chunk 84 optimal weight: 2.9990 chunk 362 optimal weight: 1.9990 chunk 510 optimal weight: 5.9990 chunk 762 optimal weight: 10.0000 chunk 807 optimal weight: 5.9990 chunk 398 optimal weight: 50.0000 chunk 722 optimal weight: 20.0000 chunk 217 optimal weight: 7.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 70 GLN 0 77 GLN 0 258 ASN 0 277 GLN 5 194 HIS 5 318 HIS C 88 ASN C 259 ASN Q 163 GLN T 136 GLN U 80 ASN ** W 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 312 GLN ** X 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 247 ASN Y 256 GLN A 19 HIS A 197 ASN 3 186 ASN D 21 ASN ** 4 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN E 96 GLN F 34 GLN 6 108 GLN H 14 GLN I 51 HIS ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.241 93925 Z= 0.289 Angle : 0.757 50.598 134131 Z= 0.444 Chirality : 0.106 6.366 16177 Planarity : 0.004 0.052 11387 Dihedral : 20.247 179.975 30028 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.21 % Allowed : 13.64 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.10), residues: 6722 helix: 1.15 (0.09), residues: 3301 sheet: 0.10 (0.20), residues: 631 loop : -0.28 (0.11), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 0 344 HIS 0.005 0.001 HIS 5 318 PHE 0.031 0.002 PHE d 176 TYR 0.018 0.002 TYR M 42 ARG 0.004 0.000 ARG V 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 842 time to evaluate : 5.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 200 GLU cc_start: 0.4953 (tm-30) cc_final: 0.3776 (tt0) REVERT: 5 49 ASP cc_start: 0.5518 (m-30) cc_final: 0.4873 (t0) REVERT: 5 53 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7576 (mp) REVERT: 5 164 TYR cc_start: 0.5745 (m-80) cc_final: 0.5455 (m-80) REVERT: C 42 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7190 (mm) REVERT: C 53 MET cc_start: 0.7382 (mmt) cc_final: 0.7136 (mmt) REVERT: d 535 ARG cc_start: 0.7067 (mtp-110) cc_final: 0.6425 (mtm-85) REVERT: P 38 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7595 (mt-10) REVERT: S 24 ARG cc_start: 0.3356 (OUTLIER) cc_final: 0.2326 (ptp-170) REVERT: T 137 ARG cc_start: 0.7663 (ttm170) cc_final: 0.7384 (ttt180) REVERT: U 57 ILE cc_start: 0.6485 (mp) cc_final: 0.6230 (mm) REVERT: U 223 LYS cc_start: 0.8144 (tppt) cc_final: 0.7825 (tptt) REVERT: A 199 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: 2 128 ASN cc_start: 0.6412 (OUTLIER) cc_final: 0.5738 (m110) REVERT: 6 58 MET cc_start: 0.8437 (ttt) cc_final: 0.8195 (ttt) REVERT: I 256 TYR cc_start: 0.8513 (t80) cc_final: 0.8225 (t80) REVERT: K 76 TYR cc_start: 0.8565 (m-80) cc_final: 0.8343 (m-80) outliers start: 136 outliers final: 95 residues processed: 921 average time/residue: 0.8152 time to fit residues: 1301.6903 Evaluate side-chains 903 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 803 time to evaluate : 5.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 63 ARG Chi-restraints excluded: chain 0 residue 128 VAL Chi-restraints excluded: chain 0 residue 209 LEU Chi-restraints excluded: chain 0 residue 261 SER Chi-restraints excluded: chain 0 residue 518 GLU Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 5 residue 102 LEU Chi-restraints excluded: chain 5 residue 190 MET Chi-restraints excluded: chain 5 residue 230 ILE Chi-restraints excluded: chain 5 residue 318 HIS Chi-restraints excluded: chain 5 residue 324 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain d residue 450 MET Chi-restraints excluded: chain d residue 519 VAL Chi-restraints excluded: chain d residue 729 CYS Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain P residue 118 GLU Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain S residue 24 ARG Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain T residue 123 ILE Chi-restraints excluded: chain T residue 136 GLN Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 138 LEU Chi-restraints excluded: chain U residue 145 ASP Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain U residue 203 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain W residue 194 ASP Chi-restraints excluded: chain W residue 254 THR Chi-restraints excluded: chain W residue 324 MET Chi-restraints excluded: chain W residue 418 THR Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 46 SER Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 206 THR Chi-restraints excluded: chain Y residue 266 THR Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 62 THR Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 392 ASN Chi-restraints excluded: chain 2 residue 128 ASN Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 97 LEU Chi-restraints excluded: chain 3 residue 167 THR Chi-restraints excluded: chain D residue 21 ASN Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain 4 residue 103 THR Chi-restraints excluded: chain 4 residue 286 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain 6 residue 331 ASP Chi-restraints excluded: chain 6 residue 334 ILE Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 106 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 835 random chunks: chunk 672 optimal weight: 10.0000 chunk 458 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 600 optimal weight: 4.9990 chunk 333 optimal weight: 9.9990 chunk 688 optimal weight: 10.0000 chunk 557 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 412 optimal weight: 0.0570 chunk 724 optimal weight: 10.0000 chunk 203 optimal weight: 0.0770 overall best weight: 4.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 212 GLN ** 0 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 295 HIS 0 387 ASN 0 442 ASN 0 476 ASN ** 5 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 489 GLN ** M 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 GLN N 63 ASN ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 163 GLN T 136 GLN U 68 HIS U 80 ASN V 93 GLN ** W 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 HIS A 233 ASN D 21 ASN E 244 HIS F 34 GLN H 14 GLN ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.240 93925 Z= 0.331 Angle : 0.773 50.602 134131 Z= 0.450 Chirality : 0.106 6.376 16177 Planarity : 0.005 0.052 11387 Dihedral : 20.181 179.932 30026 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.78 % Allowed : 14.27 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: 0.61 (0.10), residues: 6722 helix: 1.11 (0.09), residues: 3316 sheet: 0.15 (0.20), residues: 627 loop : -0.29 (0.11), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 74 HIS 0.027 0.001 HIS 5 318 PHE 0.036 0.002 PHE d 176 TYR 0.019 0.002 TYR M 42 ARG 0.005 0.000 ARG d 531 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 816 time to evaluate : 5.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 279 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6166 (tt) REVERT: 5 49 ASP cc_start: 0.5242 (m-30) cc_final: 0.4971 (t0) REVERT: 5 53 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7641 (mp) REVERT: 5 164 TYR cc_start: 0.5598 (m-80) cc_final: 0.5376 (m-80) REVERT: 5 266 GLU cc_start: 0.1614 (OUTLIER) cc_final: 0.0234 (mm-30) REVERT: C 42 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7109 (mm) REVERT: d 535 ARG cc_start: 0.6915 (mtp-110) cc_final: 0.6230 (mtm-85) REVERT: P 38 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7642 (mt-10) REVERT: S 24 ARG cc_start: 0.3518 (OUTLIER) cc_final: 0.2400 (ptp-170) REVERT: T 137 ARG cc_start: 0.7634 (ttm170) cc_final: 0.7408 (ttt180) REVERT: U 57 ILE cc_start: 0.6589 (mp) cc_final: 0.6332 (mm) REVERT: U 223 LYS cc_start: 0.8139 (tppt) cc_final: 0.7806 (tptt) REVERT: W 174 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7683 (mp) REVERT: 4 208 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.5267 (p90) REVERT: F 36 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7248 (ttm-80) REVERT: L 54 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7334 (mt0) outliers start: 171 outliers final: 117 residues processed: 917 average time/residue: 0.8497 time to fit residues: 1349.8110 Evaluate side-chains 907 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 781 time to evaluate : 5.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 63 ARG Chi-restraints excluded: chain 0 residue 128 VAL Chi-restraints excluded: chain 0 residue 209 LEU Chi-restraints excluded: chain 0 residue 279 LEU Chi-restraints excluded: chain 0 residue 307 VAL Chi-restraints excluded: chain 0 residue 370 ILE Chi-restraints excluded: chain 0 residue 545 TRP Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 5 residue 94 VAL Chi-restraints excluded: chain 5 residue 102 LEU Chi-restraints excluded: chain 5 residue 103 ASN Chi-restraints excluded: chain 5 residue 178 VAL Chi-restraints excluded: chain 5 residue 190 MET Chi-restraints excluded: chain 5 residue 193 LEU Chi-restraints excluded: chain 5 residue 230 ILE Chi-restraints excluded: chain 5 residue 232 VAL Chi-restraints excluded: chain 5 residue 266 GLU Chi-restraints excluded: chain 5 residue 310 GLU Chi-restraints excluded: chain 5 residue 324 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain d residue 519 VAL Chi-restraints excluded: chain d residue 771 VAL Chi-restraints excluded: chain d residue 794 GLU Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain P residue 118 GLU Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain S residue 24 ARG Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain T residue 123 ILE Chi-restraints excluded: chain T residue 136 GLN Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 138 LEU Chi-restraints excluded: chain U residue 145 ASP Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain U residue 203 VAL Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 113 LYS Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain W residue 174 ILE Chi-restraints excluded: chain W residue 254 THR Chi-restraints excluded: chain W residue 324 MET Chi-restraints excluded: chain W residue 418 THR Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 46 SER Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 206 THR Chi-restraints excluded: chain Y residue 266 THR Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 62 THR Chi-restraints excluded: chain Z residue 87 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 293 GLN Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 392 ASN Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 70 THR Chi-restraints excluded: chain 3 residue 97 LEU Chi-restraints excluded: chain 3 residue 125 ASP Chi-restraints excluded: chain 3 residue 247 VAL Chi-restraints excluded: chain D residue 6 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain 4 residue 80 ILE Chi-restraints excluded: chain 4 residue 103 THR Chi-restraints excluded: chain 4 residue 208 PHE Chi-restraints excluded: chain 4 residue 286 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 36 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain 6 residue 331 ASP Chi-restraints excluded: chain 6 residue 334 ILE Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain K residue 125 SER Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 140 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 835 random chunks: chunk 271 optimal weight: 7.9990 chunk 726 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 473 optimal weight: 1.9990 chunk 199 optimal weight: 0.0020 chunk 807 optimal weight: 9.9990 chunk 670 optimal weight: 10.0000 chunk 374 optimal weight: 0.6980 chunk 67 optimal weight: 0.0020 chunk 267 optimal weight: 5.9990 chunk 424 optimal weight: 2.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 277 GLN 0 387 ASN 0 476 ASN ** 5 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 318 HIS C 174 ASN C 259 ASN ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 GLN Q 163 GLN ** R 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 HIS U 80 ASN V 93 GLN W 106 HIS ** W 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 HIS ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS 3 199 GLN ** 4 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN H 14 GLN L 77 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.244 93925 Z= 0.229 Angle : 0.711 50.531 134131 Z= 0.423 Chirality : 0.105 6.322 16177 Planarity : 0.004 0.058 11387 Dihedral : 20.026 179.944 30026 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.89 % Allowed : 15.83 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: 1.05 (0.10), residues: 6722 helix: 1.50 (0.09), residues: 3317 sheet: 0.27 (0.21), residues: 629 loop : -0.09 (0.12), residues: 2776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 243 HIS 0.006 0.001 HIS 5 318 PHE 0.034 0.001 PHE d 176 TYR 0.015 0.001 TYR J 127 ARG 0.014 0.000 ARG Y 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 993 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 877 time to evaluate : 5.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 200 GLU cc_start: 0.4723 (tm-30) cc_final: 0.3901 (tt0) REVERT: 5 53 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7648 (mp) REVERT: 5 89 GLN cc_start: 0.3376 (OUTLIER) cc_final: 0.1994 (mt0) REVERT: 5 164 TYR cc_start: 0.5530 (m-80) cc_final: 0.5265 (m-80) REVERT: 5 194 HIS cc_start: 0.3352 (OUTLIER) cc_final: 0.2839 (m170) REVERT: C 42 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7028 (mt) REVERT: d 482 LYS cc_start: 0.5177 (ptpt) cc_final: 0.4795 (mptt) REVERT: d 501 MET cc_start: 0.7975 (mmt) cc_final: 0.7567 (mmt) REVERT: d 535 ARG cc_start: 0.6773 (mtp-110) cc_final: 0.6110 (mtm-85) REVERT: S 24 ARG cc_start: 0.3471 (OUTLIER) cc_final: 0.2355 (ptp-170) REVERT: U 223 LYS cc_start: 0.8141 (tppt) cc_final: 0.7848 (tptt) REVERT: V 126 GLN cc_start: 0.6838 (mm110) cc_final: 0.6380 (mm-40) REVERT: W 174 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7615 (mp) REVERT: Z 17 LYS cc_start: 0.8572 (tttp) cc_final: 0.8063 (tttp) REVERT: D 475 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6917 (mt-10) REVERT: 4 208 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.5270 (p90) REVERT: E 75 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6734 (tpt) REVERT: 6 112 ASP cc_start: 0.5827 (p0) cc_final: 0.5550 (p0) REVERT: I 256 TYR cc_start: 0.8484 (t80) cc_final: 0.8207 (t80) outliers start: 116 outliers final: 68 residues processed: 947 average time/residue: 0.8109 time to fit residues: 1332.3545 Evaluate side-chains 890 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 814 time to evaluate : 5.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 63 ARG Chi-restraints excluded: chain 0 residue 128 VAL Chi-restraints excluded: chain 0 residue 196 LEU Chi-restraints excluded: chain 0 residue 209 LEU Chi-restraints excluded: chain 0 residue 261 SER Chi-restraints excluded: chain 0 residue 307 VAL Chi-restraints excluded: chain 0 residue 370 ILE Chi-restraints excluded: chain 0 residue 545 TRP Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 5 residue 89 GLN Chi-restraints excluded: chain 5 residue 94 VAL Chi-restraints excluded: chain 5 residue 102 LEU Chi-restraints excluded: chain 5 residue 190 MET Chi-restraints excluded: chain 5 residue 194 HIS Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain d residue 265 THR Chi-restraints excluded: chain d residue 794 GLU Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain S residue 24 ARG Chi-restraints excluded: chain U residue 138 LEU Chi-restraints excluded: chain U residue 145 ASP Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 83 GLN Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain W residue 174 ILE Chi-restraints excluded: chain W residue 324 MET Chi-restraints excluded: chain W residue 418 THR Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 62 THR Chi-restraints excluded: chain Z residue 87 ASP Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain 2 residue 30 THR Chi-restraints excluded: chain 3 residue 70 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain 4 residue 80 ILE Chi-restraints excluded: chain 4 residue 208 PHE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 120 MET Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 140 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 835 random chunks: chunk 778 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 460 optimal weight: 8.9990 chunk 589 optimal weight: 8.9990 chunk 457 optimal weight: 9.9990 chunk 680 optimal weight: 10.0000 chunk 451 optimal weight: 1.9990 chunk 804 optimal weight: 3.9990 chunk 503 optimal weight: 10.0000 chunk 490 optimal weight: 2.9990 chunk 371 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 295 HIS 0 387 ASN 5 72 GLN ** 5 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 489 GLN ** M 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 132 GLN Q 163 GLN ** R 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 HIS U 80 ASN V 93 GLN ** W 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 HIS ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 199 GLN 3 229 HIS ** 4 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN H 14 GLN L 77 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.241 93925 Z= 0.269 Angle : 0.728 50.573 134131 Z= 0.429 Chirality : 0.105 6.346 16177 Planarity : 0.004 0.047 11387 Dihedral : 19.940 179.471 30026 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.38 % Allowed : 15.69 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: 1.05 (0.10), residues: 6722 helix: 1.51 (0.09), residues: 3308 sheet: 0.30 (0.21), residues: 632 loop : -0.11 (0.12), residues: 2782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 74 HIS 0.025 0.001 HIS A 19 PHE 0.035 0.001 PHE d 620 TYR 0.017 0.001 TYR O 218 ARG 0.008 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 825 time to evaluate : 5.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 200 GLU cc_start: 0.4875 (tm-30) cc_final: 0.4023 (tt0) REVERT: 0 279 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6171 (tt) REVERT: 0 306 ILE cc_start: 0.6548 (OUTLIER) cc_final: 0.6315 (tp) REVERT: 5 53 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7652 (mp) REVERT: 5 89 GLN cc_start: 0.3300 (OUTLIER) cc_final: 0.1974 (mt0) REVERT: 5 164 TYR cc_start: 0.5516 (m-80) cc_final: 0.5237 (m-80) REVERT: 5 194 HIS cc_start: 0.3262 (OUTLIER) cc_final: 0.2662 (m170) REVERT: 5 266 GLU cc_start: 0.1405 (OUTLIER) cc_final: 0.0139 (mm-30) REVERT: C 42 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.7051 (mt) REVERT: d 482 LYS cc_start: 0.5257 (ptpt) cc_final: 0.4810 (mptt) REVERT: d 535 ARG cc_start: 0.6828 (mtp-110) cc_final: 0.6148 (mtm-85) REVERT: d 720 ILE cc_start: 0.5965 (OUTLIER) cc_final: 0.5757 (tp) REVERT: O 145 ARG cc_start: 0.7388 (mtt180) cc_final: 0.7095 (mtt90) REVERT: S 24 ARG cc_start: 0.3400 (OUTLIER) cc_final: 0.2251 (ptp-170) REVERT: V 126 GLN cc_start: 0.6838 (mm110) cc_final: 0.6403 (mm-40) REVERT: W 174 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7605 (mp) REVERT: X 54 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6937 (tt) REVERT: Z 17 LYS cc_start: 0.8569 (tttp) cc_final: 0.8065 (tttp) REVERT: A 256 PHE cc_start: 0.4902 (OUTLIER) cc_final: 0.4362 (m-80) REVERT: A 293 MET cc_start: 0.8025 (mtm) cc_final: 0.7737 (mtm) REVERT: 2 128 ASN cc_start: 0.6033 (m110) cc_final: 0.5468 (m110) REVERT: D 475 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6814 (mt-10) REVERT: 4 208 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.5207 (p90) REVERT: E 75 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.6637 (tpt) REVERT: I 256 TYR cc_start: 0.8511 (t80) cc_final: 0.8252 (t80) REVERT: L 54 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7292 (mt0) outliers start: 146 outliers final: 96 residues processed: 916 average time/residue: 0.8174 time to fit residues: 1300.5821 Evaluate side-chains 913 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 802 time to evaluate : 5.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 63 ARG Chi-restraints excluded: chain 0 residue 113 GLN Chi-restraints excluded: chain 0 residue 128 VAL Chi-restraints excluded: chain 0 residue 196 LEU Chi-restraints excluded: chain 0 residue 209 LEU Chi-restraints excluded: chain 0 residue 261 SER Chi-restraints excluded: chain 0 residue 279 LEU Chi-restraints excluded: chain 0 residue 306 ILE Chi-restraints excluded: chain 0 residue 307 VAL Chi-restraints excluded: chain 0 residue 370 ILE Chi-restraints excluded: chain 0 residue 545 TRP Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 5 residue 89 GLN Chi-restraints excluded: chain 5 residue 94 VAL Chi-restraints excluded: chain 5 residue 102 LEU Chi-restraints excluded: chain 5 residue 190 MET Chi-restraints excluded: chain 5 residue 194 HIS Chi-restraints excluded: chain 5 residue 266 GLU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain d residue 265 THR Chi-restraints excluded: chain d residue 301 HIS Chi-restraints excluded: chain d residue 720 ILE Chi-restraints excluded: chain d residue 771 VAL Chi-restraints excluded: chain d residue 794 GLU Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain S residue 24 ARG Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 138 LEU Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 161 SER Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 174 ILE Chi-restraints excluded: chain W residue 324 MET Chi-restraints excluded: chain W residue 418 THR Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 62 THR Chi-restraints excluded: chain Z residue 87 ASP Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain 2 residue 30 THR Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 218 THR Chi-restraints excluded: chain D residue 6 ASN Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain 4 residue 80 ILE Chi-restraints excluded: chain 4 residue 103 THR Chi-restraints excluded: chain 4 residue 119 THR Chi-restraints excluded: chain 4 residue 208 PHE Chi-restraints excluded: chain 4 residue 286 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain 6 residue 331 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 140 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 835 random chunks: chunk 497 optimal weight: 9.9990 chunk 321 optimal weight: 3.9990 chunk 480 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 511 optimal weight: 20.0000 chunk 548 optimal weight: 6.9990 chunk 397 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 632 optimal weight: 0.8980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 295 HIS 0 387 ASN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 296 ASN ** d 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 GLN Q 163 GLN U 68 HIS U 80 ASN V 93 GLN ** W 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 HIS ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 199 GLN ** 4 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN H 14 GLN L 77 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.242 93925 Z= 0.253 Angle : 0.719 50.574 134131 Z= 0.425 Chirality : 0.105 6.336 16177 Planarity : 0.004 0.046 11387 Dihedral : 19.892 179.751 30026 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.26 % Allowed : 16.37 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: 1.09 (0.10), residues: 6722 helix: 1.53 (0.09), residues: 3311 sheet: 0.31 (0.21), residues: 635 loop : -0.06 (0.12), residues: 2776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 243 HIS 0.034 0.001 HIS A 19 PHE 0.036 0.001 PHE d 620 TYR 0.026 0.001 TYR 0 365 ARG 0.010 0.000 ARG Y 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 814 time to evaluate : 5.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 200 GLU cc_start: 0.4684 (tm-30) cc_final: 0.3939 (tt0) REVERT: 0 279 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6227 (tt) REVERT: 0 306 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.6324 (tp) REVERT: 0 326 ILE cc_start: 0.7484 (mm) cc_final: 0.7221 (mm) REVERT: 5 53 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7685 (mp) REVERT: 5 89 GLN cc_start: 0.3314 (OUTLIER) cc_final: 0.1928 (mt0) REVERT: 5 164 TYR cc_start: 0.5477 (m-80) cc_final: 0.5179 (m-80) REVERT: 5 194 HIS cc_start: 0.3332 (OUTLIER) cc_final: 0.2715 (m170) REVERT: C 42 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7079 (mt) REVERT: d 482 LYS cc_start: 0.5251 (ptpt) cc_final: 0.4798 (mptt) REVERT: d 535 ARG cc_start: 0.6801 (mtp-110) cc_final: 0.6150 (mtm-85) REVERT: S 24 ARG cc_start: 0.3320 (OUTLIER) cc_final: 0.2164 (ptp-170) REVERT: V 126 GLN cc_start: 0.6810 (mm110) cc_final: 0.6394 (mm-40) REVERT: W 174 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7607 (mp) REVERT: X 54 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6887 (tt) REVERT: Z 17 LYS cc_start: 0.8589 (tttp) cc_final: 0.8081 (tttp) REVERT: A 256 PHE cc_start: 0.4827 (OUTLIER) cc_final: 0.4305 (m-80) REVERT: A 293 MET cc_start: 0.8020 (mtm) cc_final: 0.7738 (mtm) REVERT: 2 128 ASN cc_start: 0.6114 (m110) cc_final: 0.5551 (m110) REVERT: D 475 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6813 (mt-10) REVERT: 4 208 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.5224 (p90) REVERT: E 75 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.6493 (tpt) REVERT: E 94 GLN cc_start: 0.6837 (mp10) cc_final: 0.6426 (pm20) REVERT: 6 112 ASP cc_start: 0.5730 (p0) cc_final: 0.5466 (p0) REVERT: I 256 TYR cc_start: 0.8493 (t80) cc_final: 0.8268 (t80) REVERT: L 54 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7290 (mt0) outliers start: 139 outliers final: 107 residues processed: 908 average time/residue: 0.9272 time to fit residues: 1472.0562 Evaluate side-chains 919 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 799 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 63 ARG Chi-restraints excluded: chain 0 residue 113 GLN Chi-restraints excluded: chain 0 residue 128 VAL Chi-restraints excluded: chain 0 residue 196 LEU Chi-restraints excluded: chain 0 residue 209 LEU Chi-restraints excluded: chain 0 residue 258 ASN Chi-restraints excluded: chain 0 residue 261 SER Chi-restraints excluded: chain 0 residue 279 LEU Chi-restraints excluded: chain 0 residue 306 ILE Chi-restraints excluded: chain 0 residue 307 VAL Chi-restraints excluded: chain 0 residue 449 LEU Chi-restraints excluded: chain 0 residue 545 TRP Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 5 residue 89 GLN Chi-restraints excluded: chain 5 residue 94 VAL Chi-restraints excluded: chain 5 residue 102 LEU Chi-restraints excluded: chain 5 residue 190 MET Chi-restraints excluded: chain 5 residue 194 HIS Chi-restraints excluded: chain 5 residue 310 GLU Chi-restraints excluded: chain 5 residue 324 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain d residue 265 THR Chi-restraints excluded: chain d residue 771 VAL Chi-restraints excluded: chain d residue 794 GLU Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 55 LEU Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain S residue 24 ARG Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain U residue 138 LEU Chi-restraints excluded: chain U residue 145 ASP Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 161 SER Chi-restraints excluded: chain W residue 84 ASP Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 174 ILE Chi-restraints excluded: chain W residue 254 THR Chi-restraints excluded: chain W residue 324 MET Chi-restraints excluded: chain W residue 418 THR Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 206 THR Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 62 THR Chi-restraints excluded: chain Z residue 87 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain 2 residue 30 THR Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 97 LEU Chi-restraints excluded: chain 3 residue 218 THR Chi-restraints excluded: chain D residue 6 ASN Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain 4 residue 80 ILE Chi-restraints excluded: chain 4 residue 103 THR Chi-restraints excluded: chain 4 residue 119 THR Chi-restraints excluded: chain 4 residue 208 PHE Chi-restraints excluded: chain 4 residue 286 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain 6 residue 331 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 61 LEU Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 140 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 835 random chunks: chunk 732 optimal weight: 10.0000 chunk 771 optimal weight: 30.0000 chunk 703 optimal weight: 10.0000 chunk 749 optimal weight: 10.0000 chunk 770 optimal weight: 20.0000 chunk 451 optimal weight: 2.9990 chunk 326 optimal weight: 10.0000 chunk 588 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 677 optimal weight: 10.0000 chunk 709 optimal weight: 10.0000 overall best weight: 7.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 96 HIS 0 284 GLN 0 295 HIS 0 387 ASN ** 5 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 78 ASN ** N 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 163 GLN R 133 GLN V 93 GLN W 62 ASN ** W 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 449 HIS ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 GLN H 14 GLN ** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 GLN L 124 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.238 93925 Z= 0.494 Angle : 0.876 50.704 134131 Z= 0.492 Chirality : 0.109 6.438 16177 Planarity : 0.006 0.089 11387 Dihedral : 20.091 178.415 30026 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.52 % Allowed : 16.57 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: 0.31 (0.10), residues: 6722 helix: 0.82 (0.09), residues: 3323 sheet: 0.09 (0.20), residues: 623 loop : -0.40 (0.11), residues: 2776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 74 HIS 0.012 0.002 HIS 0 295 PHE 0.039 0.003 PHE d 620 TYR 0.025 0.003 TYR M 42 ARG 0.010 0.001 ARG I 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 786 time to evaluate : 5.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 200 GLU cc_start: 0.5191 (tm-30) cc_final: 0.4345 (tt0) REVERT: 0 279 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6297 (tt) REVERT: 5 53 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7627 (mp) REVERT: 5 89 GLN cc_start: 0.3025 (OUTLIER) cc_final: 0.1896 (mt0) REVERT: 5 164 TYR cc_start: 0.5440 (m-80) cc_final: 0.5144 (m-80) REVERT: 5 266 GLU cc_start: 0.1425 (OUTLIER) cc_final: 0.0122 (mm-30) REVERT: C 42 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7316 (mm) REVERT: d 535 ARG cc_start: 0.6727 (mtp-110) cc_final: 0.6160 (mtm-85) REVERT: S 24 ARG cc_start: 0.3731 (OUTLIER) cc_final: 0.2347 (ptp-170) REVERT: U 137 MET cc_start: 0.8309 (ttm) cc_final: 0.8009 (ttm) REVERT: X 33 LYS cc_start: 0.6569 (pttt) cc_final: 0.6159 (pttt) REVERT: X 54 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7004 (tt) REVERT: X 65 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6786 (m-30) REVERT: A 256 PHE cc_start: 0.5053 (OUTLIER) cc_final: 0.4576 (m-80) REVERT: 2 128 ASN cc_start: 0.6272 (OUTLIER) cc_final: 0.5700 (m110) REVERT: D 38 SER cc_start: 0.8826 (p) cc_final: 0.8561 (m) REVERT: 4 208 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.5188 (p90) REVERT: E 75 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.6999 (tpt) REVERT: I 256 TYR cc_start: 0.8627 (t80) cc_final: 0.8396 (t80) REVERT: L 54 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7392 (mt0) outliers start: 155 outliers final: 119 residues processed: 892 average time/residue: 0.8176 time to fit residues: 1261.1208 Evaluate side-chains 900 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 768 time to evaluate : 5.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 63 ARG Chi-restraints excluded: chain 0 residue 128 VAL Chi-restraints excluded: chain 0 residue 209 LEU Chi-restraints excluded: chain 0 residue 261 SER Chi-restraints excluded: chain 0 residue 279 LEU Chi-restraints excluded: chain 0 residue 307 VAL Chi-restraints excluded: chain 0 residue 370 ILE Chi-restraints excluded: chain 0 residue 449 LEU Chi-restraints excluded: chain 0 residue 545 TRP Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 5 residue 89 GLN Chi-restraints excluded: chain 5 residue 94 VAL Chi-restraints excluded: chain 5 residue 102 LEU Chi-restraints excluded: chain 5 residue 103 ASN Chi-restraints excluded: chain 5 residue 190 MET Chi-restraints excluded: chain 5 residue 194 HIS Chi-restraints excluded: chain 5 residue 230 ILE Chi-restraints excluded: chain 5 residue 232 VAL Chi-restraints excluded: chain 5 residue 266 GLU Chi-restraints excluded: chain 5 residue 293 GLN Chi-restraints excluded: chain 5 residue 310 GLU Chi-restraints excluded: chain 5 residue 324 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain d residue 265 THR Chi-restraints excluded: chain d residue 301 HIS Chi-restraints excluded: chain d residue 519 VAL Chi-restraints excluded: chain d residue 771 VAL Chi-restraints excluded: chain d residue 794 GLU Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 36 GLU Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain S residue 24 ARG Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 138 LEU Chi-restraints excluded: chain U residue 145 ASP Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain U residue 207 GLU Chi-restraints excluded: chain U residue 211 GLN Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 161 SER Chi-restraints excluded: chain W residue 84 ASP Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 254 THR Chi-restraints excluded: chain W residue 324 MET Chi-restraints excluded: chain W residue 418 THR Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 93 THR Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 206 THR Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 62 THR Chi-restraints excluded: chain Z residue 87 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain 2 residue 30 THR Chi-restraints excluded: chain 2 residue 128 ASN Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 76 GLN Chi-restraints excluded: chain 3 residue 97 LEU Chi-restraints excluded: chain 3 residue 218 THR Chi-restraints excluded: chain D residue 6 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain 4 residue 80 ILE Chi-restraints excluded: chain 4 residue 103 THR Chi-restraints excluded: chain 4 residue 119 THR Chi-restraints excluded: chain 4 residue 208 PHE Chi-restraints excluded: chain 4 residue 286 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 104 GLN Chi-restraints excluded: chain 6 residue 331 ASP Chi-restraints excluded: chain 6 residue 334 ILE Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 140 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 835 random chunks: chunk 747 optimal weight: 10.0000 chunk 492 optimal weight: 3.9990 chunk 793 optimal weight: 4.9990 chunk 484 optimal weight: 0.3980 chunk 376 optimal weight: 1.9990 chunk 551 optimal weight: 0.0670 chunk 831 optimal weight: 3.9990 chunk 765 optimal weight: 7.9990 chunk 662 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 511 optimal weight: 10.0000 overall best weight: 2.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 295 HIS 0 387 ASN C 259 ASN ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 GLN Q 163 GLN Q 187 GLN U 80 ASN V 215 GLN ** W 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 449 HIS ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 199 GLN ** 4 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN H 14 GLN L 77 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.244 93925 Z= 0.254 Angle : 0.739 50.595 134131 Z= 0.434 Chirality : 0.105 6.348 16177 Planarity : 0.004 0.067 11387 Dihedral : 19.979 179.990 30026 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.90 % Allowed : 17.23 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: 0.75 (0.10), residues: 6722 helix: 1.23 (0.09), residues: 3319 sheet: 0.15 (0.21), residues: 625 loop : -0.22 (0.12), residues: 2778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 0 344 HIS 0.006 0.001 HIS 5 318 PHE 0.046 0.001 PHE d 620 TYR 0.020 0.001 TYR 0 365 ARG 0.008 0.000 ARG B 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13444 Ramachandran restraints generated. 6722 Oldfield, 0 Emsley, 6722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 806 time to evaluate : 5.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 200 GLU cc_start: 0.4725 (tm-30) cc_final: 0.4077 (tt0) REVERT: 0 279 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6169 (tt) REVERT: 0 288 GLN cc_start: 0.6215 (tm-30) cc_final: 0.6012 (tm-30) REVERT: 0 326 ILE cc_start: 0.7506 (mm) cc_final: 0.7227 (mm) REVERT: 5 53 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7872 (mp) REVERT: 5 89 GLN cc_start: 0.3075 (OUTLIER) cc_final: 0.1708 (mt0) REVERT: 5 164 TYR cc_start: 0.5569 (m-80) cc_final: 0.5284 (m-80) REVERT: 5 266 GLU cc_start: 0.1425 (OUTLIER) cc_final: 0.0148 (mm-30) REVERT: C 42 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7124 (mm) REVERT: C 329 ILE cc_start: 0.5339 (mp) cc_final: 0.4990 (mt) REVERT: d 535 ARG cc_start: 0.6736 (mtp-110) cc_final: 0.6100 (mtm-85) REVERT: S 24 ARG cc_start: 0.3693 (OUTLIER) cc_final: 0.2699 (ptp-170) REVERT: V 126 GLN cc_start: 0.6783 (mm110) cc_final: 0.6389 (mm-40) REVERT: X 33 LYS cc_start: 0.6489 (pttt) cc_final: 0.6014 (pttt) REVERT: X 37 GLU cc_start: 0.7017 (tp30) cc_final: 0.6770 (tp30) REVERT: X 54 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6936 (tt) REVERT: Z 17 LYS cc_start: 0.8696 (tttp) cc_final: 0.8207 (tttp) REVERT: A 256 PHE cc_start: 0.4920 (OUTLIER) cc_final: 0.4440 (m-80) REVERT: A 293 MET cc_start: 0.8051 (mtm) cc_final: 0.7823 (mtm) REVERT: 2 128 ASN cc_start: 0.6164 (m110) cc_final: 0.5593 (m110) REVERT: D 475 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6854 (mt-10) REVERT: 4 208 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.5350 (p90) REVERT: E 75 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.6915 (tpt) REVERT: 6 112 ASP cc_start: 0.5783 (p0) cc_final: 0.5554 (p0) REVERT: L 54 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7327 (mt0) outliers start: 117 outliers final: 96 residues processed: 884 average time/residue: 0.8262 time to fit residues: 1262.0993 Evaluate side-chains 896 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 789 time to evaluate : 5.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 63 ARG Chi-restraints excluded: chain 0 residue 128 VAL Chi-restraints excluded: chain 0 residue 196 LEU Chi-restraints excluded: chain 0 residue 209 LEU Chi-restraints excluded: chain 0 residue 261 SER Chi-restraints excluded: chain 0 residue 279 LEU Chi-restraints excluded: chain 0 residue 307 VAL Chi-restraints excluded: chain 0 residue 449 LEU Chi-restraints excluded: chain 0 residue 518 GLU Chi-restraints excluded: chain 0 residue 545 TRP Chi-restraints excluded: chain 5 residue 53 ILE Chi-restraints excluded: chain 5 residue 58 ASP Chi-restraints excluded: chain 5 residue 89 GLN Chi-restraints excluded: chain 5 residue 94 VAL Chi-restraints excluded: chain 5 residue 102 LEU Chi-restraints excluded: chain 5 residue 190 MET Chi-restraints excluded: chain 5 residue 194 HIS Chi-restraints excluded: chain 5 residue 266 GLU Chi-restraints excluded: chain 5 residue 310 GLU Chi-restraints excluded: chain 5 residue 324 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain d residue 265 THR Chi-restraints excluded: chain d residue 794 GLU Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 90 ASP Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 160 THR Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 105 SER Chi-restraints excluded: chain R residue 106 THR Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain S residue 24 ARG Chi-restraints excluded: chain S residue 41 THR Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 138 LEU Chi-restraints excluded: chain U residue 145 ASP Chi-restraints excluded: chain U residue 185 THR Chi-restraints excluded: chain V residue 36 VAL Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain V residue 161 SER Chi-restraints excluded: chain W residue 84 ASP Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 254 THR Chi-restraints excluded: chain W residue 324 MET Chi-restraints excluded: chain W residue 418 THR Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 15 SER Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 22 ILE Chi-restraints excluded: chain Z residue 23 ILE Chi-restraints excluded: chain Z residue 62 THR Chi-restraints excluded: chain Z residue 87 ASP Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 256 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain 2 residue 30 THR Chi-restraints excluded: chain 3 residue 67 LEU Chi-restraints excluded: chain 3 residue 97 LEU Chi-restraints excluded: chain 3 residue 218 THR Chi-restraints excluded: chain D residue 6 ASN Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain 4 residue 80 ILE Chi-restraints excluded: chain 4 residue 103 THR Chi-restraints excluded: chain 4 residue 119 THR Chi-restraints excluded: chain 4 residue 208 PHE Chi-restraints excluded: chain 4 residue 286 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 287 ASP Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 306 SER Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain 6 residue 331 ASP Chi-restraints excluded: chain G residue 156 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 183 LEU Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 147 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 253 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain K residue 90 THR Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 75 SER Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 140 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 835 random chunks: chunk 406 optimal weight: 3.9990 chunk 526 optimal weight: 1.9990 chunk 705 optimal weight: 10.0000 chunk 202 optimal weight: 0.0570 chunk 610 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 184 optimal weight: 30.0000 chunk 663 optimal weight: 10.0000 chunk 277 optimal weight: 0.9980 chunk 681 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 295 HIS 0 387 ASN ** C 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 ASN V 93 GLN ** W 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 247 ASN ** A 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 169 ASN ** 4 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN H 14 GLN L 77 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.115694 restraints weight = 145202.812| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.63 r_work: 0.3146 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.243 93925 Z= 0.234 Angle : 0.709 50.548 134131 Z= 0.421 Chirality : 0.105 6.322 16177 Planarity : 0.004 0.050 11387 Dihedral : 19.759 179.702 30026 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.72 % Allowed : 17.62 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.63 % 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: 1.10 (0.10), residues: 6722 helix: 1.55 (0.09), residues: 3318 sheet: 0.26 (0.21), residues: 636 loop : -0.06 (0.12), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 243 HIS 0.009 0.001 HIS 0 295 PHE 0.046 0.001 PHE d 620 TYR 0.017 0.001 TYR G 142 ARG 0.016 0.000 ARG Y 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20992.73 seconds wall clock time: 371 minutes 2.17 seconds (22262.17 seconds total)