Starting phenix.real_space_refine on Wed Mar 20 04:14:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdu_37465/03_2024/8wdu_37465_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdu_37465/03_2024/8wdu_37465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdu_37465/03_2024/8wdu_37465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdu_37465/03_2024/8wdu_37465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdu_37465/03_2024/8wdu_37465_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wdu_37465/03_2024/8wdu_37465_updated.pdb" } resolution = 2.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 8 Type Number sf(0) Gaussians Ca 6 9.91 5 Fe 5 7.16 5 P 21 5.49 5 Mg 37 5.21 5 S 96 5.16 5 C 18084 2.51 5 N 3529 2.21 5 O 4496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 76": "OD1" <-> "OD2" Residue "L GLU 88": "OE1" <-> "OE2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "M GLU 138": "OE1" <-> "OE2" Residue "M GLU 309": "OE1" <-> "OE2" Residue "A PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 13": "OD1" <-> "OD2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 13": "OD1" <-> "OD2" Residue "F PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 13": "OE1" <-> "OE2" Residue "G PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 13": "OD1" <-> "OD2" Residue "K PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "T GLU 17": "OE1" <-> "OE2" Residue "U GLU 41": "OE1" <-> "OE2" Residue "U GLU 46": "OE1" <-> "OE2" Residue "V GLU 17": "OE1" <-> "OE2" Residue "V PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 4": "OD1" <-> "OD2" Residue "Y ASP 4": "OD1" <-> "OD2" Residue "Z PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 13": "OD1" <-> "OD2" Residue "4 GLU 17": "OE1" <-> "OE2" Residue "5 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 13": "OD1" <-> "OD2" Residue "8 GLU 14": "OE1" <-> "OE2" Residue "8 GLU 17": "OE1" <-> "OE2" Residue "0 GLU 12": "OE1" <-> "OE2" Residue "0 GLU 14": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26274 Number of models: 1 Model: "" Number of chains: 98 Chain: "C" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2429 Classifications: {'peptide': 311} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 283} Chain: "L" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2210 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "M" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2533 Classifications: {'peptide': 318} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 298} Chain: "H" Number of atoms: 1993 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 259, 1991 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 235} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 259, 1991 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 235} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2041 Chain: "A" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 397 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Chain: "E" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "F" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 397 Classifications: {'peptide': 49} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 45} Chain: "G" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 335 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "I" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 324 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "O" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 41} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "Q" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 331 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "S" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Chain: "T" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "U" Number of atoms: 407 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Conformer: "B" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} bond proxies already assigned to first conformer: 408 Chain: "V" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 335 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "W" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 402 Classifications: {'peptide': 50} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 46} Chain: "X" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "Y" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 470 Classifications: {'peptide': 59} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 54} Chain breaks: 1 Chain: "Z" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 343 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "1" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "2" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 339 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "3" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 498 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 57} Chain: "4" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 345 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "5" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 355 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "6" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 320 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "7" Number of atoms: 359 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 39} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 42, 351 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 39} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 354 Chain: "8" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 339 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "9" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 359 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "0" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 251 Unusual residues: {' MG': 1, 'HEM': 4, 'PGV': 1, 'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PLM:plan-1': 1, 'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 552 Unusual residues: {'BCL': 2, 'BPH': 1, 'CDL': 1, 'LMT': 1, 'PGV': 3, 'UQ8': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 88 Planarities with less than four sites: {'PGV:plan-3': 3, 'UQ8:plan-6': 1, 'UQ8:plan-7': 1, 'UQ8:plan-8': 1, 'UQ8:plan-9': 1} Unresolved non-hydrogen planarities: 31 Chain: "M" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 515 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CDL': 2, 'CRT': 1, 'LMT': 2, 'MQ8': 1, 'PGV': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'CDL': 1, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'BCL': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PGV:plan-3': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 125 Unusual residues: {' CA': 1, 'BCL': 1, 'CDL': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 42 Chain: "E" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {' CA': 1, 'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'BCL': 1, 'LDA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'BCL': 1, 'LDA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {' CA': 1, 'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "T" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {' CA': 1, 'BCL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 111 Unusual residues: {' CA': 1, 'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "1" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'BCL': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "2" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCL': 1, 'CRT': 1, 'LMT': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "5" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "6" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 136 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "9" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "0" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Classifications: {'water': 119} Link IDs: {None: 118} Chain: "L" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Classifications: {'water': 50} Link IDs: {None: 49} Chain: "M" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "T" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "V" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Y" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "3" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "9" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 16.71, per 1000 atoms: 0.64 Number of scatterers: 26274 At special positions: 0 Unit cell: (132.714, 121.806, 135.138, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 5 26.01 Ca 6 19.99 S 96 16.00 P 21 15.00 Mg 37 11.99 O 4496 8.00 N 3529 7.00 C 18084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=50, symmetry=0 Number of additional bonds: simple=50, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.35 Conformation dependent library (CDL) restraints added in 4.1 seconds 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4774 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 107 helices and 5 sheets defined 60.2% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.78 Creating SS restraints... Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 72 through 75 No H-bonds generated for 'chain 'C' and resid 72 through 75' Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 122 through 140 Processing helix chain 'C' and resid 142 through 145 No H-bonds generated for 'chain 'C' and resid 142 through 145' Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 226 through 243 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 264 through 282 Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 317 through 320 Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 328 through 330 No H-bonds generated for 'chain 'C' and resid 328 through 330' Processing helix chain 'L' and resid 8 through 10 No H-bonds generated for 'chain 'L' and resid 8 through 10' Processing helix chain 'L' and resid 33 through 56 Processing helix chain 'L' and resid 77 through 79 No H-bonds generated for 'chain 'L' and resid 77 through 79' Processing helix chain 'L' and resid 86 through 88 No H-bonds generated for 'chain 'L' and resid 86 through 88' Processing helix chain 'L' and resid 90 through 117 Processing helix chain 'L' and resid 122 through 138 removed outlier: 3.590A pdb=" N PHE L 129 " --> pdb=" O PHE L 125 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA L 130 " --> pdb=" O ALA L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 145 Processing helix chain 'L' and resid 148 through 150 No H-bonds generated for 'chain 'L' and resid 148 through 150' Processing helix chain 'L' and resid 158 through 170 removed outlier: 3.995A pdb=" N PHE L 170 " --> pdb=" O VAL L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 175 No H-bonds generated for 'chain 'L' and resid 173 through 175' Processing helix chain 'L' and resid 177 through 204 Processing helix chain 'L' and resid 215 through 226 removed outlier: 3.667A pdb=" N PHE L 222 " --> pdb=" O GLU L 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 255 Processing helix chain 'L' and resid 265 through 273 removed outlier: 4.041A pdb=" N TRP L 269 " --> pdb=" O TRP L 265 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN L 270 " --> pdb=" O PRO L 266 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TRP L 271 " --> pdb=" O GLU L 267 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TRP L 272 " --> pdb=" O TRP L 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 43 removed outlier: 3.722A pdb=" N ILE M 43 " --> pdb=" O TRP M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 79 Processing helix chain 'M' and resid 83 through 88 Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 109 through 111 No H-bonds generated for 'chain 'M' and resid 109 through 111' Processing helix chain 'M' and resid 113 through 140 Processing helix chain 'M' and resid 145 through 161 Processing helix chain 'M' and resid 163 through 167 Processing helix chain 'M' and resid 171 through 173 No H-bonds generated for 'chain 'M' and resid 171 through 173' Processing helix chain 'M' and resid 179 through 192 Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'M' and resid 200 through 229 removed outlier: 4.585A pdb=" N ARG M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N PHE M 229 " --> pdb=" O ALA M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 256 Processing helix chain 'M' and resid 264 through 286 removed outlier: 3.801A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 300 Processing helix chain 'M' and resid 316 through 318 No H-bonds generated for 'chain 'M' and resid 316 through 318' Processing helix chain 'H' and resid 11 through 36 removed outlier: 3.718A pdb=" N ARG H 36 " --> pdb=" O ARG H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 48 Processing helix chain 'H' and resid 70 through 72 No H-bonds generated for 'chain 'H' and resid 70 through 72' Processing helix chain 'H' and resid 106 through 108 No H-bonds generated for 'chain 'H' and resid 106 through 108' Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 197 through 199 No H-bonds generated for 'chain 'H' and resid 197 through 199' Processing helix chain 'H' and resid 217 through 221 removed outlier: 3.513A pdb=" N ALA H 220 " --> pdb=" O ALA H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 249 removed outlier: 3.638A pdb=" N GLY H 246 " --> pdb=" O TYR H 242 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS H 247 " --> pdb=" O TYR H 243 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU H 248 " --> pdb=" O ALA H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 255 Processing helix chain 'A' and resid 7 through 10 Processing helix chain 'A' and resid 14 through 38 Processing helix chain 'B' and resid 12 through 43 Processing helix chain 'D' and resid 5 through 11 Processing helix chain 'D' and resid 14 through 38 Processing helix chain 'E' and resid 12 through 43 removed outlier: 3.526A pdb=" N LYS E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 10 Processing helix chain 'F' and resid 14 through 38 Processing helix chain 'G' and resid 12 through 43 Processing helix chain 'I' and resid 7 through 10 removed outlier: 3.508A pdb=" N GLN I 10 " --> pdb=" O LYS I 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 7 through 10' Processing helix chain 'I' and resid 14 through 38 Processing helix chain 'J' and resid 12 through 43 Processing helix chain 'K' and resid 14 through 38 Processing helix chain 'N' and resid 12 through 43 removed outlier: 4.004A pdb=" N GLU N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE N 21 " --> pdb=" O GLU N 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 10 Processing helix chain 'O' and resid 14 through 38 Processing helix chain 'P' and resid 12 through 43 Processing helix chain 'Q' and resid 7 through 9 No H-bonds generated for 'chain 'Q' and resid 7 through 9' Processing helix chain 'Q' and resid 14 through 38 Processing helix chain 'R' and resid 12 through 43 Processing helix chain 'S' and resid 7 through 10 Processing helix chain 'S' and resid 14 through 37 Processing helix chain 'T' and resid 12 through 43 Processing helix chain 'U' and resid 5 through 10 removed outlier: 3.824A pdb=" N ILE U 8 " --> pdb=" O LEU U 5 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP U 9 " --> pdb=" O TRP U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 38 Processing helix chain 'V' and resid 14 through 43 removed outlier: 3.555A pdb=" N HIS V 19 " --> pdb=" O ALA V 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 10 removed outlier: 3.574A pdb=" N TRP W 9 " --> pdb=" O TRP W 6 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU W 10 " --> pdb=" O LYS W 7 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 38 Processing helix chain 'X' and resid 12 through 43 removed outlier: 3.521A pdb=" N GLY X 20 " --> pdb=" O LYS X 16 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE X 21 " --> pdb=" O GLU X 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 10 removed outlier: 3.610A pdb=" N TRP Y 9 " --> pdb=" O TRP Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 37 Processing helix chain 'Z' and resid 12 through 43 removed outlier: 3.564A pdb=" N GLU Z 17 " --> pdb=" O GLU Z 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY Z 20 " --> pdb=" O LYS Z 16 " (cutoff:3.500A) Processing helix chain '1' and resid 7 through 11 Processing helix chain '1' and resid 14 through 38 Processing helix chain '2' and resid 12 through 43 removed outlier: 3.600A pdb=" N GLU 2 17 " --> pdb=" O GLN 2 13 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL 2 23 " --> pdb=" O HIS 2 19 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLN 2 24 " --> pdb=" O GLY 2 20 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 11 Processing helix chain '3' and resid 14 through 38 Processing helix chain '3' and resid 44 through 46 No H-bonds generated for 'chain '3' and resid 44 through 46' Processing helix chain '4' and resid 14 through 43 Processing helix chain '5' and resid 7 through 11 Processing helix chain '5' and resid 14 through 38 Processing helix chain '5' and resid 40 through 42 No H-bonds generated for 'chain '5' and resid 40 through 42' Processing helix chain '6' and resid 12 through 43 Processing helix chain '7' and resid 7 through 11 Processing helix chain '7' and resid 14 through 38 removed outlier: 3.967A pdb=" N VAL 7 19 " --> pdb=" O ARG 7 15 " (cutoff:3.500A) Processing helix chain '8' and resid 14 through 43 Processing helix chain '9' and resid 7 through 11 Processing helix chain '9' and resid 14 through 38 Processing helix chain '0' and resid 12 through 43 Processing sheet with id= A, first strand: chain 'C' and resid 29 through 32 Processing sheet with id= B, first strand: chain 'H' and resid 66 through 68 Processing sheet with id= C, first strand: chain 'H' and resid 89 through 91 Processing sheet with id= D, first strand: chain 'H' and resid 133 through 135 removed outlier: 6.788A pdb=" N GLU H 183 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL H 170 " --> pdb=" O TYR H 181 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR H 181 " --> pdb=" O VAL H 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 201 through 203 removed outlier: 6.463A pdb=" N THR H 155 " --> pdb=" O VAL H 209 " (cutoff:3.500A) 1153 hydrogen bonds defined for protein. 3364 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.35 Time building geometry restraints manager: 13.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 9182 1.38 - 1.56: 17396 1.56 - 1.75: 43 1.75 - 1.93: 180 1.93 - 2.11: 156 Bond restraints: 26957 Sorted by residual: bond pdb=" CB7 CDL D 101 " pdb=" OB8 CDL D 101 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL M 407 " pdb=" OA8 CDL M 407 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CA7 CDL M 409 " pdb=" OA8 CDL M 409 " ideal model delta sigma weight residual 1.334 1.453 -0.119 1.10e-02 8.26e+03 1.17e+02 bond pdb=" CB7 CDL L 311 " pdb=" OB8 CDL L 311 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 bond pdb=" CA7 CDL L 311 " pdb=" OA8 CDL L 311 " ideal model delta sigma weight residual 1.334 1.451 -0.117 1.10e-02 8.26e+03 1.13e+02 ... (remaining 26952 not shown) Histogram of bond angle deviations from ideal: 82.41 - 101.81: 447 101.81 - 121.20: 29671 121.20 - 140.60: 6838 140.60 - 160.00: 38 160.00 - 179.39: 80 Bond angle restraints: 37074 Sorted by residual: angle pdb=" N PRO Y 59 " pdb=" CD PRO Y 59 " pdb=" CG PRO Y 59 " ideal model delta sigma weight residual 103.20 84.37 18.83 1.50e+00 4.44e-01 1.58e+02 angle pdb=" CA PRO Y 59 " pdb=" CB PRO Y 59 " pdb=" CG PRO Y 59 " ideal model delta sigma weight residual 104.50 86.85 17.65 1.90e+00 2.77e-01 8.63e+01 angle pdb=" C39 CRT V 102 " pdb=" C38 CRT V 102 " pdb=" O2 CRT V 102 " ideal model delta sigma weight residual 111.76 86.65 25.11 3.00e+00 1.11e-01 7.01e+01 angle pdb=" C40 CRT M 406 " pdb=" C38 CRT M 406 " pdb=" O2 CRT M 406 " ideal model delta sigma weight residual 111.40 86.96 24.44 3.00e+00 1.11e-01 6.64e+01 angle pdb=" C3 CRT J 103 " pdb=" C1 CRT J 103 " pdb=" C4 CRT J 103 " ideal model delta sigma weight residual 108.82 84.72 24.10 3.00e+00 1.11e-01 6.46e+01 ... (remaining 37069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 14291 36.00 - 72.00: 926 72.00 - 108.00: 179 108.00 - 144.00: 59 144.00 - 180.00: 14 Dihedral angle restraints: 15469 sinusoidal: 8098 harmonic: 7371 Sorted by residual: dihedral pdb=" C1 BCL T 101 " pdb=" CGA BCL T 101 " pdb=" O2A BCL T 101 " pdb=" CBA BCL T 101 " ideal model delta sinusoidal sigma weight residual -180.00 -74.32 -105.68 1 6.00e+00 2.78e-02 3.39e+02 dihedral pdb=" C1 BCL F 502 " pdb=" C2 BCL F 502 " pdb=" C3 BCL F 502 " pdb=" C5 BCL F 502 " ideal model delta sinusoidal sigma weight residual -180.00 -0.00 -180.00 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL 3 101 " pdb=" C2 BCL 3 101 " pdb=" C3 BCL 3 101 " pdb=" C5 BCL 3 101 " ideal model delta sinusoidal sigma weight residual -180.00 -0.04 -179.96 1 8.00e+00 1.56e-02 3.00e+02 ... (remaining 15466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3333 0.080 - 0.160: 354 0.160 - 0.241: 65 0.241 - 0.321: 13 0.321 - 0.401: 7 Chirality restraints: 3772 Sorted by residual: chirality pdb=" CBD BCL M 403 " pdb=" CAD BCL M 403 " pdb=" CGD BCL M 403 " pdb=" CHA BCL M 403 " both_signs ideal model delta sigma weight residual False 2.62 3.02 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CBD BCL R 101 " pdb=" CAD BCL R 101 " pdb=" CGD BCL R 101 " pdb=" CHA BCL R 101 " both_signs ideal model delta sigma weight residual False 2.62 2.26 0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CBD BCL V 101 " pdb=" CAD BCL V 101 " pdb=" CGD BCL V 101 " pdb=" CHA BCL V 101 " both_signs ideal model delta sigma weight residual False 2.62 2.26 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 3769 not shown) Planarity restraints: 4374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL 0 101 " 0.370 3.00e-02 1.11e+03 3.09e-01 5.30e+02 pdb=" CBA BCL 0 101 " 0.121 3.00e-02 1.11e+03 pdb=" CGA BCL 0 101 " -0.077 3.00e-02 1.11e+03 pdb=" O1A BCL 0 101 " 0.134 3.00e-02 1.11e+03 pdb=" O2A BCL 0 101 " -0.549 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL W 101 " 0.352 3.00e-02 1.11e+03 2.86e-01 4.55e+02 pdb=" CBA BCL W 101 " 0.185 3.00e-02 1.11e+03 pdb=" CGA BCL W 101 " -0.082 3.00e-02 1.11e+03 pdb=" O1A BCL W 101 " 0.038 3.00e-02 1.11e+03 pdb=" O2A BCL W 101 " -0.493 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL K 102 " -0.354 3.00e-02 1.11e+03 2.86e-01 4.54e+02 pdb=" CBA BCL K 102 " -0.194 3.00e-02 1.11e+03 pdb=" CGA BCL K 102 " 0.085 3.00e-02 1.11e+03 pdb=" O1A BCL K 102 " -0.024 3.00e-02 1.11e+03 pdb=" O2A BCL K 102 " 0.488 3.00e-02 1.11e+03 ... (remaining 4371 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 111 2.39 - 3.02: 14566 3.02 - 3.65: 43074 3.65 - 4.27: 72296 4.27 - 4.90: 112914 Nonbonded interactions: 242961 Sorted by model distance: nonbonded pdb=" OE2 GLU M 96 " pdb=" O HOH M 501 " model vdw 1.765 2.440 nonbonded pdb=" OE1 GLU M 96 " pdb=" O HOH M 502 " model vdw 1.806 2.440 nonbonded pdb=" OE1 GLN C 183 " pdb="MG MG C 405 " model vdw 2.031 2.170 nonbonded pdb=" NE2 HIS L 196 " pdb="FE FE M 401 " model vdw 2.071 2.340 nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 401 " model vdw 2.073 2.260 ... (remaining 242956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '0' and resid 10 through 47) selection = (chain '2' and resid 10 through 47) selection = (chain '4' and resid 10 through 47) selection = (chain '6' and resid 10 through 47) selection = (chain '8' and resid 10 through 47) selection = (chain 'B' and resid 10 through 47) selection = (chain 'J' and resid 10 through 47) selection = (chain 'N' and resid 10 through 47) selection = (chain 'P' and resid 10 through 47) selection = (chain 'R' and resid 10 through 47) } ncs_group { reference = (chain '1' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain '5' and (resid 5 through 21 or resid 23 through 46)) selection = (chain '7' and (resid 5 through 21 or resid 23 through 46)) selection = (chain '9' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'A' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'I' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'K' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'O' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) selection = (chain 'Q' and (resid 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 21 or resid 23 through 46)) } ncs_group { reference = (chain 'D' and (resid 2 through 33 or resid 35 through 50 or resid 102 through 1 \ 03)) selection = (chain 'F' and (resid 2 through 33 or resid 35 through 50 or resid 502 through 5 \ 03)) selection = (chain 'S' and (resid 2 through 33 or resid 35 through 50 or resid 102 through 1 \ 03)) selection = (chain 'U' and (resid 2 through 33 or resid 35 through 50 or resid 101 through 1 \ 02)) selection = (chain 'W' and (resid 2 through 33 or resid 35 through 50 or resid 101 through 1 \ 02)) } ncs_group { reference = (chain 'E' and resid 8 through 47) selection = (chain 'G' and resid 8 through 47) selection = (chain 'T' and resid 8 through 47) selection = (chain 'V' and resid 8 through 47) selection = (chain 'X' and resid 8 through 47) selection = (chain 'Z' and resid 8 through 47) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 24.830 Check model and map are aligned: 0.390 Set scattering table: 0.210 Process input model: 73.490 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.190 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.019 0.268 26957 Z= 0.921 Angle : 1.894 25.111 37074 Z= 0.819 Chirality : 0.057 0.401 3772 Planarity : 0.017 0.309 4374 Dihedral : 24.811 179.998 10695 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.73 % Allowed : 18.61 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.17), residues: 2494 helix: 1.98 (0.13), residues: 1511 sheet: -0.76 (0.77), residues: 41 loop : 0.51 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP S 6 HIS 0.011 0.002 HIS R 19 PHE 0.026 0.002 PHE V 30 TYR 0.020 0.002 TYR C 319 ARG 0.007 0.001 ARG 1 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 270 time to evaluate : 2.518 Fit side-chains REVERT: H 75 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7286 (p) REVERT: F 41 GLU cc_start: 0.7606 (tp30) cc_final: 0.7252 (tp30) REVERT: I 8 ILE cc_start: 0.5850 (OUTLIER) cc_final: 0.5524 (pt) REVERT: P 27 THR cc_start: 0.7498 (m) cc_final: 0.7023 (m) REVERT: X 28 MET cc_start: 0.6580 (tpt) cc_final: 0.6213 (tpt) REVERT: Y 59 PRO cc_start: 0.6371 (Cg_exo) cc_final: 0.5699 (Cg_endo) REVERT: 4 44 ARG cc_start: 0.7735 (ttp-110) cc_final: 0.7456 (ttm170) outliers start: 37 outliers final: 26 residues processed: 301 average time/residue: 1.1891 time to fit residues: 424.8633 Evaluate side-chains 284 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 256 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain M residue 312 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 48 SER Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 4 ASP Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain Z residue 33 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 103 optimal weight: 0.0050 chunk 63 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 192 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 222 optimal weight: 20.0000 overall best weight: 1.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 ASN C 206 GLN L 207 GLN L 219 ASN M 145 HIS H 71 HIS H 103 ASN H 192 ASN A 6 HIS B 4 ASN ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 6 HIS 2 16 GLN ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 10 GLN 0 24 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 26957 Z= 0.210 Angle : 0.781 17.560 37074 Z= 0.303 Chirality : 0.042 0.424 3772 Planarity : 0.005 0.067 4374 Dihedral : 21.182 179.996 6184 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.47 % Allowed : 16.51 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.17), residues: 2494 helix: 2.42 (0.12), residues: 1512 sheet: -0.67 (0.79), residues: 41 loop : 0.38 (0.21), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 6 HIS 0.010 0.002 HIS L 159 PHE 0.022 0.002 PHE L 41 TYR 0.017 0.002 TYR C 200 ARG 0.005 0.000 ARG 1 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 266 time to evaluate : 2.188 Fit side-chains REVERT: L 13 ARG cc_start: 0.7738 (ttt180) cc_final: 0.7515 (ttt180) REVERT: H 237 ASP cc_start: 0.8905 (OUTLIER) cc_final: 0.8575 (t70) REVERT: H 259 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5580 (tp) REVERT: F 41 GLU cc_start: 0.7588 (tp30) cc_final: 0.7294 (tp30) REVERT: I 8 ILE cc_start: 0.5904 (OUTLIER) cc_final: 0.5633 (pt) REVERT: P 23 VAL cc_start: 0.7052 (OUTLIER) cc_final: 0.6608 (t) REVERT: P 27 THR cc_start: 0.7823 (m) cc_final: 0.7408 (m) REVERT: S 10 LEU cc_start: 0.4561 (OUTLIER) cc_final: 0.4339 (mt) REVERT: S 17 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7213 (mp) REVERT: V 17 GLU cc_start: 0.3435 (OUTLIER) cc_final: 0.3129 (pp20) REVERT: Y 59 PRO cc_start: 0.6279 (Cg_exo) cc_final: 0.5902 (Cg_endo) REVERT: 4 7 MET cc_start: 0.4052 (OUTLIER) cc_final: 0.3668 (mtt) REVERT: 6 23 VAL cc_start: 0.7679 (t) cc_final: 0.7283 (p) REVERT: 7 8 ILE cc_start: 0.7066 (tt) cc_final: 0.6675 (tp) outliers start: 53 outliers final: 18 residues processed: 305 average time/residue: 1.1518 time to fit residues: 418.3007 Evaluate side-chains 280 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 254 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain S residue 10 LEU Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain V residue 17 GLU Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 7 MET Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 185 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 222 optimal weight: 20.0000 chunk 240 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN P 13 GLN ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26957 Z= 0.304 Angle : 0.836 16.992 37074 Z= 0.333 Chirality : 0.045 0.423 3772 Planarity : 0.005 0.066 4374 Dihedral : 19.953 179.794 6163 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.26 % Allowed : 15.44 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.16), residues: 2494 helix: 2.17 (0.12), residues: 1505 sheet: -0.55 (0.79), residues: 41 loop : 0.25 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 9 9 HIS 0.011 0.002 HIS L 159 PHE 0.028 0.002 PHE L 41 TYR 0.024 0.003 TYR C 319 ARG 0.005 0.001 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 267 time to evaluate : 2.487 Fit side-chains revert: symmetry clash REVERT: L 208 LYS cc_start: 0.5744 (OUTLIER) cc_final: 0.5086 (mppt) REVERT: H 75 THR cc_start: 0.7885 (OUTLIER) cc_final: 0.7319 (p) REVERT: H 259 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5564 (tp) REVERT: F 15 ARG cc_start: 0.5881 (tmt90) cc_final: 0.5300 (tmm160) REVERT: F 41 GLU cc_start: 0.7578 (tp30) cc_final: 0.7240 (tp30) REVERT: I 8 ILE cc_start: 0.5854 (OUTLIER) cc_final: 0.5608 (pt) REVERT: N 26 MET cc_start: 0.6430 (OUTLIER) cc_final: 0.5929 (mtt) REVERT: P 13 GLN cc_start: 0.4251 (OUTLIER) cc_final: 0.3891 (tm-30) REVERT: P 24 GLN cc_start: 0.6523 (OUTLIER) cc_final: 0.6061 (mp-120) REVERT: P 27 THR cc_start: 0.7807 (m) cc_final: 0.7361 (m) REVERT: Q 15 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6801 (mtp180) REVERT: S 17 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7255 (mp) REVERT: Y 59 PRO cc_start: 0.6313 (Cg_exo) cc_final: 0.5976 (Cg_endo) REVERT: 2 25 SER cc_start: 0.6836 (t) cc_final: 0.6319 (p) REVERT: 2 27 THR cc_start: 0.7552 (OUTLIER) cc_final: 0.7201 (m) REVERT: 4 44 ARG cc_start: 0.7704 (ttp-110) cc_final: 0.7417 (ttm170) REVERT: 7 8 ILE cc_start: 0.7015 (tt) cc_final: 0.6619 (tp) outliers start: 70 outliers final: 35 residues processed: 320 average time/residue: 1.1861 time to fit residues: 450.0998 Evaluate side-chains 301 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 256 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 11 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain P residue 13 GLN Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain X residue 7 MET Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 149 optimal weight: 7.9990 chunk 223 optimal weight: 0.9980 chunk 236 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 212 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN P 13 GLN ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 GLN ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 26957 Z= 0.337 Angle : 0.864 16.779 37074 Z= 0.346 Chirality : 0.046 0.421 3772 Planarity : 0.005 0.066 4374 Dihedral : 20.030 179.988 6163 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.01 % Allowed : 14.69 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.16), residues: 2494 helix: 1.98 (0.12), residues: 1508 sheet: -0.61 (0.78), residues: 41 loop : 0.18 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 9 9 HIS 0.012 0.002 HIS L 159 PHE 0.030 0.003 PHE L 41 TYR 0.026 0.003 TYR C 319 ARG 0.005 0.001 ARG 9 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 262 time to evaluate : 3.061 Fit side-chains revert: symmetry clash REVERT: L 208 LYS cc_start: 0.5754 (OUTLIER) cc_final: 0.5080 (mppt) REVERT: H 75 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7311 (p) REVERT: H 259 LEU cc_start: 0.6104 (OUTLIER) cc_final: 0.5651 (tp) REVERT: F 16 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5783 (mtt90) REVERT: F 41 GLU cc_start: 0.7582 (tp30) cc_final: 0.7234 (tp30) REVERT: I 8 ILE cc_start: 0.5885 (OUTLIER) cc_final: 0.5596 (pt) REVERT: N 26 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.5963 (mtt) REVERT: O 10 GLN cc_start: 0.6377 (OUTLIER) cc_final: 0.6166 (mt0) REVERT: P 23 VAL cc_start: 0.7161 (OUTLIER) cc_final: 0.6692 (t) REVERT: P 24 GLN cc_start: 0.6524 (OUTLIER) cc_final: 0.6091 (mp-120) REVERT: P 27 THR cc_start: 0.7755 (m) cc_final: 0.7324 (m) REVERT: Q 15 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6794 (mtp180) REVERT: S 15 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.5357 (ttp-170) REVERT: S 17 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.7206 (mp) REVERT: Y 41 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6930 (tm-30) REVERT: Y 59 PRO cc_start: 0.6324 (Cg_exo) cc_final: 0.6018 (Cg_endo) REVERT: 2 25 SER cc_start: 0.7066 (OUTLIER) cc_final: 0.6603 (p) REVERT: 2 27 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.7121 (m) REVERT: 4 44 ARG cc_start: 0.7693 (ttp-110) cc_final: 0.7421 (ttm170) REVERT: 7 8 ILE cc_start: 0.6995 (tt) cc_final: 0.6601 (tp) REVERT: 7 13 ASP cc_start: 0.7302 (t0) cc_final: 0.7072 (t0) REVERT: 8 26 MET cc_start: 0.8212 (ttm) cc_final: 0.7947 (ttm) outliers start: 86 outliers final: 42 residues processed: 323 average time/residue: 1.2112 time to fit residues: 463.7298 Evaluate side-chains 315 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 258 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain O residue 10 GLN Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 4 residue 35 ILE Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26957 Z= 0.258 Angle : 0.782 16.756 37074 Z= 0.311 Chirality : 0.042 0.417 3772 Planarity : 0.005 0.065 4374 Dihedral : 19.379 179.837 6163 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.17 % Allowed : 15.49 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.16), residues: 2494 helix: 2.14 (0.12), residues: 1503 sheet: -0.56 (0.79), residues: 41 loop : 0.26 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 9 9 HIS 0.012 0.002 HIS L 159 PHE 0.027 0.002 PHE L 41 TYR 0.021 0.002 TYR C 319 ARG 0.003 0.000 ARG M 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 261 time to evaluate : 2.562 Fit side-chains revert: symmetry clash REVERT: L 3 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8542 (mtt) REVERT: L 208 LYS cc_start: 0.5747 (OUTLIER) cc_final: 0.5091 (mppt) REVERT: H 259 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5612 (tp) REVERT: B 13 GLN cc_start: 0.6436 (OUTLIER) cc_final: 0.6102 (tp40) REVERT: B 26 MET cc_start: 0.8441 (ttp) cc_final: 0.8163 (ttp) REVERT: F 41 GLU cc_start: 0.7581 (tp30) cc_final: 0.7263 (tp30) REVERT: I 8 ILE cc_start: 0.5891 (OUTLIER) cc_final: 0.5611 (pt) REVERT: N 26 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.5929 (mtt) REVERT: P 23 VAL cc_start: 0.7125 (OUTLIER) cc_final: 0.6643 (t) REVERT: P 24 GLN cc_start: 0.6495 (OUTLIER) cc_final: 0.6047 (mp-120) REVERT: P 27 THR cc_start: 0.7820 (m) cc_final: 0.7401 (m) REVERT: Q 15 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6804 (mtp180) REVERT: S 17 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7203 (mp) REVERT: Y 41 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6922 (tm-30) REVERT: Y 59 PRO cc_start: 0.6287 (Cg_exo) cc_final: 0.5975 (Cg_endo) REVERT: 2 25 SER cc_start: 0.7064 (OUTLIER) cc_final: 0.6552 (p) REVERT: 2 35 ILE cc_start: 0.7726 (pp) cc_final: 0.7486 (mm) REVERT: 8 26 MET cc_start: 0.8251 (ttm) cc_final: 0.7967 (ttm) outliers start: 68 outliers final: 35 residues processed: 310 average time/residue: 1.1097 time to fit residues: 411.7770 Evaluate side-chains 298 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 251 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain L residue 3 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 15 ARG Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 35 ILE Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 9.9990 chunk 213 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 237 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26957 Z= 0.280 Angle : 0.809 16.560 37074 Z= 0.321 Chirality : 0.043 0.416 3772 Planarity : 0.005 0.065 4374 Dihedral : 19.365 179.830 6163 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.54 % Allowed : 15.39 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % 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: 1.98 (0.16), residues: 2494 helix: 2.10 (0.12), residues: 1501 sheet: -0.58 (0.79), residues: 41 loop : 0.21 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 6 HIS 0.012 0.002 HIS L 159 PHE 0.028 0.002 PHE L 41 TYR 0.023 0.002 TYR C 319 ARG 0.004 0.001 ARG M 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 256 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 208 LYS cc_start: 0.5755 (OUTLIER) cc_final: 0.5093 (mppt) REVERT: H 75 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7256 (p) REVERT: H 253 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6264 (mm-30) REVERT: H 259 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5635 (tp) REVERT: B 13 GLN cc_start: 0.6398 (OUTLIER) cc_final: 0.6105 (tp40) REVERT: F 41 GLU cc_start: 0.7572 (tp30) cc_final: 0.7254 (tp30) REVERT: I 8 ILE cc_start: 0.5906 (OUTLIER) cc_final: 0.5680 (pt) REVERT: P 23 VAL cc_start: 0.7112 (OUTLIER) cc_final: 0.6634 (t) REVERT: P 24 GLN cc_start: 0.6494 (OUTLIER) cc_final: 0.6077 (mp-120) REVERT: P 27 THR cc_start: 0.7821 (m) cc_final: 0.7408 (m) REVERT: S 15 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5334 (ttp-170) REVERT: S 17 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7184 (mp) REVERT: Y 59 PRO cc_start: 0.6271 (Cg_exo) cc_final: 0.5966 (Cg_endo) REVERT: 2 25 SER cc_start: 0.7020 (OUTLIER) cc_final: 0.6574 (p) REVERT: 2 27 THR cc_start: 0.7457 (t) cc_final: 0.7133 (m) REVERT: 2 35 ILE cc_start: 0.7720 (pp) cc_final: 0.7481 (mm) REVERT: 4 44 ARG cc_start: 0.7695 (ttp-110) cc_final: 0.7413 (ttm170) REVERT: 7 13 ASP cc_start: 0.7338 (t0) cc_final: 0.7111 (t0) REVERT: 8 26 MET cc_start: 0.8237 (ttm) cc_final: 0.7991 (ttm) REVERT: 0 12 GLU cc_start: 0.7215 (tp30) cc_final: 0.6970 (tp30) outliers start: 76 outliers final: 40 residues processed: 318 average time/residue: 1.1809 time to fit residues: 445.4456 Evaluate side-chains 303 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 253 time to evaluate : 4.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 8 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 35 ILE Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 173 optimal weight: 0.0010 chunk 134 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 10 GLN ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 26957 Z= 0.339 Angle : 0.874 16.470 37074 Z= 0.349 Chirality : 0.046 0.420 3772 Planarity : 0.005 0.065 4374 Dihedral : 19.733 179.801 6163 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.50 % Allowed : 15.72 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.16), residues: 2494 helix: 1.94 (0.12), residues: 1503 sheet: -0.64 (0.78), residues: 41 loop : 0.14 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP S 6 HIS 0.012 0.002 HIS L 159 PHE 0.031 0.003 PHE L 41 TYR 0.026 0.003 TYR C 319 ARG 0.005 0.001 ARG L 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 265 time to evaluate : 2.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 208 LYS cc_start: 0.5733 (OUTLIER) cc_final: 0.5080 (mppt) REVERT: H 75 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7304 (p) REVERT: H 77 MET cc_start: 0.7388 (mmt) cc_final: 0.6919 (mmm) REVERT: H 253 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6241 (mm-30) REVERT: H 259 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5574 (tp) REVERT: B 13 GLN cc_start: 0.6388 (OUTLIER) cc_final: 0.6074 (tp40) REVERT: F 16 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5750 (mtt90) REVERT: F 41 GLU cc_start: 0.7581 (tp30) cc_final: 0.7221 (tp30) REVERT: J 24 GLN cc_start: 0.6313 (tt0) cc_final: 0.5924 (tp40) REVERT: N 26 MET cc_start: 0.6455 (OUTLIER) cc_final: 0.5959 (mtt) REVERT: P 23 VAL cc_start: 0.7099 (OUTLIER) cc_final: 0.6621 (t) REVERT: P 24 GLN cc_start: 0.6517 (OUTLIER) cc_final: 0.6076 (mp-120) REVERT: P 27 THR cc_start: 0.7740 (m) cc_final: 0.7315 (m) REVERT: S 15 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.5324 (ttp-170) REVERT: S 17 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7199 (mp) REVERT: Y 41 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.6940 (tm-30) REVERT: Y 59 PRO cc_start: 0.6303 (Cg_exo) cc_final: 0.6015 (Cg_endo) REVERT: 2 25 SER cc_start: 0.7071 (OUTLIER) cc_final: 0.6658 (p) REVERT: 2 35 ILE cc_start: 0.7744 (pp) cc_final: 0.7458 (mm) REVERT: 4 44 ARG cc_start: 0.7679 (ttp-110) cc_final: 0.7422 (ttm170) REVERT: 7 13 ASP cc_start: 0.7270 (t0) cc_final: 0.7041 (t0) REVERT: 8 26 MET cc_start: 0.8250 (ttm) cc_final: 0.8023 (ttm) REVERT: 0 12 GLU cc_start: 0.7256 (tp30) cc_final: 0.7046 (tp30) outliers start: 75 outliers final: 41 residues processed: 324 average time/residue: 1.1848 time to fit residues: 455.1056 Evaluate side-chains 312 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 259 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 26 MET Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 4 residue 35 ILE Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 26957 Z= 0.373 Angle : 0.910 16.410 37074 Z= 0.363 Chirality : 0.048 0.425 3772 Planarity : 0.005 0.065 4374 Dihedral : 19.871 179.734 6161 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.64 % Allowed : 15.72 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.16), residues: 2494 helix: 1.80 (0.12), residues: 1509 sheet: -0.65 (0.78), residues: 41 loop : 0.08 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP S 6 HIS 0.014 0.002 HIS R 19 PHE 0.032 0.003 PHE L 41 TYR 0.026 0.003 TYR C 319 ARG 0.006 0.001 ARG M 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 261 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 208 LYS cc_start: 0.5757 (OUTLIER) cc_final: 0.5100 (mppt) REVERT: H 75 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7283 (p) REVERT: H 253 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6228 (mm-30) REVERT: H 259 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5578 (tp) REVERT: B 13 GLN cc_start: 0.6383 (OUTLIER) cc_final: 0.6103 (tp40) REVERT: D 41 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7486 (tp30) REVERT: F 16 ARG cc_start: 0.6258 (OUTLIER) cc_final: 0.5712 (mtt90) REVERT: F 41 GLU cc_start: 0.7588 (tp30) cc_final: 0.7233 (tp30) REVERT: J 24 GLN cc_start: 0.6311 (tt0) cc_final: 0.5935 (tp40) REVERT: N 26 MET cc_start: 0.6479 (OUTLIER) cc_final: 0.5984 (mtt) REVERT: P 23 VAL cc_start: 0.7146 (OUTLIER) cc_final: 0.6672 (t) REVERT: P 24 GLN cc_start: 0.6532 (OUTLIER) cc_final: 0.6090 (mp-120) REVERT: P 27 THR cc_start: 0.7745 (m) cc_final: 0.7323 (m) REVERT: R 10 LEU cc_start: 0.4129 (OUTLIER) cc_final: 0.3640 (tp) REVERT: S 15 ARG cc_start: 0.6214 (OUTLIER) cc_final: 0.5351 (ttp-170) REVERT: S 17 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7203 (mp) REVERT: Y 41 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: Y 59 PRO cc_start: 0.6328 (Cg_exo) cc_final: 0.6046 (Cg_endo) REVERT: 2 25 SER cc_start: 0.7032 (OUTLIER) cc_final: 0.6720 (p) REVERT: 2 27 THR cc_start: 0.7407 (t) cc_final: 0.7107 (m) REVERT: 4 7 MET cc_start: 0.4762 (mtm) cc_final: 0.4532 (mpt) REVERT: 4 12 GLU cc_start: 0.4982 (OUTLIER) cc_final: 0.4754 (tp30) REVERT: 4 44 ARG cc_start: 0.7704 (ttp-110) cc_final: 0.7425 (ttm170) REVERT: 7 13 ASP cc_start: 0.7286 (t0) cc_final: 0.6995 (t0) REVERT: 8 26 MET cc_start: 0.8264 (ttm) cc_final: 0.8062 (ttm) REVERT: 0 12 GLU cc_start: 0.7225 (tp30) cc_final: 0.7017 (tp30) outliers start: 78 outliers final: 44 residues processed: 320 average time/residue: 1.2106 time to fit residues: 468.4376 Evaluate side-chains 317 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 258 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 48 ARG Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 12 GLU Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 4 residue 35 ILE Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 chunk 208 optimal weight: 30.0000 chunk 219 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 26957 Z= 0.327 Angle : 0.860 16.349 37074 Z= 0.345 Chirality : 0.045 0.420 3772 Planarity : 0.005 0.066 4374 Dihedral : 19.587 179.745 6161 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.03 % Allowed : 16.46 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.16), residues: 2494 helix: 1.86 (0.12), residues: 1509 sheet: -0.67 (0.77), residues: 41 loop : 0.11 (0.21), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP S 6 HIS 0.016 0.002 HIS R 19 PHE 0.030 0.003 PHE L 41 TYR 0.025 0.003 TYR C 319 ARG 0.005 0.001 ARG M 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 260 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 208 LYS cc_start: 0.5729 (OUTLIER) cc_final: 0.5064 (mppt) REVERT: L 211 GLU cc_start: 0.7677 (pt0) cc_final: 0.7283 (mt-10) REVERT: H 75 THR cc_start: 0.7857 (OUTLIER) cc_final: 0.7256 (p) REVERT: H 77 MET cc_start: 0.7356 (mmt) cc_final: 0.6878 (mmm) REVERT: H 253 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6236 (mm-30) REVERT: H 259 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5571 (tp) REVERT: B 13 GLN cc_start: 0.6384 (OUTLIER) cc_final: 0.6037 (tp40) REVERT: F 16 ARG cc_start: 0.6272 (OUTLIER) cc_final: 0.5748 (mtt90) REVERT: F 41 GLU cc_start: 0.7584 (tp30) cc_final: 0.7270 (tp30) REVERT: J 24 GLN cc_start: 0.6293 (tt0) cc_final: 0.5913 (tp40) REVERT: P 23 VAL cc_start: 0.7107 (OUTLIER) cc_final: 0.6632 (t) REVERT: P 24 GLN cc_start: 0.6529 (OUTLIER) cc_final: 0.6088 (mp-120) REVERT: P 27 THR cc_start: 0.7750 (m) cc_final: 0.7336 (m) REVERT: S 15 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5341 (ttp-170) REVERT: S 17 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7204 (mp) REVERT: Y 41 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6966 (tm-30) REVERT: Y 59 PRO cc_start: 0.6328 (Cg_exo) cc_final: 0.6040 (Cg_endo) REVERT: 2 25 SER cc_start: 0.7019 (OUTLIER) cc_final: 0.6696 (p) REVERT: 2 27 THR cc_start: 0.7437 (t) cc_final: 0.7150 (m) REVERT: 4 44 ARG cc_start: 0.7684 (ttp-110) cc_final: 0.7431 (ttm170) REVERT: 7 13 ASP cc_start: 0.7310 (t0) cc_final: 0.7035 (t0) REVERT: 8 26 MET cc_start: 0.8252 (ttm) cc_final: 0.8048 (ttm) outliers start: 65 outliers final: 41 residues processed: 311 average time/residue: 1.1810 time to fit residues: 435.5181 Evaluate side-chains 312 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 260 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 307 CYS Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 4 residue 35 ILE Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 8.9990 chunk 232 optimal weight: 0.5980 chunk 142 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26957 Z= 0.252 Angle : 0.783 16.289 37074 Z= 0.313 Chirality : 0.042 0.412 3772 Planarity : 0.005 0.066 4374 Dihedral : 19.021 179.845 6161 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.66 % Allowed : 16.88 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % 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: 1.94 (0.16), residues: 2494 helix: 2.04 (0.12), residues: 1511 sheet: -0.66 (0.78), residues: 41 loop : 0.21 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP S 6 HIS 0.015 0.002 HIS R 19 PHE 0.026 0.002 PHE L 41 TYR 0.021 0.002 TYR C 319 ARG 0.003 0.000 ARG N 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4988 Ramachandran restraints generated. 2494 Oldfield, 0 Emsley, 2494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 261 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 208 LYS cc_start: 0.5761 (OUTLIER) cc_final: 0.5105 (mppt) REVERT: L 211 GLU cc_start: 0.7670 (pt0) cc_final: 0.7260 (mt-10) REVERT: H 253 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6241 (mm-30) REVERT: H 259 LEU cc_start: 0.6019 (OUTLIER) cc_final: 0.5564 (tp) REVERT: B 13 GLN cc_start: 0.6376 (OUTLIER) cc_final: 0.6063 (tp40) REVERT: F 15 ARG cc_start: 0.5914 (tmt90) cc_final: 0.5212 (tmm160) REVERT: F 41 GLU cc_start: 0.7564 (tp30) cc_final: 0.7244 (tp30) REVERT: J 24 GLN cc_start: 0.6264 (tt0) cc_final: 0.5892 (tp40) REVERT: P 23 VAL cc_start: 0.7109 (OUTLIER) cc_final: 0.6637 (t) REVERT: P 24 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.6081 (mp-120) REVERT: P 27 THR cc_start: 0.7782 (m) cc_final: 0.7387 (m) REVERT: S 15 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5321 (ttp-170) REVERT: S 17 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.7181 (mp) REVERT: Y 41 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6913 (tm-30) REVERT: Y 59 PRO cc_start: 0.6328 (Cg_exo) cc_final: 0.6030 (Cg_endo) REVERT: 2 25 SER cc_start: 0.7073 (OUTLIER) cc_final: 0.6710 (p) REVERT: 2 27 THR cc_start: 0.7410 (t) cc_final: 0.7127 (m) REVERT: 2 35 ILE cc_start: 0.7680 (pp) cc_final: 0.7459 (mm) REVERT: 3 16 MET cc_start: 0.5628 (mmt) cc_final: 0.5242 (tpt) REVERT: 8 26 MET cc_start: 0.8236 (ttm) cc_final: 0.7968 (ttm) outliers start: 57 outliers final: 41 residues processed: 306 average time/residue: 1.2097 time to fit residues: 438.4061 Evaluate side-chains 305 residues out of total 2142 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 255 time to evaluate : 5.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 203 VAL Chi-restraints excluded: chain L residue 208 LYS Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 237 ASP Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain B residue 4 ASN Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain F residue 16 ARG Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain J residue 21 ILE Chi-restraints excluded: chain K residue 7 LYS Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain P residue 23 VAL Chi-restraints excluded: chain P residue 24 GLN Chi-restraints excluded: chain Q residue 38 SER Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 15 ARG Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 27 THR Chi-restraints excluded: chain U residue 17 ILE Chi-restraints excluded: chain V residue 23 THR Chi-restraints excluded: chain W residue 17 ILE Chi-restraints excluded: chain Y residue 41 GLU Chi-restraints excluded: chain Y residue 60 VAL Chi-restraints excluded: chain Z residue 11 THR Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 2 residue 25 SER Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain 3 residue 66 ARG Chi-restraints excluded: chain 4 residue 26 MET Chi-restraints excluded: chain 4 residue 35 ILE Chi-restraints excluded: chain 8 residue 10 LEU Chi-restraints excluded: chain 0 residue 10 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 199 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 206 GLN L 219 ASN H 71 HIS ** I 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.108681 restraints weight = 35826.496| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.30 r_work: 0.2854 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2705 r_free = 0.2705 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 26957 Z= 0.421 Angle : 0.958 16.430 37074 Z= 0.384 Chirality : 0.050 0.426 3772 Planarity : 0.006 0.064 4374 Dihedral : 19.909 179.755 6161 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.80 % Allowed : 16.60 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.16), residues: 2494 helix: 1.75 (0.12), residues: 1501 sheet: -0.74 (0.77), residues: 41 loop : 0.07 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP S 6 HIS 0.019 0.003 HIS R 19 PHE 0.034 0.003 PHE L 41 TYR 0.027 0.003 TYR C 319 ARG 0.007 0.001 ARG M 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9194.71 seconds wall clock time: 164 minutes 8.07 seconds (9848.07 seconds total)